SOLID DOSAGE FORMS CONTAINING BACTERIA AND MICROBIAL EXTRACELLULAR VESICLES

Abstract
Enterically-coated solid dosage forms containing a pharmaceutical agent which includes bacteria and/or microbial extracellular vesicles (mEVs) are provided. Methods of treatment using such solid dosage forms are also provided.
Description
SUMMARY

In certain aspects, provided herein are solid dosage forms of a pharmaceutical agent. In certain embodiments, such solid dose forms include capsules, tablets, and minitablets. In some embodiments, the capsules, tablets, or minitablets are coated with one layer of enteric coating or with two layers of enteric coatings (e.g., an inner enteric coating and an outer enteric coating). In some embodiments, the enterically-coated minitablets (with one layer of enteric coating or with two layers of enteric coatings) can be loaded into a capsule.


Aspects of the disclosure are based, in part, on the discovery that certain solid dosage forms of a pharmaceutical agent provide an increase in therapeutic efficacy and/or physiological effect as compared to other dosage forms of the pharmaceutical agent (e.g., as compared to the same dose of the pharmaceutical agent administered in a form that does not comprise the enteric coating, e.g., a non-enterically coated tablet or non-enterically coated minitablet or a suspension of biomass or powder). The solid dosage forms can be formulated to contain a lower dose (e.g., 1/10 or less of a dose) of the pharmaceutical agent than other dosage forms (e.g., as compared to the same dose of the pharmaceutical agent administered in a form that does not comprise the enteric coating, e.g., a non-enterically coated tablet or non-enterically coated minitablet or a suspension of biomass or powder), yet result in comparable therapeutic efficacy and/or physiological effect. Such solid dosage forms can alternatively be formulated to contain the same dose of a pharmaceutical agent as other dosage forms (e.g., as compared to the same dose of the pharmaceutical agent administered in a form that does not comprise the enteric coating, e.g., a non-enterically coated tablet or non-enterically coated minitablet or a suspension of biomass or powder), yet result in greater therapeutic efficacy or physiological effect (e.g., 10-fold or more therapeutic efficacy or physiological effect). The solid dosage forms of a pharmaceutical agent as described herein can provide release in the small intestine of the pharmaceutical agent contained therein. The solid dosage forms can be prepared to allow release of the pharmaceutical agent at specific locations in the small intestine. Release of the pharmaceutical agent at particular locations in the small intestine allows the pharmaceutical agent to target and affect cells (e.g., epithelial cells and/or immune cells) located at these specific locations, e.g., which can cause a local effect in the gastrointestinal tract and/or cause a systemic effect (e.g., an effect outside of the gastrointestinal tract).


In certain embodiments, the solid dosage forms of a pharmaceutical agent as described herein can be used to deliver a variety of pharmaceutical agents that can act on immune cells and/or epithelial cells in the small intestine to cause a systemic effect (e.g., an effect outside of the gastrointestinal tract) and/or can cause a local effect in the gastrointestinal tract.


In some embodiments, the pharmaceutical agent can be of bacterial origin (e.g., mixture of selected strains or components thereof, such as microbial extracellular vesicles (mEVs) of the mixture of selected strains). The pharmaceutical agent can be of bacterial origin (e.g., a single selected strain and/or components thereof, such as microbial extracellular vesicles (mEVs) of that single selected strain).


As described herein, improved therapeutic effects were seen with certain solid dosage forms of a pharmaceutical agent that contained one layer of enteric coating, as compared to the same dose of the pharmaceutical agent administered in a form that does not comprise the enteric coating, e.g., a non-enterically coated tablet or non-enterically coated minitablet or a suspension of biomass or powder.


In some embodiments, a solid dosage form described herein can provide, inter alia, a pharmaceutical agent (e.g., a formulation of a pharmaceutical agent) which enhances the pharmacological potency of the pharmaceutical agent by 10-fold or more in preclinical in vivo models, as compared to the same dose of the pharmaceutical agent administered in a form that does not comprise the enteric coating, e.g., a non-enterically coated tablet or non-enterically coated minitablet or a suspension of biomass or powder). For example, for a given level of therapeutic efficacy and/or physiological effect obtained with a comparator formulation of the pharmaceutical agent, the dose can be reduced (e.g., to 1/10 or less) when prepared in a solid dosage form described herein.


In some embodiments, or a given dose of a pharmaceutical agent, target engagement (e.g., in the small intestine) can be increased such that for a given dose of a pharmaceutical agent, target engagement (e.g., in the small intestine) can be increased for better efficacy when the pharmaceutical agent is prepared in a solid dosage form described herein.


In some aspects, the disclosure provides a solid dosage form (e.g., for oral administration) (e.g., for therapeutic use) comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), and wherein the solid dosage form is enterically coated (e.g., comprises an enteric coating; e.g., is coated with an enteric coating).


In certain embodiments, the solid dosage form comprises a capsule. In some embodiments, the capsule is a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule. In some embodiments, the capsule is a size 0 capsule.


In some embodiments, the solid dosage form comprises a tablet. In some embodiments, the tablet (e.g., enterically coated tablet) is a 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm, 11 mm, 12 mm, 13 mm, 14 mm, 15 mm, 16 mm, 17 mm, or 18 mm tablet.


In some embodiments, the solid dosage form comprises a minitablet. In some embodiments, the minitablet (e.g., enterically coated minitablet) is a 1 mm minitablet, 1.5 mm minitablet, 2 mm minitablet, 3 mm minitablet, or 4 mm minitablet. In some embodiments, a plurality of enterically coated minitablets are contained in a capsule (e.g., a size 0 capsule can contain about 31 to about 35 (e.g., 33) minitablets, wherein the minitablets are 3 mm in size). In some embodiments, the capsule is a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule. In some embodiments, the capsule comprises HPMC (hydroxyl propyl methyl cellulose) or gelatin.


In some embodiments, the enteric coating comprises one enteric coating.


In some embodiments, the enteric coating comprises an inner enteric coating and an outer enteric coating, and wherein the inner and outer enteric coatings are not identical (e.g., the inner and outer enteric coatings do not contain identical components in identical amounts).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a polymethacrylate-based copolymer.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1).


In some embodiments, the one enteric coating comprises methacrylic acid ethyl acrylate (MAE) copolymer (1:1) (such as Kollicoat MAE 100P).


In some embodiments, the one enteric coating comprises a Eudragit copolymer, e.g., a Eudragit L (e.g., Eudragit L 100-55; Eudragit L 30 D-55), a Eudragit S, a Eudragit RL, a Eudragit RS, a Eudragit E, or a Eudragit FS (e.g., Eudragit FS 30 D).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises cellulose acetate phthalate (CAP), cellulose acetate trimellitate (CAT), poly(vinyl acetate phthalate) (PVAP), hydroxypropyl methylcellulose phthalate (HPMCP), a fatty acid, a wax, shellac (esters of aleurtic acid), a plastic, a plant fiber, zein, Aqua-Zein (an aqueous zein formulation containing no alcohol), amylose starch, a starch derivative, a dextrin, a methyl acrylate-methacrylic acid copolymer, cellulose acetate succinate, hydroxypropyl methyl cellulose acetate succinate (hypromellose acetate succinate), a methyl methacrylate-methacrylic acid copolymer, or sodium alginate.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises an anionic polymeric material.


In some embodiments, the solid dosage form comprises a sub-coat, e.g., under the enteric coating (e.g., one enteric coating). The sub-coat can be used, e.g., to visually mask the appearance of the pharmaceutical agent.


In some embodiments, the pharmaceutical agent comprises bacteria.


In some embodiments, the pharmaceutical agent comprises microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent comprises bacteria and microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent has one or more beneficial immune effects outside the gastrointestinal tract, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent modulates immune effects outside the gastrointestinal tract (e.g., outside of the small intestine) in the subject, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent causes a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent acts on immune cells and/or epithelial cells in the small intestine e.g., causing a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent comprises isolated bacteria (e.g., from one or more strains of bacteria (e.g., bacteria of interest) (e.g., a therapeutically effective amount thereof)). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is the isolated bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises live bacteria.


In some embodiments, the pharmaceutical agent comprises dead bacteria.


In some embodiments, the pharmaceutical agent comprises non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises bacteria from one strain of bacteria.


In some embodiments, the bacteria are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient) (e.g., a powder form).


In some embodiments, the bacteria are gamma irradiated.


In some embodiments, the bacteria are UV irradiated.


In some embodiments, the bacteria are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the bacteria are acid treated.


In some embodiments, the bacteria are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the bacteria are Gram positive bacteria.


In some embodiments, the bacteria are Gram negative bacteria.


In some embodiments, the bacteria are aerobic bacteria.


In some embodiments, the bacteria are anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the bacteria are acidophile bacteria.


In some embodiments, the bacteria are alkaliphile bacteria.


In some embodiments, the bacteria are neutralophile bacteria.


In some embodiments, the bacteria are fastidious bacteria.


In some embodiments, the bacteria are nonfastidious bacteria.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the bacteria are a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the bacteria are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the bacteria are of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria.


In some embodiments, the bacteria are Prevotella histicola bacteria.


In some embodiments, the bacteria are Bifidobacterium animalis bacteria.


In some embodiments, the bacteria are Veillonella parvula bacteria.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the bacteria are Prevotella bacteria. In some embodiments, the Prevotella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the bacteria are Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the bacteria are Veillonella bacteria. In some embodiments, the Veillonella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the bacteria are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the bacteria are Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the bacteria are Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the bacteria are Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the bacteria are of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bifidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the bacteria are of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the bacteria are Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the bacteria are BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the bacteria are Blautia hydrogenotrophica bacteria.


In some embodiments, the bacteria are Blautia stercoris bacteria.


In some embodiments, the bacteria are Blautia wexlerae bacteria.


In some embodiments, the bacteria are Enterococcus gallinarum bacteria.


In some embodiments, the bacteria are Enterococcus faecium bacteria.


In some embodiments, the bacteria are Bifidobacterium bifidium bacteria.


In some embodiments, the bacteria are Bifidobacterium breve bacteria.


In some embodiments, the bacteria are Bifidobacterium longum bacteria.


In some embodiments, the bacteria are Roseburia hominis bacteria.


In some embodiments, the bacteria are Bacteroides thetaiotaomicron bacteria.


In some embodiments, the bacteria are Bacteroides coprocola bacteria.


In some embodiments, the bacteria are Erysipelatoclostridium ramosum bacteria.


In some embodiments, the bacteria are Megasphera massiliensis bacteria.


In some embodiments, the bacteria are Eubacterium bacteria.


In some embodiments, the bacteria are Parabacteroides distasonis bacteria.


In some embodiments, the bacteria are Lactobacillus plantarum bacteria.


In some embodiments, the bacteria are bacteria of the Negativicutes class.


In some embodiments, the bacteria are of the Veillonellaceae family.


In some embodiments, the bacteria are of the Selenomonadaceae family.


In some embodiments, the bacteria are of the Acidaminococcaceae family.


In some embodiments, the bacteria are of the Sporomusaceae family.


In some embodiments, the bacteria are of the Megasphaera genus.


In some embodiments, the bacteria are of the Selenomonas genus.


In some embodiments, the bacteria are of the Propionospora genus.


In some embodiments, the bacteria are of the Acidaminococcus genus.


In some embodiments, the bacteria are Megasphaera sp. bacteria.


In some embodiments, the bacteria are Selenomonas felix bacteria.


In some embodiments, the bacteria are Acidaminococcus intestini bacteria.


In some embodiments, the bacteria are Propionospora sp. bacteria.


In some embodiments, the bacteria are bacteria of the Clostridia class.


In some embodiments, the bacteria are of the Oscillospriraceae family.


In some embodiments, the bacteria are of the Faecalibacterium genus.


In some embodiments, the bacteria are of the Fournierella genus.


In some embodiments, the bacteria are of the Harryflintia genus.


In some embodiments, the bacteria are of the Agathobaculum genus.


In some embodiments, the bacteria are Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the bacteria are Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the bacteria are Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the bacteria are Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the bacteria are a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the bacteria are of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the bacteria are of order Bacteroidales. In some embodiments, the bacteria are of the family Porphyromonoadaceae. In some embodiments, the bacteria are of the family Prevotellaceae. In some embodiments, the bacteria are of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Bacteroidia that stain Gram negative. In some embodiments, the bacteria are of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Clostridia [phylum Firmicutes]. In some embodiments, the bacteria are of the order Eubacteriales. In some embodiments, the bacteria are of the family Oscillispiraceae. In some embodiments, the bacteria are of the family Lachnospiraceae. In some embodiments, the bacteria are of the family Peptostreptococcaceae. In some embodiments, the bacteria are of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the bacteria are of the class Clostridia that stain Gram negative. In some embodiments, the bacteria are of the class Clostridia that stain Gram positive. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the bacteria are of the class Negativicutes [phylum Firmicutes]. In some embodiments, the bacteria are of the order Veillonellales. In some embodiments, the bacteria are of the family Veillonelloceae. In some embodiments, the bacteria are of the order Selenomonadales. In some embodiments, the bacteria are of the family Selenomonadaceae. In some embodiments, the bacteria are of the family Sporomusaceae. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Negativicutes that stain Gram negative. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Synergistia [phylum Synergistota]. In some embodiments, the bacteria are of the order Synergistales. In some embodiments, the bacteria are of the family Synergistaceae. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Synergistia that stain Gram negative. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the bacteria are bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises isolated mEVs (e.g., from one or more strains of bacteria (e.g., bacteria of interest)) (e.g., a therapeutically effective amount thereof). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is isolated mEV of bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise secreted mEVs (smEVs).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise processed mEVs (pmEVs).


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from live bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from dead bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs are from one strain of bacteria.


In some embodiments, the mEVs are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient).


In some embodiments, the mEVs are gamma irradiated.


In some embodiments, the mEVs are UV irradiated.


In some embodiments, the mEVs are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the mEVs are acid treated.


In some embodiments, the mEVs are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the mEVs are from Gram positive bacteria.


In some embodiments, the mEVs are from Gram negative bacteria.


In some embodiments, the mEVs are from aerobic bacteria.


In some embodiments, the mEVs are from anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the mEVs are from acidophile bacteria.


In some embodiments, the mEVs are from alkaliphile bacteria.


In some embodiments, the mEVs are from neutralophile bacteria.


In some embodiments, the mEVs are from fastidious bacteria.


In some embodiments, the mEVs are from nonfastidious bacteria.


In some embodiments, the mEVs are from bacteria of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the mEVs are from a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the mEVs are from bacteria of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the mEVs are from a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the mEVs are from bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the mEVs are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria.


In some embodiments, the mEVs are from Prevotella histicola bacteria.


In some embodiments, the mEVs are from Bifidobacterium animalis bacteria.


In some embodiments, the mEVs are from Veillonella parvula bacteria.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the mEVs are from Prevotella bacteria. In some embodiments, the Prevotella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the mEVs are from Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the mEVs are from Veillonella bacteria. In some embodiments, the Veillonella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the mEVs are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the mEVs are from Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the mEVs are from Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the mEVs are from Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the mEVs are from bacteria of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bifidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the mEVs are from bacteria of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the mEVs are from Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the mEVs are from Blautia hydrogenotrophica bacteria.


In some embodiments, the mEVs are from Blautia stercoris bacteria.


In some embodiments, the mEVs are from Blautia wexlerae bacteria.


In some embodiments, the mEVs are from Enterococcus gallinarum bacteria.


In some embodiments, the mEVs are from Enterococcus faecium bacteria.


In some embodiments, the mEVs are from Bifidobacterium bifidium bacteria.


In some embodiments, the mEVs are from Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from Bifidobacterium longum bacteria.


In some embodiments, the mEVs are from Roseburia hominis bacteria.


In some embodiments, the mEVs are from Bacteroides thetaiotaomicron bacteria.


In some embodiments, the mEVs are from Bacteroides coprocola bacteria.


In some embodiments, the mEVs are from Erysipelatoclostridium ramosum bacteria.


In some embodiments, the mEVs are from Megasphera massiliensis bacteria.


In some embodiments, the mEVs are from Eubacterium bacteria.


In some embodiments, the mEVs are from Parabacteroides distasonis bacteria.


In some embodiments, the mEVs are from Lactobacillus plantarum bacteria.


In some embodiments, the mEVs are from bacteria of the Negativicutes class.


In some embodiments, the mEVs are from bacteria of the Veillonellaceae family.


In some embodiments, the mEVs are from bacteria of the Selenomonadaceae family.


In some embodiments, the mEVs are from bacteria of the Acidaminococcaceae family.


In some embodiments, the mEVs are from bacteria of the Sporomusaceae family.


In some embodiments, the mEVs are from bacteria of the Megasphaera genus.


In some embodiments, the mEVs are from bacteria of the Selenomonas genus.


In some embodiments, the mEVs are from bacteria of the Propionospora genus.


In some embodiments, the mEVs are from bacteria of the Acidaminococcus genus.


In some embodiments, the mEVs are from Megasphaera sp. bacteria.


In some embodiments, the mEVs are from Selenomonas felix bacteria.


In some embodiments, the mEVs are from Acidaminococcus intestini bacteria.


In some embodiments, the mEVs are from Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the Clostridia class.


In some embodiments, the mEVs are from bacteria of the Oscillospriraceae family.


In some embodiments, the mEVs are from bacteria of the Faecalibacterium genus.


In some embodiments, the mEVs are from bacteria of the Fournierella genus.


In some embodiments, the mEVs are from bacteria of the Harryflintia genus.


In some embodiments, the mEVs are from bacteria of the Agathobaculum genus.


In some embodiments, the mEVs are from Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the mEVs are from Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the mEVs are from Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the mEVs are from Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the mEVs are from a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the mEVs are from bacteria of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the mEVs are from bacteria of order Bacteroidales. In some embodiments, the mEVs are from bacteria of the family Porphyromonoadaceae. In some embodiments, the mEVs are from bacteria of the family Prevotellaceae. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Bacteroidia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Clostridia [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Eubacteriales. In some embodiments, the mEVs are from bacteria of the family Oscillispiraceae. In some embodiments, the mEVs are from bacteria of the family Lachnospiraceae. In some embodiments, the mEVs are from bacteria of the family Peptostreptococcaceae. In some embodiments, the mEVs are from bacteria of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram positive. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the mEVs are from bacteria of the class Negativicutes [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Veillonellales. In some embodiments, the mEVs are from bacteria of the family Veillonelloceae. In some embodiments, the mEVs are from bacteria of the order Selenomonadales. In some embodiments, the mEVs are from bacteria of the family Selenomonadaceae. In some embodiments, the mEVs are from bacteria of the family Sporomusaceae. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Negativicutes that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Synergistia [phylum Synergistota]. In some embodiments, the mEVs are from bacteria of the order Synergistales. In some embodiments, the mEVs are from bacteria of the family Synergistaceae. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Synergistia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the mEVs are from bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×107 to about 2×1012 (e.g., about 3×1010 or about 1.5×1011 or about 1.5×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×1010 to about 2×1012 (e.g., about 1.6×1011 or about 8×1011 or about 9.6×1011 about 12.8×1011 or about 1.6×1012) cells (e.g., wherein cell number is determined by total cell count, e.g., as determined by Coulter counter), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×109, about 3×109, about 5×109, about 1.5×1010, about 3×1010, about 5×1010, about 1.5×1011, about 1.5×1012, or about 2×1012 cells, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×105 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×1010 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of the pharmaceutical agent (e.g., bacteria and/or mEVs) is about 10 mg to about 3500 mg, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of the pharmaceutical agent (e.g., bacteria and/or mEVs) is about 30 mg to about 1300 mg (by weight of bacteria and/or mEVs) (about 25, about 30, about 35, about 50, about 75, about 100, about 120, about 150, about 250, about 300, about 350, about 400, about 500, about 600, about 700, about 750, about 800, about 900, about 1000, about 1100, about 1200, about 1250, about 1300, about 2000, about 2500, about 3000, or about 3500 mg wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 2×106 to about 2×1016 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 5 mg to about 900 mg total protein (e.g., wherein total protein is determined by Bradford assay or BCA), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the solid dosage form further comprises one or more additional pharmaceutical agents.


In some embodiments, the solid dosage form further comprises an excipient (e.g., an excipient described herein, e.g., a diluent, a binder and/or an adhesive, a disintegrant, a lubricant and/or a glidant, a coloring agent, a flavoring agent, and/or a sweetening agent).


In some aspects, the disclosure provides a method of treating a subject (e.g., human) (e.g., a subject in need of treatment), the method comprising:

    • administering to the subject a solid dosage form, wherein the solid dosage form comprises a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), and wherein the solid dosage form is enterically coated (e.g., comprises an enteric coating; e.g., is coated with an enteric coating).


In some aspects, the disclosure provides a solid dosage form for use in treating a subject (e.g., human) (e.g., a subject in need of treatment), wherein the solid dosage form comprises a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), and wherein the solid dosage form is enterically coated (e.g., comprises an enteric coating; e.g., is coated with an enteric coating).


In some aspects, the disclosure provides use of a solid dosage form for the preparation of a medicament for treating a subject (e.g., human) (e.g., a subject in need of treatment), wherein the solid dosage form comprises a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), and wherein the solid dosage form is enterically coated (e.g., comprises an enteric coating; e.g., is coated with an enteric coating).


In some embodiments, the solid dosage form is orally administered (e.g., is for oral administration).


In some embodiments, the solid dosage form (e.g., a capsule, a tablet, or a plurality of minitablets (e.g., contained in a capsule)) is administered (e.g., is for administration) 1, 2, 3, or 4 times a day.


In some embodiments, the solid dosage form comprises a capsule, a tablet, or a plurality of minitablets (e.g., contained in a capsule) and 1, 2, 3, or 4 solid dosage forms (e.g., a capsule, a tablet, or a plurality of minitablets (e.g., contained in a capsule)) are administered (e.g., are for administration) 1, 2, 3, or 4 times a day.


In some embodiments, the solid dosage form provides an increase in efficacy or in physiological effect of the pharmaceutical agent (e.g., 10-fold or more) as compared to other dosage forms (e.g., as compared to the same dose of the pharmaceutical agent administered in a form that does not comprise the enteric coating, e.g., a non-enterically coated tablet or non-enterically coated minitablet or a suspension of biomass or powder).


In some embodiments, the solid dosage form provides release in the small intestine of the pharmaceutical agent contained in the solid dosage form.


In some embodiments, the solid dosage form delivers the pharmaceutical agent to the small intestine, wherein the pharmaceutical agent can act on immune cells and/or epithelial cells in the small intestine, e.g., to cause a systemic effect (e.g., an effect outside of the gastrointestinal tract).


In some embodiments, the solid dosage form provides increased efficacy or increased physiological effect (10-fold or more increased efficacy) (e.g., as measured by a systemic effect (e.g., outside of the gastrointestinal tract) of the pharmaceutical agent, e.g., in ear thickness in DTH model for inflammation; tumor size in cancer model), e.g., as compared to the same dose of the pharmaceutical agent administered in a form that does not comprise the enteric coating, e.g., a suspension or non-enterically coated tablet or non-enterically coated minitablet).


In some embodiments, the pharmaceutical agent provides one or more beneficial immune effects outside the gastrointestinal tract (e.g., outside of the small intestine), e.g., when orally administered.


In some embodiments, the pharmaceutical agent modulates immune effects outside the gastrointestinal tract (e.g., outside of the small intestine) in the subject, e.g., when orally administered.


In some embodiments, the pharmaceutical agent causes a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when orally administered.


In some embodiments, the pharmaceutical agent acts on immune cells and/or epithelial cells in the small intestine (e.g., causing a systemic effect (e.g., an effect outside of the gastrointestinal tract)), e.g., when orally administered.


In some embodiments, the solid dosage form is administered orally and has one or more beneficial immune effects outside the gastrointestinal tract (e.g., interaction between the pharmaceutical agent and cells in the small intestine modulates a systemic immune response).


In some embodiments, the solid dosage form is administered orally and modulates immune effects outside the gastrointestinal tract (e.g., interaction between agent and cells in the small intestine modulates a systemic immune response).


In some embodiments, the solid dosage form is administered orally and activates innate antigen presenting cells (e.g., in the small intestine).


In some embodiments, the subject is in need of treatment (and/or prevention) of a cancer.


In some embodiments, the subject is in need of treatment (and/or prevention) of an autoimmune disease.


In some embodiments, the subject is in need of treatment (and/or prevention) of an inflammatory disease.


In some embodiments, the subject is in need of treatment (and/or prevention) of a metabolic disease.


In some embodiments, the subject is in need of treatment (and/or prevention) of dysbiosis.


In some embodiments, the solid dosage form is administered in combination with an additional pharmaceutical agent.


In certain embodiments, the solid dosage form comprises a capsule. In some embodiments, the capsule is a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule. In some embodiments, the capsule is a size 0 capsule.


In some embodiments, the solid dosage form comprises a tablet. In some embodiments, the tablet (e.g., enterically coated tablet) is a 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm, 11 mm, 12 mm, 13 mm, 14 mm, 15 mm, 16 mm, 17 mm, or 18 mm tablet.


In some embodiments, the solid dosage form comprises a minitablet. In some embodiments, the minitablet (e.g., enterically coated minitablet) is a 1 mm minitablet, 1.5 mm minitablet, 2 mm minitablet, 3 mm minitablet, or 4 mm minitablet. In some embodiments, a plurality of enterically coated minitablets are contained in a capsule (e.g., a size 0 capsule can contain about 31 to about 35 (e.g., 33) minitablets, wherein the minitablets are 3 mm in size). In some embodiments, the capsule is a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule. In some embodiments, the capsule comprises HPMC (hydroxyl propyl methyl cellulose) or gelatin.


In some embodiments, the enteric coating comprises one enteric coating.


In some embodiments, the enteric coating comprises an inner enteric coating and an outer enteric coating, and wherein the inner and outer enteric coatings are not identical (e.g., the inner and outer enteric coatings do not contain identical components in identical amounts).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a polymethacrylate-based copolymer.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1).


In some embodiments, the one enteric coating comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1) (such as Kollicoat MAE 100P).


In some embodiments, the one enteric coating comprises a Eudragit copolymer, e.g., a Eudragit L (e.g., Eudragit L 100-55; Eudragit L 30 D-55), a Eudragit S, a Eudragit RL, a Eudragit RS, a Eudragit E, or a Eudragit FS (e.g., Eudragit FS 30 D).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises cellulose acetate phthalate (CAP), cellulose acetate trimellitate (CAT), poly(vinyl acetate phthalate) (PVAP), hydroxypropyl methylcellulose phthalate (HPMCP), a fatty acid, a wax, shellac (esters of aleurtic acid), a plastic, a plant fiber, zein, Aqua-Zein (an aqueous zein formulation containing no alcohol), amylose starch, a starch derivative, a dextrin, a methyl acrylate-methacrylic acid copolymer, cellulose acetate succinate, hydroxypropyl methyl cellulose acetate succinate (hypromellose acetate succinate), a methyl methacrylate-methacrylic acid copolymer, or sodium alginate.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises an anionic polymeric material.


In some embodiments, the pharmaceutical agent agent comprises bacteria.


In some embodiments, the pharmaceutical agent comprises microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent comprises bacteria and microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent has one or more beneficial immune effects outside the gastrointestinal tract, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent modulates immune effects outside the gastrointestinal tract (e.g., outside of the small intestine) in the subject, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent causes a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent acts on immune cells and/or epithelial cells in the small intestine (e.g., causing a systemic effect (e.g., an effect outside of the gastrointestinal tract)), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent comprises isolated bacteria (e.g., from one or more strains of bacteria (e.g., bacteria of interest) (e.g., a therapeutically effective amount thereof)). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is the isolated bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises live bacteria.


In some embodiments, the pharmaceutical agent comprises dead bacteria.


In some embodiments, the pharmaceutical agent comprises non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises bacteria from one strain of microbe (e.g., bacteria).


In some embodiments, the bacteria are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient) (e.g., a powder form).


In some embodiments, the bacteria are gamma irradiated.


In some embodiments, the bacteria are UV irradiated.


In some embodiments, the bacteria are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the bacteria are acid treated.


In some embodiments, the bacteria are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the bacteria are Gram positive bacteria.


In some embodiments, the bacteria are Gram negative bacteria.


In some embodiments, the bacteria are aerobic bacteria.


In some embodiments, the bacteria are anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the bacteria are acidophile bacteria.


In some embodiments, the bacteria are alkaliphile bacteria.


In some embodiments, the bacteria are neutralophile bacteria.


In some embodiments, the bacteria are fastidious bacteria.


In some embodiments, the bacteria are nonfastidious bacteria.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the bacteria are a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the bacteria are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the bacteria are of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria.


In some embodiments, the bacteria are Prevotella histicola bacteria.


In some embodiments, the bacteria are Bifidobacterium animalis bacteria.


In some embodiments, the bacteria are Veillonella parvula bacteria.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the bacteria are Prevotella bacteria. In some embodiments, the Prevotella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the bacteria are Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the bacteria are Veillonella bacteria. In some embodiments, the Veillonella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the bacteria are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the bacteria are Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the bacteria are Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the bacteria are Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the bacteria are of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bfidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the bacteria are of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the bacteria are Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the bacteria are BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the bacteria are Blautia hydrogenotrophica bacteria.


In some embodiments, the bacteria are Blautia stercoris bacteria.


In some embodiments, the bacteria are Blautia wexlerae bacteria.


In some embodiments, the bacteria are Enterococcus gallinarum bacteria.


In some embodiments, the bacteria are Enterococcus faecium bacteria.


In some embodiments, the bacteria are Bifidobacterium bifidium bacteria.


In some embodiments, the bacteria are Bifidobacterium breve bacteria.


In some embodiments, the bacteria are Bifidobacterium longum bacteria.


In some embodiments, the bacteria are Roseburia hominis bacteria.


In some embodiments, the bacteria are Bacteroides thetaiotaomicron bacteria.


In some embodiments, the bacteria are Bacteroides coprocola bacteria.


In some embodiments, the bacteria are Erysipelatoclostridium ramosum bacteria.


In some embodiments, the bacteria are Megasphera massiliensis bacteria.


In some embodiments, the bacteria are Eubacterium bacteria.


In some embodiments, the bacteria are Parabacteroides distasonis bacteria.


In some embodiments, the bacteria are Lactobacillus plantarum bacteria.


In some embodiments, the bacteria are bacteria of the Negativicutes class.


In some embodiments, the bacteria are of the Veillonellaceae family.


In some embodiments, the bacteria are of the Selenomonadaceae family.


In some embodiments, the bacteria are of the Acidaminococcaceae family.


In some embodiments, the bacteria are of the Sporomusaceae family.


In some embodiments, the bacteria are of the Megasphaera genus.


In some embodiments, the bacteria are of the Selenomonas genus.


In some embodiments, the bacteria are of the Propionospora genus.


In some embodiments, the bacteria are of the Acidaminococcus genus.


In some embodiments, the bacteria are Megasphaera sp. bacteria.


In some embodiments, the bacteria are Selenomonas felix bacteria.


In some embodiments, the bacteria are Acidaminococcus intestini bacteria.


In some embodiments, the bacteria are Propionospora sp. bacteria.


In some embodiments, the bacteria are bacteria of the Clostridia class.


In some embodiments, the bacteria are of the Oscillospriraceae family.


In some embodiments, the bacteria are of the Faecalibacterium genus.


In some embodiments, the bacteria are of the Fournierella genus.


In some embodiments, the bacteria are of the Harryflintia genus.


In some embodiments, the bacteria are of the Agathobaculum genus.


In some embodiments, the bacteria are Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the bacteria are Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the bacteria are Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the bacteria are Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the bacteria are a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the bacteria are of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the bacteria are of order Bacteroidales. In some embodiments, the bacteria are of the family Porphyromonoadaceae. In some embodiments, the bacteria are of the family Prevotellaceae. In some embodiments, the bacteria are of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Bacteroidia that stain Gram negative. In some embodiments, the bacteria are of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Clostridia [phylum Firmicutes]. In some embodiments, the bacteria are of the order Eubacteriales. In some embodiments, the bacteria are of the family Oscillispiraceae. In some embodiments, the bacteria are of the family Lachnospiraceae. In some embodiments, the bacteria are of the family Peptostreptococcaceae. In some embodiments, the bacteria are of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the bacteria are of the class Clostridia that stain Gram negative. In some embodiments, the bacteria are of the class Clostridia that stain Gram positive. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the bacteria are of the class Negativicutes [phylum Firmicutes]. In some embodiments, the bacteria are of the order Veillonellales. In some embodiments, the bacteria are of the family Veillonelloceae. In some embodiments, the bacteria are of the order Selenomonadales. In some embodiments, the bacteria are of the family Selenomonadaceae. In some embodiments, the bacteria are of the family Sporomusaceae. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Negativicutes that stain Gram negative. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Synergistia [phylum Synergistota]. In some embodiments, the bacteria are of the order Synergistales. In some embodiments, the bacteria are of the family Synergistaceae. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Synergistia that stain Gram negative. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the bacteria are bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises isolated mEVs (e.g., from one or more strains of bacteria (e.g., bacteria of interest)) (e.g., a therapeutically effective amount thereof). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is isolated mEV of bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise secreted mEVs (smEVs).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise processed mEVs (pmEVs).


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from live bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from dead bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs are from one strain of bacteria.


In some embodiments, the mEVs are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient).


In some embodiments, the mEVs are gamma irradiated.


In some embodiments, the mEVs are UV irradiated.


In some embodiments, the mEVs are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the mEVs are acid treated.


In some embodiments, the mEVs are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the mEVs are from Gram positive bacteria.


In some embodiments, the mEVs are from Gram negative bacteria.


In some embodiments, the mEVs are from aerobic bacteria.


In some embodiments, the mEVs are from anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the mEVs are from acidophile bacteria.


In some embodiments, the mEVs are from alkaliphile bacteria.


In some embodiments, the mEVs are from neutralophile bacteria.


In some embodiments, the mEVs are from fastidious bacteria.


In some embodiments, the mEVs are from nonfastidious bacteria.


In some embodiments, the mEVs are from bacteria of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the mEVs are from a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the mEVs are from bacteria of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the mEVs are from a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the mEVs are from bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the mEVs are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria.


In some embodiments, the mEVs are from Prevotella histicola bacteria.


In some embodiments, the mEVs are from Bifidobacterium animalis bacteria.


In some embodiments, the mEVs are from Veillonella parvula bacteria.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the mEVs are from Prevotella bacteria. In some embodiments, the Prevotella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the mEVs are from Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the mEVs are from Veillonella bacteria. In some embodiments, the Veillonella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the mEVs are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the mEVs are from Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the mEVs are from Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the mEVs are from Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the mEVs are from bacteria of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bifidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the mEVs are from bacteria of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the mEVs are from Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the mEVs are from Blautia hydrogenotrophica bacteria.


In some embodiments, the mEVs are from Blautia stercoris bacteria.


In some embodiments, the mEVs are from Blautia wexlerae bacteria.


In some embodiments, the mEVs are from Enterococcus gallinarum bacteria.


In some embodiments, the mEVs are from Enterococcus faecium bacteria.


In some embodiments, the mEVs are from Bifidobacterium bifidium bacteria.


In some embodiments, the mEVs are from Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from Bifidobacterium longum bacteria.


In some embodiments, the mEVs are from Roseburia hominis bacteria.


In some embodiments, the mEVs are from Bacteroides thetaiotaomicron bacteria.


In some embodiments, the mEVs are from Bacteroides coprocola bacteria.


In some embodiments, the mEVs are from Erysipelatoclostridium ramosum bacteria.


In some embodiments, the mEVs are from Megasphera massiliensis bacteria.


In some embodiments, the mEVs are from Eubacterium bacteria.


In some embodiments, the mEVs are from Parabacteroides distasonis bacteria.


In some embodiments, the mEVs are from Lactobacillus plantarum bacteria.


In some embodiments, the mEVs are from bacteria of the Negativicutes class.


In some embodiments, the mEVs are from bacteria of the Veillonellaceae family.


In some embodiments, the mEVs are from bacteria of the Selenomonadaceae family.


In some embodiments, the mEVs are from bacteria of the Acidaminococcaceae family.


In some embodiments, the mEVs are from bacteria of the Sporomusaceae family.


In some embodiments, the mEVs are from bacteria of the Megasphaera genus.


In some embodiments, the mEVs are from bacteria of the Selenomonas genus.


In some embodiments, the mEVs are from bacteria of the Propionospora genus.


In some embodiments, the mEVs are from bacteria of the Acidaminococcus genus.


In some embodiments, the mEVs are from Megasphaera sp. bacteria.


In some embodiments, the mEVs are from Selenomonas felix bacteria.


In some embodiments, the mEVs are from Acidaminococcus intestini bacteria.


In some embodiments, the mEVs are from Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the Clostridia class.


In some embodiments, the mEVs are from bacteria of the Oscillospriraceae family.


In some embodiments, the mEVs are from bacteria of the Faecalibacterium genus.


In some embodiments, the mEVs are from bacteria of the Fournierella genus.


In some embodiments, the mEVs are from bacteria of the Harryflintia genus.


In some embodiments, the mEVs are from bacteria of the Agathobaculum genus.


In some embodiments, the mEVs are from Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the mEVs are from Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the mEVs are from Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the mEVs are from Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the mEVs are from a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the mEVs are from bacteria of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the mEVs are from bacteria of order Bacteroidales. In some embodiments, the mEVs are from bacteria of the family Porphyromonoadaceae. In some embodiments, the mEVs are from bacteria of the family Prevotellaceae. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Bacteroidia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Clostridia [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Eubacteriales. In some embodiments, the mEVs are from bacteria of the family Oscillispiraceae. In some embodiments, the mEVs are from bacteria of the family Lachnospiraceae. In some embodiments, the mEVs are from bacteria of the family Peptostreptococcaceae. In some embodiments, the mEVs are from bacteria of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram positive. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the mEVs are from bacteria of the class Negativicutes [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Veillonellales. In some embodiments, the mEVs are from bacteria of the family Veillonelloceae. In some embodiments, the mEVs are from bacteria of the order Selenomonadales. In some embodiments, the mEVs are from bacteria of the family Selenomonadaceae. In some embodiments, the mEVs are from bacteria of the family Sporomusaceae. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Negativicutes that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Synergistia [phylum Synergistota]. In some embodiments, the mEVs are from bacteria of the order Synergistales. In some embodiments, the mEVs are from bacteria of the family Synergistaceae. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Synergistia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the mEVs are from bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×107 to about 2×1012 (e.g., about 3×1010 or about 1.5×1011 or about 1.5×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×1010 to about 2×1012 (e.g., about 1.6×1011 or about 8×1011 or about 9.6×1011 about 12.8×1011 or about 1.6×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×109, about 3×109, about 5×109, about 1.5×1010, about 3×1010, about 5×1010, about 1.5×1011, about 1.5×1012, or about 2×1012 cells, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×105 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×1010 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of drug substance that contains the pharmaceutical agent (e.g., bacteria and/or mEVs) is about 10 mg to about 3500 mg, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of drug substance that contains the pharmaceutical agent (e.g., bacteria and/or mEVs) is about 30 mg to about 1300 mg (by weight of bacteria and/or mEVs) (about 25, about 30, about 35, about 50, about 75, about 100, about 120, about 150, about 250, about 300, about 350, about 400, about 500, about 600, about 700, about 750, about 800, about 900, about 1000, about 1100, about 1200, about 1250, about 1300, about 2000, about 2500, about 3000, or about 3500 mg, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 2×106 to about 2×1016 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of the pharmaceutical agent (e.g., bacteria and/or mEVs) is about 5 mg to about 900 mg total protein (e.g., wherein total protein is determined by Bradford assay or BCA), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the solid dosage form further comprises one or more additional pharmaceutical agents.


In some embodiments, the solid dosage form further comprises an excipient (e.g., an excipient described herein, e.g., a diluent, a binder and/or an adhesive, a disintegrant, a lubricant and/or a glidant, a coloring agent, a flavoring agent, and/or a sweetening agent).


In some aspects, the disclosure provides a method for preparing an enterically coated capsule comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) loading the pharmaceutical agent into a capsule; and
    • b) enterically coating the capsule, thereby preparing the enterically coated capsule.


In some embodiments, the method comprises combining the pharmaceutical agent with a pharmaceutically acceptable excipient prior to loading into the capsule.


In some embodiments, the method for preparing an enterically coated capsule comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), comprises:

    • a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;
    • b) loading the pharmaceutical agent and pharmaceutically acceptable excipient into a capsule; and
    • c) enterically coating the capsule, thereby preparing the enterically coated capsule.


In some embodiments, the method further comprises banding the capsule after loading the capsule and prior to enterically coating the capsule. In some embodiments, the capsule is banded with an HPMC-based banding solution.


In some embodiments, the disclosure provides a method for preparing an enterically coated capsule comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) loading the pharmaceutical agent into a capsule;
    • b) banding the capsule; and
    • c) enterically coating the capsule, thereby preparing the enterically coated capsule.


In some embodiments, the disclosure provides a method for preparing an enterically coated capsule comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;
    • b) loading the pharmaceutical agent and pharmaceutically acceptable excipient into a capsule;
    • c) banding the capsule; and
    • d) enterically coating the capsule, thereby preparing the enterically coated capsule.


In certain embodiments, the solid dosage form comprises a capsule. In some embodiments, the capsule is a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule. In some embodiments, the capsule is a size 0 capsule.


In some embodiments, the capsule comprises HPMC or gelatin. In some embodiments, the capsule comprises HPMC.


In some embodiments, the enteric coating comprises an inner enteric coating and an outer enteric coating, and wherein the inner and outer enteric coatings are not identical (e.g., the inner and outer enteric coatings do not contain identical components in identical amounts).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a polymethacrylate-based copolymer.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1).


In some embodiments, the one enteric coating comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1) (such as Kollicoat MAE 100P).


In some embodiments, the one enteric coating comprises a Eudragit copolymer, e.g., a Eudragit L (e.g., Eudragit L 100-55; Eudragit L 30 D-55), a Eudragit S, a Eudragit RL, a Eudragit RS, a Eudragit E, or a Eudragit FS (e.g., Eudragit FS 30 D).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises cellulose acetate phthalate (CAP), cellulose acetate trimellitate (CAT), poly(vinyl acetate phthalate) (PVAP), hydroxypropyl methylcellulose phthalate (HPMCP), a fatty acid, a wax, shellac (esters of aleurtic acid), a plastic, a plant fiber, zein, Aqua-Zein (an aqueous zein formulation containing no alcohol), amylose starch, a starch derivative, a dextrin, a methyl acrylate-methacrylic acid copolymer, cellulose acetate succinate, hydroxypropyl methyl cellulose acetate succinate (hypromellose acetate succinate), a methyl methacrylate-methacrylic acid copolymer, or sodium alginate.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises an anionic polymeric material.


In some embodiments, the pharmaceutical agent comprises bacteria.


In some embodiments, the pharmaceutical agent comprises microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent comprises bacteria and microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent has one or more beneficial immune effects outside the gastrointestinal tract, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent modulates immune effects outside the gastrointestinal tract (e.g., outside of the small intestine) in the subject, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent causes a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent acts on immune cells and/or epithelial cells in the small intestine (e.g., causing a systemic effect (e.g., an effect outside of the gastrointestinsl tract), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent comprises isolated bacteria (e.g., from one or more strains of bacteria (e.g., bacteria of interest) (e.g., a therapeutically effective amount thereof)). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is the isolated bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises live bacteria.


In some embodiments, the pharmaceutical agent comprises dead bacteria.


In some embodiments, the pharmaceutical agent comprises non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises bacteria from one strain of microbe (e.g., bacteria).


In some embodiments, the bacteria are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient) (e.g., a powder form).


In some embodiments, the bacteria are gamma irradiated.


In some embodiments, the bacteria are UV irradiated.


In some embodiments, the bacteria are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the bacteria are acid treated.


In some embodiments, the bacteria are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the bacteria are Gram positive bacteria.


In some embodiments, the bacteria are Gram negative bacteria.


In some embodiments, the bacteria are aerobic bacteria.


In some embodiments, the bacteria are anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the bacteria are acidophile bacteria.


In some embodiments, the bacteria are alkaliphile bacteria.


In some embodiments, the bacteria are neutralophile bacteria.


In some embodiments, the bacteria are fastidious bacteria.


In some embodiments, the bacteria are nonfastidious bacteria.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the bacteria are a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the bacteria are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the bacteria are of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria.


In some embodiments, the bacteria are Prevotella histicola bacteria.


In some embodiments, the bacteria are Bifidobacterium animalis bacteria.


In some embodiments, the bacteria are Veillonella parvula bacteria.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the bacteria are Prevotella bacteria. In some embodiments, the Prevotella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the bacteria are Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the bacteria are Veillonella bacteria. In some embodiments, the Veillonella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the bacteria are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the bacteria are Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the bacteria are Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the bacteria are Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the bacteria are of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bfidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the bacteria are of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the bacteria are Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the bacteria are BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the bacteria are Blautia hydrogenotrophica bacteria.


In some embodiments, the bacteria are Blautia stercoris bacteria.


In some embodiments, the bacteria are Blautia wexlerae bacteria.


In some embodiments, the bacteria are Enterococcus gallinarum bacteria.


In some embodiments, the bacteria are Enterococcus faecium bacteria.


In some embodiments, the bacteria are Bifidobacterium bifidium bacteria.


In some embodiments, the bacteria are Bifidobacterium breve bacteria.


In some embodiments, the bacteria are Bifidobacterium longum bacteria.


In some embodiments, the bacteria are Roseburia hominis bacteria.


In some embodiments, the bacteria are Bacteroides thetaiotaomicron bacteria.


In some embodiments, the bacteria are Bacteroides coprocola bacteria.


In some embodiments, the bacteria are Erysipelatoclostridium ramosum bacteria.


In some embodiments, the bacteria are Megasphera massiliensis bacteria.


In some embodiments, the bacteria are Eubacterium bacteria.


In some embodiments, the bacteria are Parabacteroides distasonis bacteria.


In some embodiments, the bacteria are Lactobacillus plantarum bacteria.


In some embodiments, the bacteria are bacteria of the Negativicutes class.


In some embodiments, the bacteria are of the Veillonellaceae family.


In some embodiments, the bacteria are of the Selenomonadaceae family.


In some embodiments, the bacteria are of the Acidaminococcaceae family.


In some embodiments, the bacteria are of the Sporomusaceae family.


In some embodiments, the bacteria are of the Megasphaera genus.


In some embodiments, the bacteria are of the Selenomonas genus.


In some embodiments, the bacteria are of the Propionospora genus.


In some embodiments, the bacteria are of the Acidaminococcus genus.


In some embodiments, the bacteria are Megasphaera sp. bacteria.


In some embodiments, the bacteria are Selenomonas felix bacteria.


In some embodiments, the bacteria are Acidaminococcus intestini bacteria.


In some embodiments, the bacteria are Propionospora sp. bacteria.


In some embodiments, the bacteria are bacteria of the Clostridia class.


In some embodiments, the bacteria are of the Oscillospriraceae family.


In some embodiments, the bacteria are of the Faecalibacterium genus.


In some embodiments, the bacteria are of the Fournierella genus.


In some embodiments, the bacteria are of the Harryflintia genus.


In some embodiments, the bacteria are of the Agathobaculum genus.


In some embodiments, the bacteria are Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the bacteria are Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the bacteria are Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the bacteria are Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the bacteria are a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the bacteria are of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the bacteria are of order Bacteroidales. In some embodiments, the bacteria are of the family Porphyromonoadaceae. In some embodiments, the bacteria are of the family Prevotellaceae. In some embodiments, the bacteria are of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Bacteroidia that stain Gram negative. In some embodiments, the bacteria are of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Clostridia [phylum Firmicutes]. In some embodiments, the bacteria are of the order Eubacteriales. In some embodiments, the bacteria are of the family Oscillispiraceae. In some embodiments, the bacteria are of the family Lachnospiraceae. In some embodiments, the bacteria are of the family Peptostreptococcaceae. In some embodiments, the bacteria are of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the bacteria are of the class Clostridia that stain Gram negative. In some embodiments, the bacteria are of the class Clostridia that stain Gram positive. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the bacteria are of the class Negativicutes [phylum Firmicutes]. In some embodiments, the bacteria are of the order Veillonellales. In some embodiments, the bacteria are of the family Veillonelloceae. In some embodiments, the bacteria are of the order Selenomonadales. In some embodiments, the bacteria are of the family Selenomonadaceae. In some embodiments, the bacteria are of the family Sporomusaceae. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Negativicutes that stain Gram negative. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Synergistia [phylum Synergistota]. In some embodiments, the bacteria are of the order Synergistales. In some embodiments, the bacteria are of the family Synergistaceae. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Synergistia that stain Gram negative. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the bacteria are bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises isolated mEVs (e.g., from one or more strains of bacteria (e.g., bacteria of interest)) (e.g., a therapeutically effective amount thereof). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is isolated mEV of bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise secreted mEVs (smEVs).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise processed mEVs (pmEVs).


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from live bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from dead bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs are from one strain of bacteria.


In some embodiments, the mEVs are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient).


In some embodiments, the mEVs are gamma irradiated.


In some embodiments, the mEVs are UV irradiated.


In some embodiments, the mEVs are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the mEVs are acid treated.


In some embodiments, the mEVs are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the mEVs are from Gram positive bacteria.


In some embodiments, the mEVs are from Gram negative bacteria.


In some embodiments, the mEVs are from aerobic bacteria.


In some embodiments, the mEVs are from anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the mEVs are from acidophile bacteria.


In some embodiments, the mEVs are from alkaliphile bacteria.


In some embodiments, the mEVs are from neutralophile bacteria.


In some embodiments, the mEVs are from fastidious bacteria.


In some embodiments, the mEVs are from nonfastidious bacteria.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the bacteria are a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the mEVs are from bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the mEVs are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria.


In some embodiments, the mEVs are from Prevotella histicola bacteria.


In some embodiments, the mEVs are from Bifidobacterium animalis bacteria.


In some embodiments, the mEVs are from Veillonella parvula bacteria.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the mEVs are from Prevotella bacteria. In some embodiments, the Prevotella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the mEVs are from Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the mEVs are from Veillonella bacteria. In some embodiments, the Veillonella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the mEVs are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the mEVs are from Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the mEVs are from Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the mEVs are from Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the mEVs are from bacteria of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bifidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the mEVs are from bacteria of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the mEVs are from Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the mEVs are from Blautia hydrogenotrophica bacteria.


In some embodiments, the mEVs are from Blautia stercoris bacteria.


In some embodiments, the mEVs are from Blautia wexlerae bacteria.


In some embodiments, the mEVs are from Enterococcus gallinarum bacteria.


In some embodiments, the mEVs are from Enterococcus faecium bacteria.


In some embodiments, the mEVs are from Bifidobacterium bifidium bacteria.


In some embodiments, the mEVs are from Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from Bifidobacterium longum bacteria.


In some embodiments, the mEVs are from Roseburia hominis bacteria.


In some embodiments, the mEVs are from Bacteroides thetaiotaomicron bacteria.


In some embodiments, the mEVs are from Bacteroides coprocola bacteria.


In some embodiments, the mEVs are from Erysipelatoclostridium ramosum bacteria.


In some embodiments, the mEVs are from Megasphera massiliensis bacteria.


In some embodiments, the mEVs are from Eubacterium bacteria.


In some embodiments, the mEVs are from Parabacteroides distasonis bacteria.


In some embodiments, the mEVs are from Lactobacillus plantarum bacteria.


In some embodiments, the mEVs are from bacteria of the Negativicutes class.


In some embodiments, the mEVs are from bacteria of the Veillonellaceae family.


In some embodiments, the mEVs are from bacteria of the Selenomonadaceae family.


In some embodiments, the mEVs are from bacteria of the Acidaminococcaceae family.


In some embodiments, the mEVs are from bacteria of the Sporomusaceae family.


In some embodiments, the mEVs are from bacteria of the Megasphaera genus.


In some embodiments, the mEVs are from bacteria of the Selenomonas genus.


In some embodiments, the mEVs are from bacteria of the Propionospora genus.


In some embodiments, the mEVs are from bacteria of the Acidaminococcus genus.


In some embodiments, the mEVs are from Megasphaera sp. bacteria.


In some embodiments, the mEVs are from Selenomonas felix bacteria.


In some embodiments, the mEVs are from Acidaminococcus intestini bacteria.


In some embodiments, the mEVs are from Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the Clostridia class.


In some embodiments, the mEVs are from bacteria of the Oscillospriraceae family.


In some embodiments, the mEVs are from bacteria of the Faecalibacterium genus.


In some embodiments, the mEVs are from bacteria of the Fournierella genus.


In some embodiments, the mEVs are from bacteria of the Harryflintia genus.


In some embodiments, the mEVs are from bacteria of the Agathobaculum genus.


In some embodiments, the mEVs are from Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the mEVs are from Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the mEVs are from Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the mEVs are from Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the mEVs are from a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the mEVs are from bacteria of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the mEVs are from bacteria of order Bacteroidales. In some embodiments, the mEVs are from bacteria of the family Porphyromonoadaceae. In some embodiments, the mEVs are from bacteria of the family Prevotellaceae. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Bacteroidia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Clostridia [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Eubacteriales. In some embodiments, the mEVs are from bacteria of the family Oscillispiraceae. In some embodiments, the mEVs are from bacteria of the family Lachnospiraceae. In some embodiments, the mEVs are from bacteria of the family Peptostreptococcaceae. In some embodiments, the mEVs are from bacteria of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram positive. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the mEVs are from bacteria of the class Negativicutes [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Veillonellales. In some embodiments, the mEVs are from bacteria of the family Veillonelloceae. In some embodiments, the mEVs are from bacteria of the order Selenomonadales. In some embodiments, the mEVs are from bacteria of the family Selenomonadaceae. In some embodiments, the mEVs are from bacteria of the family Sporomusaceae. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Negativicutes that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Synergistia [phylum Synergistota]. In some embodiments, the mEVs are from bacteria of the order Synergistales. In some embodiments, the mEVs are from bacteria of the family Synergistaceae. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Synergistia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the mEVs are from bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×107 to about 2×1012 (e. g about 3×1010 or about 1.5×1011 or about 1.5×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule. In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×1010 to about 2×1012 (e.g., about 1.6×1011 or about 8×1011 or about 9.6×1011 about 12.8×1011 or about 1.6×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×109, about 3×109, about 5×109, about 1.5×1010, about 3×1010, about 5×1010, about 1.5×1011, about 1.5×1012, or about 2×1012 cells, wherein the dose is per capsule.


In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×105 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×1010 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 10 mg to about 3500 mg, wherein the dose is per tablet.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of drug substance that contains the pharmaceutical agent (e.g., bacteria and/or mEVs) is about 30 mg to about 1300 mg (by weight of bacteria and/or mEVs) (about 25, about 30, about 35, about 50, about 75, about 100, about 120, about 150, about 250, about 300, about 350, about 400, about 500, about 600, about 700, about 750, about 800, about 900, about 1000, about 1100, about 1200, about 1250, about 1300, about 2000, about 2500, about 3000, or about 3500 mg, wherein the dose is per capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 2×106 to about 2×1016 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 5 mg to about 900 mg total protein (e.g., wherein total protein is determined by Bradford assay or BCA), wherein the dose is per capsule.


In some embodiments, the can be (or be present in) a medicinal product, medical food, a food product, or a dietary supplement.


In some embodiments, the solid dosage form further comprises one or more additional pharmaceutical agents.


In some embodiments, the solid dosage form further comprises an excipient (e.g., an excipient described herein, e.g., a diluent, a binder and/or an adhesive, a disintegrant, a lubricant and/or a glidant, a coloring agent, a flavoring agent, and/or a sweetening agent).


In some aspects, the disclosure provides a method for preparing an enterically coated tablet comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;
    • b) compressing the pharmaceutical agent and pharmaceutically acceptable excipient, thereby forming a tablet; and
    • c) enterically coating the tablet, thereby preparing the enterically coated tablet.


In some embodiments, the tablet (e.g., enterically coated tablet) is a 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm, 11 mm, 12 mm, 13 mm, 14 mm, 15 mm, 16 mm, 17 mm, or 18 mm tablet.


In some embodiments, the enteric coating comprises one enteric coating.


In some embodiments, the enteric coating comprises an inner enteric coating and an outer enteric coating, and wherein the inner and outer enteric coatings are not identical (e.g., the inner and outer enteric coatings do not contain identical components in identical amounts).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a polymethacrylate-based copolymer.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1).


In some embodiments, the one enteric coating comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1) (such as Kollicoat MAE 100P).


In some embodiments, the one enteric coating comprises a Eudragit copolymer, e.g., a Eudragit L (e.g., Eudragit L 100-55; Eudragit L 30 D-55), a Eudragit S, a Eudragit RL, a Eudragit RS, a Eudragit E, or a Eudragit FS (e.g., Eudragit FS 30 D).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises cellulose acetate phthalate (CAP), cellulose acetate trimellitate (CAT), poly(vinyl acetate phthalate) (PVAP), hydroxypropyl methylcellulose phthalate (HPMCP), a fatty acid, a wax, shellac (esters of aleurtic acid), a plastic, a plant fiber, zein, Aqua-Zein (an aqueous zein formulation containing no alcohol), amylose starch, a starch derivative, a dextrin, a methyl acrylate-methacrylic acid copolymer, cellulose acetate succinate, hydroxypropyl methyl cellulose acetate succinate (hypromellose acetate succinate), a methyl methacrylate-methacrylic acid copolymer, or sodium alginate.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises an anionic polymeric material.


In some embodiments, the pharmaceutical agent comprises bacteria.


In some embodiments, the pharmaceutical agent comprises microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent comprises bacteria and microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent has one or more beneficial immune effects outside the gastrointestinal tract, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent modulates immune effects outside the gastrointestinal tract (e.g., outside of the small intestine) in the subject, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent causes a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent acts on immune cells and/or epithelial cells in the small intestine (e.g., causing a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent comprises isolated bacteria (e.g., from one or more strains of bacteria (e.g., bacteria of interest) (e.g., a therapeutically effective amount thereof)). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is the isolated bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises live bacteria.


In some embodiments, the pharmaceutical agent comprises dead bacteria.


In some embodiments, the pharmaceutical agent comprises non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises bacteria from one strain of microbe (e.g., bacteria).


In some embodiments, the bacteria are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient) (e.g., a powder form).


In some embodiments, the bacteria are gamma irradiated.


In some embodiments, the bacteria are UV irradiated.


In some embodiments, the bacteria are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the bacteria are acid treated.


In some embodiments, the bacteria are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the bacteria are Gram positive bacteria.


In some embodiments, the bacteria are Gram negative bacteria.


In some embodiments, the bacteria are aerobic bacteria.


In some embodiments, the bacteria are anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the bacteria are acidophile bacteria.


In some embodiments, the bacteria are alkaliphile bacteria.


In some embodiments, the bacteria are neutralophile bacteria.


In some embodiments, the bacteria are fastidious bacteria.


In some embodiments, the bacteria are nonfastidious bacteria.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the bacteria are a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the bacteria are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the bacteria are of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria.


In some embodiments, the bacteria are Prevotella histicola bacteria.


In some embodiments, the bacteria are Bifidobacterium animalis bacteria.


In some embodiments, the bacteria are Veillonella parvula bacteria.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the bacteria are Prevotella bacteria. In some embodiments, the Prevotella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the bacteria are Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the bacteria are Veillonella bacteria. In some embodiments, the Veillonella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the bacteria are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the bacteria are Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the bacteria are Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the bacteria are Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the bacteria are of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bifidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the bacteria are of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the bacteria are Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the bacteria are BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the bacteria are Blautia hydrogenotrophica bacteria.


In some embodiments, the bacteria are Blautia stercoris bacteria.


In some embodiments, the bacteria are Blautia wexlerae bacteria.


In some embodiments, the bacteria are Enterococcus gallinarum bacteria.


In some embodiments, the bacteria are Enterococcus faecium bacteria.


In some embodiments, the bacteria are Bifidobacterium bifidium bacteria.


In some embodiments, the bacteria are Bifidobacterium breve bacteria.


In some embodiments, the bacteria are Bifidobacterium longum bacteria.


In some embodiments, the bacteria are Roseburia hominis bacteria.


In some embodiments, the bacteria are Bacteroides thetaiotaomicron bacteria.


In some embodiments, the bacteria are Bacteroides coprocola bacteria.


In some embodiments, the bacteria are Erysipelatoclostridium ramosum bacteria.


In some embodiments, the bacteria are Megasphera massiliensis bacteria.


In some embodiments, the bacteria are Eubacterium bacteria.


In some embodiments, the bacteria are Parabacteroides distasonis bacteria.


In some embodiments, the bacteria are Lactobacillus plantarum bacteria.


In some embodiments, the bacteria are bacteria of the Negativicutes class.


In some embodiments, the bacteria are of the Veillonellaceae family.


In some embodiments, the bacteria are of the Selenomonadaceae family.


In some embodiments, the bacteria are of the Acidaminococcaceae family.


In some embodiments, the bacteria are of the Sporomusaceae family.


In some embodiments, the bacteria are of the Megasphaera genus.


In some embodiments, the bacteria are of the Selenomonas genus.


In some embodiments, the bacteria are of the Propionospora genus.


In some embodiments, the bacteria are of the Acidaminococcus genus.


In some embodiments, the bacteria are Megasphaera sp. bacteria.


In some embodiments, the bacteria are Selenomonas felix bacteria.


In some embodiments, the bacteria are Acidaminococcus intestini bacteria.


In some embodiments, the bacteria are Propionospora sp. bacteria.


In some embodiments, the bacteria are bacteria of the Clostridia class.


In some embodiments, the bacteria are of the Oscillospriraceae family.


In some embodiments, the bacteria are of the Faecalibacterium genus.


In some embodiments, the bacteria are of the Fournierella genus.


In some embodiments, the bacteria are of the Harryflintia genus.


In some embodiments, the bacteria are of the Agathobaculum genus.


In some embodiments, the bacteria are Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the bacteria are Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the bacteria are Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the bacteria are Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the bacteria are a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the bacteria are of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the bacteria are of order Bacteroidales. In some embodiments, the bacteria are of the family Porphyromonoadaceae. In some embodiments, the bacteria are of the family Prevotellaceae. In some embodiments, the bacteria are of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Bacteroidia that stain Gram negative. In some embodiments, the bacteria are of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Clostridia [phylum Firmicutes]. In some embodiments, the bacteria are of the order Eubacteriales. In some embodiments, the bacteria are of the family Oscillispiraceae. In some embodiments, the bacteria are of the family Lachnospiraceae. In some embodiments, the bacteria are of the family Peptostreptococcaceae. In some embodiments, the bacteria are of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the bacteria are of the class Clostridia that stain Gram negative. In some embodiments, the bacteria are of the class Clostridia that stain Gram positive. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the bacteria are of the class Negativicutes [phylum Firmicutes]. In some embodiments, the bacteria are of the order Veillonellales. In some embodiments, the bacteria are of the family Veillonelloceae. In some embodiments, the bacteria are of the order Selenomonadales. In some embodiments, the bacteria are of the family Selenomonadaceae. In some embodiments, the bacteria are of the family Sporomusaceae. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Negativicutes that stain Gram negative. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Synergistia [phylum Synergistota]. In some embodiments, the bacteria are of the order Synergistales. In some embodiments, the bacteria are of the family Synergistaceae. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Synergistia that stain Gram negative. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the bacteria are bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises isolated mEVs (e.g., from one or more strains of bacteria (e.g., bacteria of interest)) (e.g., a therapeutically effective amount thereof). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is isolated mEV of bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise secreted mEVs (smEVs).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise processed mEVs (pmEVs).


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from live bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from dead bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs are from one strain of bacteria.


In some embodiments, the mEVs are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient).


In some embodiments, the mEVs are gamma irradiated.


In some embodiments, the mEVs are UV irradiated.


In some embodiments, the mEVs are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the mEVs are acid treated.


In some embodiments, the mEVs are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the mEVs are from Gram positive bacteria.


In some embodiments, the mEVs are from Gram negative bacteria.


In some embodiments, the mEVs are from aerobic bacteria.


In some embodiments, the mEVs are from anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the mEVs are from acidophile bacteria.


In some embodiments, the mEVs are from alkaliphile bacteria.


In some embodiments, the mEVs are from neutralophile bacteria.


In some embodiments, the mEVs are from fastidious bacteria.


In some embodiments, the mEVs are from nonfastidious bacteria.


In some embodiments, the mEVs are from bacteria of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the mEVs are from a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the mEVs are from bacteria of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the mEVs are from a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the mEVs are from bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the mEVs are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria.


In some embodiments, the mEVs are from Prevotella histicola bacteria.


In some embodiments, the mEVs are from Bifidobacterium animalis bacteria.


In some embodiments, the mEVs are from Veillonella parvula bacteria.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the mEVs are from Prevotella bacteria. In some embodiments, the Prevotella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the mEVs are from Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the mEVs are from Veillonella bacteria. In some embodiments, the Veillonella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the mEVs are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the mEVs are from Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the mEVs are from Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the mEVs are from Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the mEVs are from bacteria of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bifidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the mEVs are from bacteria of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the mEVs are from Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the mEVs are from Blautia hydrogenotrophica bacteria.


In some embodiments, the mEVs are from Blautia stercoris bacteria.


In some embodiments, the mEVs are from Blautia wexlerae bacteria.


In some embodiments, the mEVs are from Enterococcus gallinarum bacteria.


In some embodiments, the mEVs are from Enterococcus faecium bacteria.


In some embodiments, the mEVs are from Bifidobacterium bifidium bacteria.


In some embodiments, the mEVs are from Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from Bifidobacterium longum bacteria.


In some embodiments, the mEVs are from Roseburia hominis bacteria.


In some embodiments, the mEVs are from Bacteroides thetaiotaomicron bacteria.


In some embodiments, the mEVs are from Bacteroides coprocola bacteria.


In some embodiments, the mEVs are from Erysipelatoclostridium ramosum bacteria.


In some embodiments, the mEVs are from Megasphera massiliensis bacteria.


In some embodiments, the mEVs are from Eubacterium bacteria.


In some embodiments, the mEVs are from Parabacteroides distasonis bacteria.


In some embodiments, the mEVs are from Lactobacillus plantarum bacteria.


In some embodiments, the mEVs are from bacteria of the Negativicutes class.


In some embodiments, the mEVs are from bacteria of the Veillonellaceae family.


In some embodiments, the mEVs are from bacteria of the Selenomonadaceae family.


In some embodiments, the mEVs are from bacteria of the Acidaminococcaceae family.


In some embodiments, the mEVs are from bacteria of the Sporomusaceae family.


In some embodiments, the mEVs are from bacteria of the Megasphaera genus.


In some embodiments, the mEVs are from bacteria of the Selenomonas genus.


In some embodiments, the mEVs are from bacteria of the Propionospora genus.


In some embodiments, the mEVs are from bacteria of the Acidaminococcus genus.


In some embodiments, the mEVs are from Megasphaera sp. bacteria.


In some embodiments, the mEVs are from Selenomonas felix bacteria.


In some embodiments, the mEVs are from Acidaminococcus intestini bacteria.


In some embodiments, the mEVs are from Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the Clostridia class.


In some embodiments, the mEVs are from bacteria of the Oscillospriraceae family.


In some embodiments, the mEVs are from bacteria of the Faecalibacterium genus.


In some embodiments, the mEVs are from bacteria of the Fournierella genus.


In some embodiments, the mEVs are from bacteria of the Harryflintia genus.


In some embodiments, the mEVs are from bacteria of the Agathobaculum genus.


In some embodiments, the mEVs are from Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the mEVs are from Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the mEVs are from Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the mEVs are from Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the mEVs are from a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the mEVs are from bacteria of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the mEVs are from bacteria of order Bacteroidales. In some embodiments, the mEVs are from bacteria of the family Porphyromonoadaceae. In some embodiments, the mEVs are from bacteria of the family Prevotellaceae. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Bacteroidia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Clostridia [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Eubacteriales. In some embodiments, the mEVs are from bacteria of the family Oscillispiraceae. In some embodiments, the mEVs are from bacteria of the family Lachnospiraceae. In some embodiments, the mEVs are from bacteria of the family Peptostreptococcaceae. In some embodiments, the mEVs are from bacteria of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram positive. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the mEVs are from bacteria of the class Negativicutes [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Veillonellales. In some embodiments, the mEVs are from bacteria of the family Veillonelloceae. In some embodiments, the mEVs are from bacteria of the order Selenomonadales. In some embodiments, the mEVs are from bacteria of the family Selenomonadaceae. In some embodiments, the mEVs are from bacteria of the family Sporomusaceae. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Negativicutes that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Synergistia [phylum Synergistota]. In some embodiments, the mEVs are from bacteria of the order Synergistales. In some embodiments, the mEVs are from bacteria of the family Synergistaceae. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Synergistia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the mEVs are from bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×107 to about 2×1012 (e. g about 3×1010 or about 1.5×1011 or about 1.5×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per tablet. In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×1010 to about 2×1012 (e.g., about 1.6×1011 or about 8×1011 or about 9.6×1011 about 12.8×1011 or about 1.6×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per tablet.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×109, about 3×109, about 5×109, about 1.5×1010, about 3×1010, about 5×1010, about 1.5×1011, about 1.5×1012, or about 2×1012 cells, wherein the dose is per tablet.


In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×105 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×1010 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per tablet.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 10 mg to about 3500 mg, wherein the dose is per tablet.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of drug substance that contains the pharmaceutical agent (e.g., bacteria and/or mEVs) is about 30 mg to about 1300 mg (by weight of bacteria and/or mEVs) (about 25, about 30, about 35, about 50, about 75, about 100, about 120, about 150, about 250, about 300, about 350, about 400, about 500, about 600, about 700, about 750, about 800, about 900, about 1000, about 1100, about 1200, about 1250, about 1300, about 2000, about 2500, about 3000, or about 3500 mg, wherein the dose is per tablet.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 2×106 to about 2×1016 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per tablet.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 5 mg to about 900 mg total protein (e.g., wherein total protein is determined by Bradford assay or BCA), wherein the dose is per tablet.


In some embodiments, the can be (or be present in) a medicinal product, medical food, a food product, or a dietary supplement.


In some embodiments, the solid dosage form further comprises one or more additional pharmaceutical agents.


In some embodiments, the solid dosage form further comprises an excipient (e.g., an excipient described herein, e.g., a diluent, a binder and/or an adhesive, a disintegrant, a lubricant and/or a glidant, a coloring agent, a flavoring agent, and/or a sweetening agent).


In some aspects, the disclosure provides a method for preparing an enterically coated minitablet comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;
    • b) compressing the pharmaceutical agent and pharmaceutically acceptable excipient, thereby forming a minitablet; and
    • c) enterically coating the minitablet, thereby preparing the enterically coated minitablet.


In some embodiments, one or more minitablets are loaded into a capsule. In some embodiments, the method further comprises banding the capsule after loading the capsule. In some embodiments, the capsule is banded with an HPMC-based banding solution.


In some embodiments, the minitablet (e.g., enterically coated minitablet) is a 1 mm minitablet, 1.5 mm minitablet, 2 mm minitablet, 3 mm minitablet, or 4 mm minitablet. In some embodiments, a plurality of enterically coated minitablets are contained in a capsule (e.g., a size 0 capsule can contain about 31 to about 35 (e.g., 33) minitablets, wherein the minitablets are 3 mm in size). In some embodiments, the capsule is a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule. In some embodiments, the capsule comprises HPMC (hydroxyl propyl methyl cellulose) or gelatin.


In some embodiments, the enteric coating comprises one enteric coating.


In some embodiments, the enteric coating comprises an inner enteric coating and an outer enteric coating, and wherein the inner and outer enteric coatings are not identical (e.g., the inner and outer enteric coatings do not contain identical components in identical amounts).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a polymethacrylate-based copolymer.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1).


In some embodiments, the one enteric coating comprises methacrylic acid ethyl acrylate (MAE) copolymer (1:1) (such as Kollicoat MAE 100P).


In some embodiments, the one enteric coating comprises a Eudragit copolymer, e.g., a Eudragit L (e.g., Eudragit L 100-55; Eudragit L 30 D-55), a Eudragit S, a Eudragit RL, a Eudragit RS, a Eudragit E, or a Eudragit FS (e.g., Eudragit FS 30 D).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises cellulose acetate phthalate (CAP), cellulose acetate trimellitate (CAT), poly(vinyl acetate phthalate) (PVAP), hydroxypropyl methylcellulose phthalate (HPMCP), a fatty acid, a wax, shellac (esters of aleurtic acid), a plastic, a plant fiber, zein, Aqua-Zein (an aqueous zein formulation containing no alcohol), amylose starch, a starch derivative, a dextrin, a methyl acrylate-methacrylic acid copolymer, cellulose acetate succinate, hydroxypropyl methyl cellulose acetate succinate (hypromellose acetate succinate), a methyl methacrylate-methacrylic acid copolymer, or sodium alginate.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises an anionic polymeric material.


In some embodiments, the pharmaceutical agent comprises bacteria.


In some embodiments, the pharmaceutical agent comprises microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent comprises bacteria and microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent has one or more beneficial immune effects outside the gastrointestinal tract, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent modulates immune effects outside the gastrointestinal tract (e.g., outside of the small intestine) in the subject, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent causes a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent acts on immune cells and/or epithelial cells in the small intestine (e.g., causing a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent comprises isolated bacteria (e.g., from one or more strains of bacteria (e.g., bacteria of interest) (e.g., a therapeutically effective amount thereof)). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is the isolated bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises live bacteria.


In some embodiments, the pharmaceutical agent comprises dead bacteria.


In some embodiments, the pharmaceutical agent comprises non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises bacteria from one strain of microbe (e.g., bacteria).


In some embodiments, the bacteria are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient) (e.g., a powder form).


In some embodiments, the bacteria are gamma irradiated.


In some embodiments, the bacteria are UV irradiated.


In some embodiments, the bacteria are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the bacteria are acid treated.


In some embodiments, the bacteria are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the bacteria are Gram positive bacteria.


In some embodiments, the bacteria are Gram negative bacteria.


In some embodiments, the bacteria are aerobic bacteria.


In some embodiments, the bacteria are anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the bacteria are acidophile bacteria.


In some embodiments, the bacteria are alkaliphile bacteria.


In some embodiments, the bacteria are neutralophile bacteria.


In some embodiments, the bacteria are fastidious bacteria.


In some embodiments, the bacteria are nonfastidious bacteria.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the bacteria are a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the bacteria are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the bacteria are of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria.


In some embodiments, the bacteria are Prevotella histicola bacteria.


In some embodiments, the bacteria are Bifidobacterium animalis bacteria.


In some embodiments, the bacteria are Veillonella parvula bacteria.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the bacteria are Prevotella bacteria. In some embodiments, the Prevotella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the bacteria are Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the bacteria are Veillonella bacteria. In some embodiments, the Veillonella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the bacteria are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the bacteria are Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the bacteria are Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the bacteria are Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the bacteria are of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bfidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the bacteria are of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the bacteria are Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the bacteria are BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the bacteria are Blautia hydrogenotrophica bacteria.


In some embodiments, the bacteria are Blautia stercoris bacteria.


In some embodiments, the bacteria are Blautia wexlerae bacteria.


In some embodiments, the bacteria are Enterococcus gallinarum bacteria.


In some embodiments, the bacteria are Enterococcus faecium bacteria.


In some embodiments, the bacteria are Bifidobacterium bifidium bacteria.


In some embodiments, the bacteria are Bifidobacterium breve bacteria.


In some embodiments, the bacteria are Bifidobacterium longum bacteria.


In some embodiments, the bacteria are Roseburia hominis bacteria.


In some embodiments, the bacteria are Bacteroides thetaiotaomicron bacteria.


In some embodiments, the bacteria are Bacteroides coprocola bacteria.


In some embodiments, the bacteria are Erysipelatoclostridium ramosum bacteria.


In some embodiments, the bacteria are Megasphera massiliensis bacteria.


In some embodiments, the bacteria are Eubacterium bacteria.


In some embodiments, the bacteria are Parabacteroides distasonis bacteria.


In some embodiments, the bacteria are Lactobacillus plantarum bacteria.


In some embodiments, the bacteria are bacteria of the Negativicutes class.


In some embodiments, the bacteria are of the Veillonellaceae family.


In some embodiments, the bacteria are of the Selenomonadaceae family.


In some embodiments, the bacteria are of the Acidaminococcaceae family.


In some embodiments, the bacteria are of the Sporomusaceae family.


In some embodiments, the bacteria are of the Megasphaera genus.


In some embodiments, the bacteria are of the Selenomonas genus.


In some embodiments, the bacteria are of the Propionospora genus.


In some embodiments, the bacteria are of the Acidaminococcus genus.


In some embodiments, the bacteria are Megasphaera sp. bacteria.


In some embodiments, the bacteria are Selenomonas felix bacteria.


In some embodiments, the bacteria are Acidaminococcus intestini bacteria.


In some embodiments, the bacteria are Propionospora sp. bacteria.


In some embodiments, the bacteria are bacteria of the Clostridia class.


In some embodiments, the bacteria are of the Oscillospriraceae family.


In some embodiments, the bacteria are of the Faecalibacterium genus.


In some embodiments, the bacteria are of the Fournierella genus.


In some embodiments, the bacteria are of the Harryflintia genus.


In some embodiments, the bacteria are of the Agathobaculum genus.


In some embodiments, the bacteria are Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the bacteria are Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the bacteria are Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the bacteria are Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the bacteria are a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the bacteria are of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the bacteria are of order Bacteroidales. In some embodiments, the bacteria are of the family Porphyromonoadaceae. In some embodiments, the bacteria are of the family Prevotellaceae. In some embodiments, the bacteria are of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Bacteroidia that stain Gram negative. In some embodiments, the bacteria are of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Clostridia [phylum Firmicutes]. In some embodiments, the bacteria are of the order Eubacteriales. In some embodiments, the bacteria are of the family Oscillispiraceae. In some embodiments, the bacteria are of the family Lachnospiraceae. In some embodiments, the bacteria are of the family Peptostreptococcaceae. In some embodiments, the bacteria are of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the bacteria are of the class Clostridia that stain Gram negative. In some embodiments, the bacteria are of the class Clostridia that stain Gram positive. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the bacteria are of the class Negativicutes [phylum Firmicutes]. In some embodiments, the bacteria are of the order Veillonellales. In some embodiments, the bacteria are of the family Veillonelloceae. In some embodiments, the bacteria are of the order Selenomonadales. In some embodiments, the bacteria are of the family Selenomonadaceae. In some embodiments, the bacteria are of the family Sporomusaceae. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Negativicutes that stain Gram negative. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Synergistia [phylum Synergistota]. In some embodiments, the bacteria are of the order Synergistales. In some embodiments, the bacteria are of the family Synergistaceae. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Synergistia that stain Gram negative. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the bacteria are bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises isolated mEVs (e.g., from one or more strains of bacteria (e.g., bacteria of interest)) (e.g., a therapeutically effective amount thereof). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is isolated mEV of bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise secreted mEVs (smEVs).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise processed mEVs (pmEVs).


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from live bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from dead bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs are from one strain of bacteria.


In some embodiments, the mEVs are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient).


In some embodiments, the mEVs are gamma irradiated.


In some embodiments, the mEVs are UV irradiated.


In some embodiments, the mEVs are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the mEVs are acid treated.


In some embodiments, the mEVs are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the mEVs are from Gram positive bacteria.


In some embodiments, the mEVs are from Gram negative bacteria.


In some embodiments, the mEVs are from aerobic bacteria.


In some embodiments, the mEVs are from anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the mEVs are from acidophile bacteria.


In some embodiments, the mEVs are from alkaliphile bacteria.


In some embodiments, the mEVs are from neutralophile bacteria.


In some embodiments, the mEVs are from fastidious bacteria.


In some embodiments, the mEVs are from nonfastidious bacteria.


In some embodiments, the mEVs are from bacteria of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the mEVs are from a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the mEVs are from bacteria of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the mEVs are from a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the mEVs are from bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the mEVs are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria.


In some embodiments, the mEVs are from Prevotella histicola bacteria.


In some embodiments, the mEVs are from Bifidobacterium animalis bacteria.


In some embodiments, the mEVs are from Veillonella parvula bacteria.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the mEVs are from Prevotella bacteria. In some embodiments, the Prevotella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the mEVs are from Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the mEVs are from Veillonella bacteria. In some embodiments, the Veillonella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the mEVs are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the mEVs are from Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the mEVs are from Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the mEVs are from Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the mEVs are from bacteria of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bifidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the mEVs are from bacteria of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the mEVs are from Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the mEVs are from Blautia hydrogenotrophica bacteria.


In some embodiments, the mEVs are from Blautia stercoris bacteria.


In some embodiments, the mEVs are from Blautia wexlerae bacteria.


In some embodiments, the mEVs are from Enterococcus gallinarum bacteria.


In some embodiments, the mEVs are from Enterococcus faecium bacteria.


In some embodiments, the mEVs are from Bifidobacterium bifidium bacteria.


In some embodiments, the mEVs are from Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from Bifidobacterium longum bacteria.


In some embodiments, the mEVs are from Roseburia hominis bacteria.


In some embodiments, the mEVs are from Bacteroides thetaiotaomicron bacteria.


In some embodiments, the mEVs are from Bacteroides coprocola bacteria.


In some embodiments, the mEVs are from Erysipelatoclostridium ramosum bacteria.


In some embodiments, the mEVs are from Megasphera massiliensis bacteria.


In some embodiments, the mEVs are from Eubacterium bacteria.


In some embodiments, the mEVs are from Parabacteroides distasonis bacteria.


In some embodiments, the mEVs are from Lactobacillus plantarum bacteria.


In some embodiments, the mEVs are from bacteria of the Negativicutes class.


In some embodiments, the mEVs are from bacteria of the Veillonellaceae family.


In some embodiments, the mEVs are from bacteria of the Selenomonadaceae family.


In some embodiments, the mEVs are from bacteria of the Acidaminococcaceae family.


In some embodiments, the mEVs are from bacteria of the Sporomusaceae family.


In some embodiments, the mEVs are from bacteria of the Megasphaera genus.


In some embodiments, the mEVs are from bacteria of the Selenomonas genus.


In some embodiments, the mEVs are from bacteria of the Propionospora genus.


In some embodiments, the mEVs are from bacteria of the Acidaminococcus genus.


In some embodiments, the mEVs are from Megasphaera sp. bacteria.


In some embodiments, the mEVs are from Selenomonas felix bacteria.


In some embodiments, the mEVs are from Acidaminococcus intestini bacteria.


In some embodiments, the mEVs are from Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the Clostridia class.


In some embodiments, the mEVs are from bacteria of the Oscillospriraceae family.


In some embodiments, the mEVs are from bacteria of the Faecalibacterium genus.


In some embodiments, the mEVs are from bacteria of the Fournierella genus.


In some embodiments, the mEVs are from bacteria of the Harryflintia genus.


In some embodiments, the mEVs are from bacteria of the Agathobaculum genus.


In some embodiments, the mEVs are from Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the mEVs are from Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the mEVs are from Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the mEVs are from Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the mEVs are from a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the mEVs are from bacteria of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the mEVs are from bacteria of order Bacteroidales. In some embodiments, the mEVs are from bacteria of the family Porphyromonoadaceae. In some embodiments, the mEVs are from bacteria of the family Prevotellaceae. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Bacteroidia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Clostridia [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Eubacteriales. In some embodiments, the mEVs are from bacteria of the family Oscillispiraceae. In some embodiments, the mEVs are from bacteria of the family Lachnospiraceae. In some embodiments, the mEVs are from bacteria of the family Peptostreptococcaceae. In some embodiments, the mEVs are from bacteria of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram positive. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the mEVs are from bacteria of the class Negativicutes [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Veillonellales. In some embodiments, the mEVs are from bacteria of the family Veillonelloceae. In some embodiments, the mEVs are from bacteria of the order Selenomonadales. In some embodiments, the mEVs are from bacteria of the family Selenomonadaceae. In some embodiments, the mEVs are from bacteria of the family Sporomusaceae. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Negativicutes that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Synergistia [phylum Synergistota]. In some embodiments, the mEVs are from bacteria of the order Synergistales. In some embodiments, the mEVs are from bacteria of the family Synergistaceae. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Synergistia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the mEVs are from bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×107 to about 2×1012 (e.g., about 3×1010 or about 1.5×1011 or about 1.5×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×1010 to about 2×1012 (e.g., about 1.6×1011 or about 8×1011 or about 9.6×1011 about 12.8×1011 or about 1.6×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×109, about 3×109, about 5×109, about 1.5×1010, about 3×1010, about 5×1010, about 1.5×1011, about 1.5×1012, or about 2×1012 cells, wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×105 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×1010 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of the pharmaceutical agent (e.g., bacteria and/or mEVs) is about 10 mg to about 3500 mg, wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of the pharmaceutical agent (e.g., bacteria and/or mEVs) is about 30 mg to about 1300 mg (by weight of bacteria and/or mEVs) (about 25, about 30, about 35, about 50, about 75, about 100, about 120, about 150, about 250, about 300, about 350, about 400, about 500, about 600, about 700, about 750, about 800, about 900, about 1000, about 1100, about 1200, about 1250, about 1300, about 2000, about 2500, about 3000, or about 3500 mg, wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 2×106 to about 2×1016 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 5 mg to about 900 mg total protein (e.g., wherein total protein is determined by Bradford assay or BCA), wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the solid dosage form further comprises one or more additional pharmaceutical agents.


In some embodiments, the solid dosage form further comprises an excipient (e.g., an excipient described herein, e.g., a diluent, a binder and/or an adhesive, a disintegrant, a lubricant and/or a glidant, a coloring agent, a flavoring agent, and/or a sweetening agent).


In some aspects, the disclosure provides a method for preparing a capsule comprising an enterically coated minitablet comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;
    • b) compressing the pharmaceutical agent and pharmaceutically acceptable excipient, thereby forming a minitablet;
    • c) enterically coating the minitablet (e.g., thereby preparing the enterically coated minitablet), and
    • d) loading the capsule with the enterically coated minitablet (e.g., a size 0 capsule can contain about 31 to about 35 (e.g., 33) minitablets, wherein the minitablets are 3 mm in size),
    • thereby preparing the capsule.


In some embodiments, the method further comprises banding the capsule after loading the capsule. In some embodiments, the capsule is banded with an HPMC-based banding solution.


In some embodiments, the minitablet (e.g., enterically coated minitablet) is a 1 mm minitablet, 1.5 mm minitablet, 2 mm minitablet, 3 mm minitablet, or 4 mm minitablet. In some embodiments, the capsule is a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule. In some embodiments, the capsule comprises HPMC (hydroxyl propyl methyl cellulose) or gelatin.


In some embodiments, the enteric coating comprises one enteric coating.


In some embodiments, the enteric coating comprises an inner enteric coating and an outer enteric coating, and wherein the inner and outer enteric coatings are not identical (e.g., the inner and outer enteric coatings do not contain identical components in identical amounts).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a polymethacrylate-based copolymer.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1).


In some embodiments, the one enteric coating comprises methacrylic acid ethyl acrylate (MAE) copolymer (1:1) (such as Kollicoat MAE 100P).


In some embodiments, the one enteric coating comprises a Eudragit copolymer, e.g., a Eudragit L (e.g., Eudragit L 100-55; Eudragit L 30 D-55), a Eudragit S, a Eudragit RL, a Eudragit RS, a Eudragit E, or a Eudragit FS (e.g., Eudragit FS 30 D).


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises cellulose acetate phthalate (CAP), cellulose acetate trimellitate (CAT), poly(vinyl acetate phthalate) (PVAP), hydroxypropyl methylcellulose phthalate (HPMCP), a fatty acid, a wax, shellac (esters of aleurtic acid), a plastic, a plant fiber, zein, Aqua-Zein (an aqueous zein formulation containing no alcohol), amylose starch, a starch derivative, a dextrin, a methyl acrylate-methacrylic acid copolymer, cellulose acetate succinate, hydroxypropyl methyl cellulose acetate succinate (hypromellose acetate succinate), a methyl methacrylate-methacrylic acid copolymer, or sodium alginate.


In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises an anionic polymeric material.


In some embodiments, the pharmaceutical agent comprises bacteria.


In some embodiments, the pharmaceutical agent comprises microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent comprises bacteria and microbial extracellular vesicles (mEV).


In some embodiments, the pharmaceutical agent has one or more beneficial immune effects outside the gastrointestinal tract, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent modulates immune effects outside the gastrointestinal tract (e.g., outside of the small intestine) in the subject, e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent causes a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent acts on immune cells and/or epithelial cells in the small intestine (e.g., causing a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.


In some embodiments, the pharmaceutical agent comprises isolated bacteria (e.g., from one or more strains of bacteria (e.g., bacteria of interest) (e.g., a therapeutically effective amount thereof)). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is the isolated bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises live bacteria.


In some embodiments, the pharmaceutical agent comprises dead bacteria.


In some embodiments, the pharmaceutical agent comprises non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises bacteria from one strain of microbe (e.g., bacteria).


In some embodiments, the bacteria are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient) (e.g., a powder form).


In some embodiments, the bacteria are gamma irradiated.


In some embodiments, the bacteria are UV irradiated.


In some embodiments, the bacteria are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the bacteria are acid treated.


In some embodiments, the bacteria are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the bacteria are Gram positive bacteria.


In some embodiments, the bacteria are Gram negative bacteria.


In some embodiments, the bacteria are aerobic bacteria.


In some embodiments, the bacteria are anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the bacteria are acidophile bacteria.


In some embodiments, the bacteria are alkaliphile bacteria.


In some embodiments, the bacteria are neutralophile bacteria.


In some embodiments, the bacteria are fastidious bacteria.


In some embodiments, the bacteria are nonfastidious bacteria.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the bacteria are a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the bacteria are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the bacteria are of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria.


In some embodiments, the bacteria are Prevotella histicola bacteria.


In some embodiments, the bacteria are Bifidobacterium animalis bacteria.


In some embodiments, the bacteria are Veillonella parvula bacteria.


In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the bacteria are Prevotella bacteria. In some embodiments, the Prevotella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the bacteria are Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the bacteria are Veillonella bacteria. In some embodiments, the Veillonella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the bacteria are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the bacteria are Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the bacteria are Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the bacteria are Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the bacteria are of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bfidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the bacteria are of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the bacteria are Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the bacteria are BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the bacteria are Blautia hydrogenotrophica bacteria.


In some embodiments, the bacteria are Blautia stercoris bacteria.


In some embodiments, the bacteria are Blautia wexlerae bacteria.


In some embodiments, the bacteria are Enterococcus gallinarum bacteria.


In some embodiments, the bacteria are Enterococcus faecium bacteria.


In some embodiments, the bacteria are Bifidobacterium bifidium bacteria.


In some embodiments, the bacteria are Bifidobacterium breve bacteria.


In some embodiments, the bacteria are Bifidobacterium longum bacteria.


In some embodiments, the bacteria are Roseburia hominis bacteria.


In some embodiments, the bacteria are Bacteroides thetaiotaomicron bacteria.


In some embodiments, the bacteria are Bacteroides coprocola bacteria.


In some embodiments, the bacteria are Erysipelatoclostridium ramosum bacteria.


In some embodiments, the bacteria are Megasphera massiliensis bacteria.


In some embodiments, the bacteria are Eubacterium bacteria.


In some embodiments, the bacteria are Parabacteroides distasonis bacteria.


In some embodiments, the bacteria are Lactobacillus plantarum bacteria.


In some embodiments, the bacteria are bacteria of the Negativicutes class.


In some embodiments, the bacteria are of the Veillonellaceae family.


In some embodiments, the bacteria are of the Selenomonadaceae family.


In some embodiments, the bacteria are of the Acidaminococcaceae family.


In some embodiments, the bacteria are of the Sporomusaceae family.


In some embodiments, the bacteria are of the Megasphaera genus.


In some embodiments, the bacteria are of the Selenomonas genus.


In some embodiments, the bacteria are of the Propionospora genus.


In some embodiments, the bacteria are of the Acidaminococcus genus.


In some embodiments, the bacteria are Megasphaera sp. bacteria.


In some embodiments, the bacteria are Selenomonas felix bacteria.


In some embodiments, the bacteria are Acidaminococcus intestini bacteria.


In some embodiments, the bacteria are Propionospora sp. bacteria.


In some embodiments, the bacteria are bacteria of the Clostridia class.


In some embodiments, the bacteria are of the Oscillospriraceae family.


In some embodiments, the bacteria are of the Faecalibacterium genus.


In some embodiments, the bacteria are of the Fournierella genus.


In some embodiments, the bacteria are of the Harryflintia genus.


In some embodiments, the bacteria are of the Agathobaculum genus.


In some embodiments, the bacteria are Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the bacteria are Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the bacteria are Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the bacteria are Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the bacteria are a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the bacteria are of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the bacteria are of order Bacteroidales. In some embodiments, the bacteria are of the family Porphyromonoadaceae. In some embodiments, the bacteria are of the family Prevotellaceae. In some embodiments, the bacteria are of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Bacteroidia that stain Gram negative. In some embodiments, the bacteria are of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Clostridia [phylum Firmicutes]. In some embodiments, the bacteria are of the order Eubacteriales. In some embodiments, the bacteria are of the family Oscillispiraceae. In some embodiments, the bacteria are of the family Lachnospiraceae. In some embodiments, the bacteria are of the family Peptostreptococcaceae. In some embodiments, the bacteria are of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the bacteria are of the class Clostridia that stain Gram negative. In some embodiments, the bacteria are of the class Clostridia that stain Gram positive. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the bacteria are of the class Negativicutes [phylum Firmicutes]. In some embodiments, the bacteria are of the order Veillonellales. In some embodiments, the bacteria are of the family Veillonelloceae. In some embodiments, the bacteria are of the order Selenomonadales. In some embodiments, the bacteria are of the family Selenomonadaceae. In some embodiments, the bacteria are of the family Sporomusaceae. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Negativicutes that stain Gram negative. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are of the class Synergistia [phylum Synergistota]. In some embodiments, the bacteria are of the order Synergistales. In some embodiments, the bacteria are of the family Synergistaceae. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Synergistia that stain Gram negative. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria are bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the bacteria are bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises isolated mEVs (e.g., from one or more strains of bacteria (e.g., bacteria of interest)) (e.g., a therapeutically effective amount thereof). E.g., wherein at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is isolated mEV of bacteria (e.g., bacteria of interest).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise secreted mEVs (smEVs).


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs comprise processed mEVs (pmEVs).


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from live bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from dead bacteria.


In some embodiments, the pharmaceutical agent comprises pmEVs and the pmEVs are produced from non-replicating bacteria.


In some embodiments, the pharmaceutical agent comprises mEVs and the mEVs are from one strain of bacteria.


In some embodiments, the mEVs are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient).


In some embodiments, the mEVs are gamma irradiated.


In some embodiments, the mEVs are UV irradiated.


In some embodiments, the mEVs are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the mEVs are acid treated.


In some embodiments, the mEVs are oxygen sparged (e.g., at 0.1 vvm for two hours).


In some embodiments, the mEVs are from Gram positive bacteria.


In some embodiments, the mEVs are from Gram negative bacteria.


In some embodiments, the mEVs are from aerobic bacteria.


In some embodiments, the mEVs are from anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the mEVs are from acidophile bacteria.


In some embodiments, the mEVs are from alkaliphile bacteria.


In some embodiments, the mEVs are from neutralophile bacteria.


In some embodiments, the mEVs are from fastidious bacteria.


In some embodiments, the mEVs are from nonfastidious bacteria.


In some embodiments, the mEVs are from bacteria of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, or Table 3.


In some embodiments, the mEVs are from a bacterial strain listed in Table 1, Table 2, or Table 3.


In some embodiments, the mEVs are from bacteria of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.


In some embodiments, the mEVs are from a bacterial strain listed in Table J.


In some embodiments, the Gram negative bacteria belong to class Negativicutes.


In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.


In some embodiments, the mEVs are from bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.


In some embodiments, the mEVs are Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, or Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria.


In some embodiments, the mEVs are from Prevotella histicola bacteria.


In some embodiments, the mEVs are from Bifidobacterium animalis bacteria.


In some embodiments, the mEVs are from Veillonella parvula bacteria.


In some embodiments, the mEVs are from Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are from Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the mEVs are from Prevotella bacteria. In some embodiments, the Prevotella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are from Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the mEVs are from Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are from Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the mEVs are from Veillonella bacteria. In some embodiments, the Veillonella bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are from Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the mEVs are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are from Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the mEVs are from Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are from Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the mEVs are from Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are from Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the mEVs are from Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are from Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the mEVs are from bacteria of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bifidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.


In some embodiments, the mEVs are from bacteria of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.


In some embodiments, the mEVs are from Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from BCG (bacillus Calmette-Guerin), Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.


In some embodiments, the mEVs are from Blautia hydrogenotrophica bacteria.


In some embodiments, the mEVs are from Blautia stercoris bacteria.


In some embodiments, the mEVs are from Blautia wexlerae bacteria.


In some embodiments, the mEVs are from Enterococcus gallinarum bacteria.


In some embodiments, the mEVs are from Enterococcus faecium bacteria.


In some embodiments, the mEVs are from Bifidobacterium bifidium bacteria.


In some embodiments, the mEVs are from Bifidobacterium breve bacteria.


In some embodiments, the mEVs are from Bifidobacterium longum bacteria.


In some embodiments, the mEVs are from Roseburia hominis bacteria.


In some embodiments, the mEVs are from Bacteroides thetaiotaomicron bacteria.


In some embodiments, the mEVs are from Bacteroides coprocola bacteria.


In some embodiments, the mEVs are from Erysipelatoclostridium ramosum bacteria.


In some embodiments, the mEVs are from Megasphera massiliensis bacteria.


In some embodiments, the mEVs are from Eubacterium bacteria.


In some embodiments, the mEVs are from Parabacteroides distasonis bacteria.


In some embodiments, the mEVs are from Lactobacillus plantarum bacteria.


In some embodiments, the mEVs are from bacteria of the Negativicutes class.


In some embodiments, the mEVs are from bacteria of the Veillonellaceae family.


In some embodiments, the mEVs are from bacteria of the Selenomonadaceae family.


In some embodiments, the mEVs are from bacteria of the Acidaminococcaceae family.


In some embodiments, the mEVs are from bacteria of the Sporomusaceae family.


In some embodiments, the mEVs are from bacteria of the Megasphaera genus.


In some embodiments, the mEVs are from bacteria of the Selenomonas genus.


In some embodiments, the mEVs are from bacteria of the Propionospora genus.


In some embodiments, the mEVs are from bacteria of the Acidaminococcus genus.


In some embodiments, the mEVs are from Megasphaera sp. bacteria.


In some embodiments, the mEVs are from Selenomonas felix bacteria.


In some embodiments, the mEVs are from Acidaminococcus intestini bacteria.


In some embodiments, the mEVs are from Propionospora sp. bacteria.


In some embodiments, the mEVs are from bacteria of the Clostridia class.


In some embodiments, the mEVs are from bacteria of the Oscillospriraceae family.


In some embodiments, the mEVs are from bacteria of the Faecalibacterium genus.


In some embodiments, the mEVs are from bacteria of the Fournierella genus.


In some embodiments, the mEVs are from bacteria of the Harryflintia genus.


In some embodiments, the mEVs are from bacteria of the Agathobaculum genus.


In some embodiments, the mEVs are from Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the mEVs are from Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the mEVs are from Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the mEVs are from Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the mEVs are from a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the mEVs are from bacteria of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the mEVs are from bacteria of order Bacteroidales. In some embodiments, the mEVs are from bacteria of the family Porphyromonoadaceae. In some embodiments, the mEVs are from bacteria of the family Prevotellaceae. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Bacteroidia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Clostridia [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Eubacteriales. In some embodiments, the mEVs are from bacteria of the family Oscillispiraceae. In some embodiments, the mEVs are from bacteria of the family Lachnospiraceae. In some embodiments, the mEVs are from bacteria of the family Peptostreptococcaceae. In some embodiments, the mEVs are from bacteria of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia that stain Gram positive. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the mEVs are from bacteria of the class Negativicutes [phylum Firmicutes]. In some embodiments, the mEVs are from bacteria of the order Veillonellales. In some embodiments, the mEVs are from bacteria of the family Veillonelloceae. In some embodiments, the mEVs are from bacteria of the order Selenomonadales. In some embodiments, the mEVs are from bacteria of the family Selenomonadaceae. In some embodiments, the mEVs are from bacteria of the family Sporomusaceae. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Negativicutes that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria of the class Synergistia [phylum Synergistota]. In some embodiments, the mEVs are from bacteria of the order Synergistales. In some embodiments, the mEVs are from bacteria of the family Synergistaceae. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the mEVs are from bacteria of the class Synergistia that stain Gram negative. In some embodiments, the mEVs are from bacteria of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the mEVs are from bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the mEVs are from bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×107 to about 2×1012 (e.g about 3×1010 or about 1.5×1011 or about 1.5×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×1010 to about 2×1012 (e.g., about 1.6×1011 or about 8×1011 or about 9.6×1011 about 12.8×1011 or about 1.6×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×109, about 3×109, about 5×109, about 1.5×1010, about 3×1010, about 5×1010, about 1.5×1011, about 1.5×1012, or about 2×1012 cells, wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×105 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×1010 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 10 mg to about 3500 mg, wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of drug substance that contains the pharmaceutical agent (e.g., bacteria and/or mEVs) is about 30 mg to about 1300 mg (by weight of bacteria and/or mEVs) (about 25, about 30, about 35, about 50, about 75, about 100, about 120, about 150, about 250, about 300, about 350, about 400, about 500, about 600, about 700, about 750, about 800, about 900, about 1000, about 1100, about 1200, about 1250, about 1300, about 2000, about 2500, about 3000, or about 3500 mg, wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 2×106 to about 2×1016 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and/or mEVs and the dose of pharmaceutical agent (e.g., bacteria and/or mEVs) is about 5 mg to about 900 mg total protein (e.g., wherein total protein is determined by Bradford assay or BCA), wherein the dose is per capsule or per total number of minitablets in a capsule.


In some embodiments, the capsule or minitablet further comprises one or more additional pharmaceutical agents.


In some embodiments, the capsule or minitablet further comprises an excipient (e.g., an excipient described herein, e.g., a diluent, a binder and/or an adhesive, a disintegrant, a lubricant and/or a glidant, a coloring agent, a flavoring agent, and/or a sweetening agent).





BRIEF DESCRIPTION OF THE DRAWINGS


FIG. 1 is a graph showing the effects of L. Lactis spp. cremoris solid dosage forms on ear thickness 24 hours after challenge in a DTH model.





DETAILED DESCRIPTION
Definitions

“Adjuvant” or “Adjuvant therapy” broadly refers to an agent that affects an immunological or physiological response in a subject (e.g., human). For example, an adjuvant might increase the presence of an antigen over time or to an area of interest like a tumor, help absorb an antigen presenting cell antigen, activate macrophages and lymphocytes and support the production of cytokines. By changing an immune response, an adjuvant might permit a smaller dose of an immune interacting agent to increase the effectiveness or safety of a particular dose of the immune interacting agent. For example, an adjuvant might prevent T cell exhaustion and thus increase the effectiveness or safety of a particular immune interacting agent.


“Administration” broadly refers to a route of administration of a composition (e.g., a pharmaceutical composition such as a solid dosage form that contains a pharmaceutical agent as described herein) to a subject. Examples of routes of administration include oral administration, rectal administration, topical administration, inhalation (nasal) or injection. Administration by injection includes intravenous (IV), intramuscular (IM), intratumoral (IT) and subcutaneous (SC) administration. A pharmaceutical composition described herein can be administered in any form by any effective route, including but not limited to intratumoral, oral, parenteral, enteral, intravenous, intraperitoneal, topical, transdermal (e.g., using any standard patch), intradermal, ophthalmic, (intra)nasally, local, non-oral, such as aerosol, inhalation, subcutaneous, intramuscular, buccal, sublingual, (trans)rectal, vaginal, intra-arterial, and intrathecal, transmucosal (e.g., sublingual, lingual, (trans)buccal, (trans)urethral, vaginal (e.g., trans- and perivaginally), implanted, intravesical, intrapulmonary, intraduodenal, intragastrical, and intrabronchial. In preferred embodiments, a pharmaceutical composition described herein is administered orally, rectally, intratumorally, topically, intravesically, by injection into or adjacent to a draining lymph node, intravenously, by inhalation or aerosol, or subcutaneously. In another preferred embodiment, a pharmaceutical composition described herein is administered orally, intratumorally, or intravenously. In another embodiment, a pharmaceutical composition described herein is administered orally.


As used herein, the term “antibody” may refer to both an intact antibody and an antigen binding fragment thereof. Intact antibodies are glycoproteins that include at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds. Each heavy chain includes a heavy chain variable region (abbreviated herein as VH) and a heavy chain constant region. Each light chain includes a light chain variable region (abbreviated herein as VL) and a light chain constant region. The VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen. The term “antibody” includes, for example, monoclonal antibodies, polyclonal antibodies, chimeric antibodies, humanized antibodies, human antibodies, multispecific antibodies (e.g., bispecific antibodies), single-chain antibodies and antigen-binding antibody fragments.


The terms “antigen binding fragment” and “antigen-binding portion” of an antibody, as used herein, refer to one or more fragments of an antibody that retain the ability to bind to an antigen. Examples of binding fragments encompassed within the term “antigen-binding fragment” of an antibody include Fab, Fab′, F(ab′)2, Fv, scFv, disulfide linked Fv, Fd, diabodies, single-chain antibodies, NANOBODIES®, isolated CDRH3, and other antibody fragments that retain at least a portion of the variable region of an intact antibody. These antibody fragments can be obtained using conventional recombinant and/or enzymatic techniques and can be screened for antigen binding in the same manner as intact antibodies.


“Cancer” broadly refers to an uncontrolled, abnormal growth of a host's own cells leading to invasion of surrounding tissue and potentially tissue distal to the initial site of abnormal cell growth in the host. Major classes include carcinomas which are cancers of the epithelial tissue (e.g., skin, squamous cells); sarcomas which are cancers of the connective tissue (e.g., bone, cartilage, fat, muscle, blood vessels, etc.); leukemias which are cancers of blood forming tissue (e.g., bone marrow tissue); lymphomas and myelomas which are cancers of immune cells; and central nervous system cancers which include cancers from brain and spinal tissue. “Cancer(s) and” “neoplasm(s)” are used herein interchangeably. As used herein, “cancer” refers to all types of cancer or neoplasm or malignant tumors including leukemias, carcinomas and sarcomas, whether new or recurring. Specific examples of cancers are: carcinomas, sarcomas, myelomas, leukemias, lymphomas and mixed type tumors. Non-limiting examples of cancers are new or recurring cancers of the brain, melanoma, bladder, breast, cervix, colon, head and neck, kidney, lung, non-small cell lung, mesothelioma, ovary, prostate, sarcoma, stomach, uterus and medulloblastoma. In some embodiments, the cancer comprises a solid tumor. In some embodiments, the cancer comprises a metastasis.


A “carbohydrate” refers to a sugar or polymer of sugars. The terms “saccharide,” “polysaccharide,” “carbohydrate,” and “oligosaccharide” may be used interchangeably. Most carbohydrates are aldehydes or ketones with many hydroxyl groups, usually one on each carbon atom of the molecule. Carbohydrates generally have the molecular formula CnH2nOn. A carbohydrate may be a monosaccharide, a disaccharide, trisaccharide, oligosaccharide, or polysaccharide. The most basic carbohydrate is a monosaccharide, such as glucose, sucrose, galactose, mannose, ribose, arabinose, xylose, and fructose. Disaccharides are two joined monosaccharides. Exemplary disaccharides include sucrose, maltose, cellobiose, and lactose. Typically, an oligosaccharide includes between three and six monosaccharide units (e.g., raffinose, stachyose), and polysaccharides include six or more monosaccharide units. Exemplary polysaccharides include starch, glycogen, and cellulose. Carbohydrates may contain modified saccharide units such as 2′-deoxyribose wherein a hydroxyl group is removed, 2′-fluororibose wherein a hydroxyl group is replaced with a fluorine, or N-acetylglucosamine, a nitrogen-containing form of glucose (e.g., 2′-fluororibose, deoxyribose, and hexose). Carbohydrates may exist in many different forms, for example, conformers, cyclic forms, acyclic forms, stereoisomers, tautomers, anomers, and isomers.


“Cellular augmentation” broadly refers to the influx of cells or expansion of cells in an environment that are not substantially present in the environment prior to administration of a composition and not present in the composition itself. Cells that augment the environment include immune cells, stromal cells, bacterial and fungal cells. Environments of particular interest are the microenvironments where cancer cells reside or locate. In some instances, the microenvironment is a tumor microenvironment or a tumor draining lymph node. In other instances, the microenvironment is a pre-cancerous tissue site or the site of local administration of a composition or a site where the composition will accumulate after remote administration.


“Clade” refers to the OTUs or members of a phylogenetic tree that are downstream of a statistically valid node in a phylogenetic tree. The clade comprises a set of terminal leaves in the phylogenetic tree that is a distinct monophyletic evolutionary unit and that share some extent of sequence similarity.


A “combination” of bacteria from two or more strains includes the physical co-existence of the bacteria, either in the same material or product or in physically connected products, as well as the temporal co-administration or co-localization of the bacteria from the two or more strains.


A “combination” of mEVs (such as smEVs and/or pmEVs) from two or more microbial (such as bacteria) strains includes the physical co-existence of the microbes from which the mEVs (such as smEVs and/or pmEVs) are obtained, either in the same material or product or in physically connected products, as well as the temporal co-administration or co-localization of the mEVs (such as smEVs and/or pmEVs) from the two or more strains.


The term “decrease” or “deplete” means a change, such that the difference is, depending on circumstances, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 1/100, 1/1000, 1/10,000, 1/100,000, 1/1,000,000 or undetectable after treatment when compared to a pre-treatment state. Properties that may be decreased include the number of immune cells, bacterial cells, stromal cells, myeloid derived suppressor cells, fibroblasts, metabolites; the level of a cytokine; or another physical parameter (such as ear thickness (e.g., in a DTH animal model) or tumor size).


“Dysbiosis” refers to a state of the microbiota or microbiome of the gut or other body area, including, e.g., mucosal or skin surfaces (or any other microbiome niche) in which the normal diversity and/or function of the host gut microbiome ecological networks (“microbiome”) are disrupted. A state of dysbiosis may result in a diseased state, or it may be unhealthy under only certain conditions or only if present for a prolonged period. Dysbiosis may be due to a variety of factors, including, environmental factors, infectious agents host genotype, host diet and/or stress. A dysbiosis may result in: a change (e.g., increase or decrease) in the prevalence of one or more bacteria types (e.g., anaerobic), species and/or strains, change (e.g., increase or decrease) in diversity of the host microbiome population composition; a change (e.g., increase or reduction) of one or more populations of symbiont organisms resulting in a reduction or loss of one or more beneficial effects; overgrowth of one or more populations of pathogens (e.g., pathogenic bacteria); and/or the presence of, and/or overgrowth of, symbiotic organisms that cause disease only when certain conditions are present.


The term “ecological consortium” is a group of bacteria which trades metabolites and positively co-regulates one another, in contrast to two bacteria which induce host synergy through activating complementary host pathways for improved efficacy.


The term “effective dose” or “effective amount” is an amount of a pharmaceutical agent that is effective to achieve a desired therapeutic response in a subject for a particular agent, composition, and mode of administration.


As used herein, “engineered bacteria” are any bacteria that have been genetically altered from their natural state by human activities, and the progeny of any such bacteria. Engineered bacteria include, for example, the products of targeted genetic modification, the products of random mutagenesis screens and the products of directed evolution.


The term “epitope” means a protein determinant capable of specific binding to an antibody or T cell receptor. Epitopes usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains. Certain epitopes can be defined by a particular sequence of amino acids to which an antibody is capable of binding.


The term “gene” is used broadly to refer to any nucleic acid associated with a biological function. The term “gene” applies to a specific genomic sequence, as well as to a cDNA or an mRNA encoded by that genomic sequence.


“Identity” as between nucleic acid sequences of two nucleic acid molecules can be determined as a percentage of identity using known computer algorithms such as the “FASTA” program, using for example, the default parameters as in Pearson et al. (1988) Proc. Natl. Acad. Sci. USA 85:2444 (other programs include the GCG program package (Devereux, J., et al., Nucleic Acids Research 12(I):387 (1984)), BLASTP, BLASTN, FASTA Atschul, S. F., et al., J Molec Biol 215:403 (1990); Guide to Huge Computers, Mrtin J. Bishop, ed., Academic Press, San Diego, 1994, and Carillo et al. (1988) SIAM J Applied Math 48:1073). For example, the BLAST function of the National Center for Biotechnology Information database can be used to determine identity. Other commercially or publicly available programs include, DNAStar “MegAlign” program (Madison, Wis.) and the University of Wisconsin Genetics Computer Group (UWG) “Gap” program (Madison Wis.)).


As used herein, the term “immune disorder” refers to any disease, disorder or disease symptom caused by an activity of the immune system, including autoimmune diseases, inflammatory diseases and allergies. Immune disorders include, but are not limited to, autoimmune diseases (e.g., psoriasis, atopic dermatitis, lupus, scleroderma, hemolytic anemia, vasculitis, type one diabetes, Grave's disease, rheumatoid arthritis, multiple sclerosis, Goodpasture's syndrome, pernicious anemia and/or myopathy), inflammatory diseases (e.g., acne vulgaris, asthma, celiac disease, chronic prostatitis, glomerulonephritis, inflammatory bowel disease, pelvic inflammatory disease, reperfusion injury, rheumatoid arthritis, sarcoidosis, transplant rejection, vasculitis and/or interstitial cystitis), and/or an allergies (e.g., food allergies, drug allergies and/or environmental allergies).


“Immunotherapy” is treatment that uses a subject's immune system to treat disease (e.g., immune disease, inflammatory disease, metabolic disease, cancer) and includes, for example, checkpoint inhibitors, cancer vaccines, cytokines, cell therapy, CAR-T cells, and dendritic cell therapy.


The term “increase” means a change, such that the difference is, depending on circumstances, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 2-fold, 4-fold, 10-fold, 100-fold, 10{circumflex over ( )}3 fold, 10{circumflex over ( )}4 fold, 10{circumflex over ( )}5 fold, 10{circumflex over ( )}6 fold, and/or 10{circumflex over ( )}7 fold greater after treatment when compared to a pre-treatment state. Properties that may be increased include the number of immune cells, bacterial cells, stromal cells, myeloid derived suppressor cells, fibroblasts, metabolites; the level of a cytokine; or another physical parameter (such as ear thickness (e.g., in a DTH animal model) or tumor size).


“Innate immune agonists” or “immuno-adjuvants” are small molecules, proteins, or other agents that specifically target innate immune receptors including Toll-Like Receptors (TLR), NOD receptors, RLRs, C-type lectin receptors, STING-cGAS Pathway components, inflammasome complexes. For example, LPS is a TLR-4 agonist that is bacterially derived or synthesized and aluminum can be used as an immune stimulating adjuvant. immuno-adjuvants are a specific class of broader adjuvant or adjuvant therapy. Examples of STING agonists include, but are not limited to, 2′3′-cGAMP, 3′3′-cGAMP, c-di-AMP, c-di-GMP, 2′2′-cGAMP, and 2′3′-cGAM(PS)2 (Rp/Sp) (Rp, Sp-isomers of the bis-phosphorothioate analog of 2′3′-cGAMP). Examples of TLR agonists include, but are not limited to, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLRlO and TLRI 1. Examples of NOD agonists include, but are not limited to, N-acetylmuramyl-L-alanyl-D-isoglutamine (muramyldipeptide (MDP)), gamma-D-glutamyl-meso-diaminopimelic acid (iE-DAP), and desmuramylpeptides (DMP).


The “internal transcribed spacer” or “ITS” is a piece of non-functional RNA located between structural ribosomal RNAs (rRNA) on a common precursor transcript often used for identification of eukaryotic species in particular fungi. The rRNA of fungi that forms the core of the ribosome is transcribed as a signal gene and consists of the 8S, 5.8S and 28S regions with ITS4 and 5 between the 8S and 5.8S and 5.8S and 28S regions, respectively. These two intercistronic segments between the 18S and 5.8S and 5.8S and 28S regions are removed by splicing and contain significant variation between species for barcoding purposes as previously described (Schoch et al Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. PNAS 109:6241-6246. 2012). 18S rDNA is traditionally used for phylogenetic reconstruction however the ITS can serve this function as it is generally highly conserved but contains hypervariable regions that harbor sufficient nucleotide diversity to differentiate genera and species of most fungus.


The term “isolated” or “enriched” encompasses a microbe (such as a bacterium), an mEV (such as an smEV and/or pmEV) or other entity or substance that has been (1) separated from at least some of the components with which it was associated when initially produced (whether in nature or in an experimental setting), and/or (2) produced, prepared, purified, and/or manufactured by the hand of man. Isolated microbes or mEVs may be separated from at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or more of the other components with which they were initially associated. In some embodiments, isolated microbes or mEVs are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure. As used herein, a substance is “pure” if it is substantially free of other components. The terms “purify,” “purifying” and “purified” refer to a microbe or other material that has been separated from at least some of the components with which it was associated either when initially produced or generated (e.g., whether in nature or in an experimental setting), or during any time after its initial production. A microbe or a microbial population or mEVs may be considered purified if it is isolated at or after production, such as from a material or environment containing the microbe or microbial population, and a purified microbe or microbial population may contain other materials up to about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or above about 90% and still be considered “isolated.” In some embodiments, purified microbes or microbial population or mEVs are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure. In the instance of microbial compositions provided herein, the one or more microbial types present in the composition can be independently purified from one or more other microbes produced and/or present in the material or environment containing the microbial type. Microbial compositions and the microbial components thereof are generally purified from residual habitat products.


As used herein a “lipid” includes fats, oils, triglycerides, cholesterol, phospholipids, fatty acids in any form including free fatty acids. Fats, oils and fatty acids can be saturated, unsaturated (cis or trans) or partially unsaturated (cis or trans).


“Metabolite” as used herein refers to any and all molecular compounds, compositions, molecules, ions, co-factors, catalysts or nutrients used as substrates in any cellular or microbial metabolic reaction or resulting as product compounds, compositions, molecules, ions, co-factors, catalysts or nutrients from any cellular or microbial metabolic reaction.


“Microbe” refers to any natural or engineered organism characterized as an archaeaon, parasite, bacterium, fungus, microscopic alga, protozoan, and the stages of development or life cycle stages (e.g., vegetative, spore (including sporulation, dormancy, and germination), latent, biofilm) associated with the organism. Examples of gut microbes include: Actinomyces graevenitzii, Actinomyces odontolyticus, Akkermansia muciniphila, Bacteroides caccae, Bacteroides fragilis, Bacteroides putredinis, Bacteroides thetaiotaomicron, Bacteroides vultagus, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bilophila wadsworthia, Blautia, Butyrivibrio, Campylobacter gracilis, Clostridia cluster III, Clostridia cluster IV, Clostridia cluster IX (Acidaminococcaceae group), Clostridia cluster XI, Clostridia cluster XIII (Peptostreptococcus group), Clostridia cluster XIV, Clostridia cluster XV, Collinsella aerofaciens, Coprococcus, Corynebacterium sunsvallense, Desulfomonas pigra, Dorea formicigenerans, Dorea longicatena, Escherichia coli, Eubacterium hadrum, Eubacterium rectale, Faecalibacteria prausnitzii, Gemella, Lactococcus, Lanchnospira, Mollicutes cluster XVI, Mollicutes cluster XVIII, Prevotella, Rothia mucilaginosa, Ruminococcus callidus, Ruminococcus gnavus, Ruminococcus torques, and Streptococcus.


“Microbial extracellular vesicles” (mEVs) can be obtained from microbes such as bacteria, archaea, fungi, microscopic algae, protozoans, and parasites. In some embodiments, the mEVs are obtained from bacteria. mEVs include secreted microbial extracellular vesicles (smEVs) and processed microbial extracellular vesicles (pmEVs). “Secreted microbial extracellular vesicles” (smEVs) are naturally-produced vesicles derived from microbes. smEVs are comprised of microbial lipids and/or microbial proteins and/or microbial nucleic acids and/or microbial carbohydrate moieties, and are isolated from culture supernatant. The natural production of these vesicles can be artificially enhanced (e.g., increased) or decreased through manipulation of the environment in which the bacterial cells are being cultured (e.g., by media or temperature alterations). Further, smEV compositions may be modified to reduce, increase, add, or remove microbial components or foreign substances to alter efficacy, immune stimulation, stability, immune stimulatory capacity, stability, organ targeting (e.g., lymph node), absorption (e.g., gastrointestinal), and/or yield (e.g., thereby altering the efficacy). As used herein, the term “purified smEV composition” or “smEV composition” refers to a preparation of smEVs that have been separated from at least one associated substance found in a source material (e.g., separated from at least one other microbial component) or any material associated with the smEVs in any process used to produce the preparation. It can also refer to a composition that has been significantly enriched for specific components. “Processed microbial extracellular vesicles” (pmEVs) are a non-naturally-occurring collection of microbial membrane components that have been purified from artificially lysed microbes (e.g., bacteria) (e.g., microbial membrane components that have been separated from other, intracellular microbial cell components), and which may comprise particles of a varied or a selected size range, depending on the method of purification. A pool of pmEVs is obtained by chemically disrupting (e.g., by lysozyme and/or lysostaphin) and/or physically disrupting (e.g., by mechanical force) microbial cells and separating the microbial membrane components from the intracellular components through centrifugation and/or ultracentrifugation, or other methods. The resulting pmEV mixture contains an enrichment of the microbial membranes and the components thereof (e.g., peripherally associated or integral membrane proteins, lipids, glycans, polysaccharides, carbohydrates, other polymers), such that there is an increased concentration of microbial membrane components, and a decreased concentration (e.g., dilution) of intracellular contents, relative to whole microbes. For gram-positive bacteria, pmEVs may include cell or cytoplasmic membranes. For gram-negative bacteria, a pmEV may include inner and outer membranes. pmEVs may be modified to increase purity, to adjust the size of particles in the composition, and/or modified to reduce, increase, add or remove, microbial components or foreign substances to alter efficacy, immune stimulation, stability, immune stimulatory capacity, stability, organ targeting (e.g., lymph node), absorption (e.g., gastrointestinal), and/or yield (e.g., thereby altering the efficacy). pmEVs can be modified by adding, removing, enriching for, or diluting specific components, including intracellular components from the same or other microbes. As used herein, the term “purified pmEV composition” or “pmEV composition” refers to a preparation of pmEVs that have been separated from at least one associated substance found in a source material (e.g., separated from at least one other microbial component) or any material associated with the pmEVs in any process used to produce the preparation. It can also refer to a composition that has been significantly enriched for specific components.


“Microbiome” broadly refers to the microbes residing on or in body site of a subject or patient. Microbes in a microbiome may include bacteria, viruses, eukaryotic microorganisms, and/or viruses. Individual microbes in a microbiome may be metabolically active, dormant, latent, or exist as spores, may exist planktonically or in biofilms, or may be present in the microbiome in sustainable or transient manner. The microbiome may be a commensal or healthy-state microbiome or a disease-state or dysbiotic microbiome. The microbiome may be native to the subject or patient, or components of the microbiome may be modulated, introduced, or depleted due to changes in health state (e.g., precancerous or cancerous state) or treatment conditions (e.g., antibiotic treatment, exposure to different microbes). In some aspects, the microbiome occurs at a mucosal surface. In some aspects, the microbiome is a gut microbiome. In some aspects, the microbiome is a tumor microbiome.


A “microbiome profile” or a “microbiome signature” of a tissue or sample refers to an at least partial characterization of the bacterial makeup of a microbiome. In some embodiments, a microbiome profile indicates whether at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more bacterial strains are present or absent in a microbiome. In some embodiments, a microbiome profile indicates whether at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more cancer-associated bacterial strains are present in a sample. In some embodiments, the microbiome profile indicates the relative or absolute amount of each bacterial strain detected in the sample. In some embodiments, the microbiome profile is a cancer-associated microbiome profile. A cancer-associated microbiome profile is a microbiome profile that occurs with greater frequency in a subject who has cancer than in the general population. In some embodiments, the cancer-associated microbiome profile comprises a greater number of or amount of cancer-associated bacteria than is normally present in a microbiome of an otherwise equivalent tissue or sample taken from an individual who does not have cancer.


“Modified” in reference to a bacteria broadly refers to a bacteria that has undergone a change from its wild-type form. Bacterial modification can result from engineering bacteria. Examples of bacterial modifications include genetic modification, gene expression modification, phenotype modification, formulation modification, chemical modification, and dose or concentration. Examples of improved properties are described throughout this specification and include, e.g., attenuation, auxotrophy, homing, or antigenicity. Phenotype modification might include, by way of example, bacteria growth in media that modify the phenotype of a bacterium such that it increases or decreases virulence.


An “oncobiome” as used herein comprises tumorigenic and/or cancer-associated microbiota, wherein the microbiota comprises one or more of a virus, a bacterium, a fungus, a protist, a parasite, or another microbe.


“Oncotrophic” or “oncophilic” microbes and bacteria are microbes that are highly associated or present in a cancer microenvironment. They may be preferentially selected for within the environment, preferentially grow in a cancer microenvironment or hone to a said environment.


“Operational taxonomic units” and “OTU(s)” refer to a terminal leaf in a phylogenetic tree and is defined by a nucleic acid sequence, e.g., the entire genome, or a specific genetic sequence, and all sequences that share sequence identity to this nucleic acid sequence at the level of species. In some embodiments the specific genetic sequence may be the 16S sequence or a portion of the 16S sequence. In other embodiments, the entire genomes of two entities are sequenced and compared. In another embodiment, select regions such as multilocus sequence tags (MLST), specific genes, or sets of genes may be genetically compared. For 16S, OTUs that share≥97% average nucleotide identity across the entire 16S or some variable region of the 16S are considered the same OTU. See e.g., Claesson M J, Wang Q, O'Sullivan O, Greene-Diniz R, Cole J R, Ross R P, and O'Toole P W. 2010. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res 38: e200. Konstantinidis K T, Ramette A, and Tiedje J M. 2006. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361: 1929-1940. For complete genomes, MLSTs, specific genes, other than 16S, or sets of genes OTUs that share≥95% average nucleotide identity are considered the same OTU. See e.g., Achtman M, and Wagner M. 2008. Microbial diversity and the genetic nature of microbial species. Nat. Rev. Microbiol. 6: 431-440. Konstantinidis K T, Ramette A, and Tiedje J M. 2006. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361: 1929-1940. OTUs are frequently defined by comparing sequences between organisms. Generally, sequences with less than 95% sequence identity are not considered to form part of the same OTU. OTUs may also be characterized by any combination of nucleotide markers or genes, in particular highly conserved genes (e.g., “house-keeping” genes), or a combination thereof. Operational Taxonomic Units (OTUs) with taxonomic assignments made to, e.g., genus, species, and phylogenetic clade are provided herein.


As used herein, a gene is “overexpressed” in a bacteria if it is expressed at a higher level in an engineered bacteria under at least some conditions than it is expressed by a wild-type bacteria of the same species under the same conditions. Similarly, a gene is “underexpressed” in a bacteria if it is expressed at a lower level in an engineered bacteria under at least some conditions than it is expressed by a wild-type bacteria of the same species under the same conditions.


The terms “polynucleotide”, and “nucleic acid” are used interchangeably. They refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three-dimensional structure, and may perform any function. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), micro RNA (miRNA), silencing RNA (siRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. A polynucleotide may be further modified, such as by conjugation with a labeling component. In all nucleic acid sequences provided herein, U nucleotides are interchangeable with T nucleotides.


As used herein, the term “preventing” a disease or condition in a subject refers to administering to the subject to a pharmaceutical treatment, e.g., the administration of one or more agents (e.g., pharmaceutical agent), such that onset of at least one symptom of the disease or condition is delayed or prevented.


As used herein, a substance is “pure” if it is substantially free of other components. The terms “purify,” “purifying” and “purified” refer to an mEV (such as an smEV and/or a pmEV) preparation or other material that has been separated from at least some of the components with which it was associated either when initially produced or generated (e.g., whether in nature or in an experimental setting), or during any time after its initial production. An mEV (such as an smEV and/or a pmEV) preparation or compositions may be considered purified if it is isolated at or after production, such as from one or more other bacterial components, and a purified microbe or microbial population may contain other materials up to about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or above about 90% and still be considered “purified.” In some embodiments, purified mEVs (such as smEVs and/or pmEVs) are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure. mEV (such as an smEV and/or a pmEV) compositions (or preparations) are, e.g., purified from residual habitat products.


As used herein, the term “purified mEV composition” or “mEV composition” refers to a preparation that includes mEVs (such as smEVs and/or pmEVs) that have been separated from at least one associated substance found in a source material (e.g., separated from at least one other bacterial component) or any material associated with the mEVs (such as smEVs and/or pmEVs) in any process used to produce the preparation. It also refers to a composition that has been significantly enriched or concentrated. In some embodiments, the mEVs (such as smEVs and/or pmEVs) are concentrated by 2 fold, 3-fold, 4-fold, 5-fold, 10-fold, 100-fold, 1000-fold, 10,000-fold or more than 10,000 fold.


“Residual habitat products” refers to material derived from the habitat for microbiota within or on a subject. For example, fermentation cultures of microbes can contain contaminants, e.g., other microbe strains or forms (e.g., bacteria, virus, mycoplasm, and/or fungus). For example, microbes live in feces in the gastrointestinal tract, on the skin itself, in saliva, mucus of the respiratory tract, or secretions of the genitourinary tract (i.e., biological matter associated with the microbial community). Substantially free of residual habitat products means that the microbial composition no longer contains the biological matter associated with the microbial environment on or in the culture or human or animal subject and is 100% free, 99% free, 98% free, 97% free, 96% free, or 95% free of any contaminating biological matter associated with the microbial community. Residual habitat products can include abiotic materials (including undigested food) or it can include unwanted microorganisms. Substantially free of residual habitat products may also mean that the microbial composition contains no detectable cells from a culture contaminant or a human or animal and that only microbial cells are detectable. In one embodiment, substantially free of residual habitat products may also mean that the microbial composition contains no detectable viral (including bacteria, viruses (e.g., phage)), fungal, mycoplasmal contaminants. In another embodiment, it means that fewer than 1×10−2%, 1×10−3%, 1×10−4%, 1×10−5%, 1×10−6%, 1×10−7%, 1×10−8% of the viable cells in the microbial composition are human or animal, as compared to microbial cells. There are multiple ways to accomplish this degree of purity, none of which are limiting. Thus, contamination may be reduced by isolating desired constituents through multiple steps of streaking to single colonies on solid media until replicate (such as, but not limited to, two) streaks from serial single colonies have shown only a single colony morphology. Alternatively, reduction of contamination can be accomplished by multiple rounds of serial dilutions to single desired cells (e.g., a dilution of 10−8 or 10−9), such as through multiple 10-fold serial dilutions. This can further be confirmed by showing that multiple isolated colonies have similar cell shapes and Gram staining behavior. Other methods for confirming adequate purity include genetic analysis (e.g., PCR, DNA sequencing), serology and antigen analysis, enzymatic and metabolic analysis, and methods using instrumentation such as flow cytometry with reagents that distinguish desired constituents from contaminants.


As used herein, “specific binding” refers to the ability of an antibody to bind to a predetermined antigen or the ability of a polypeptide to bind to its predetermined binding partner. Typically, an antibody or polypeptide specifically binds to its predetermined antigen or binding partner with an affinity corresponding to a KD of about 10−7 M or less, and binds to the predetermined antigen/binding partner with an affinity (as expressed by KD) that is at least 10 fold less, at least 100 fold less or at least 1000 fold less than its affinity for binding to a non-specific and unrelated antigen/binding partner (e.g., BSA, casein). Alternatively, specific binding applies more broadly to a two-component system where one component is a protein, lipid, or carbohydrate or combination thereof and engages with the second component which is a protein, lipid, carbohydrate or combination thereof in a specific way.


“Strain” refers to a member of a bacterial species with a genetic signature such that it may be differentiated from closely-related members of the same bacterial species. The genetic signature may be the absence of all or part of at least one gene, the absence of all or part of at least on regulatory region (e.g., a promoter, a terminator, a riboswitch, a ribosome binding site), the absence (“curing”) of at least one native plasmid, the presence of at least one recombinant gene, the presence of at least one mutated gene, the presence of at least one foreign gene (a gene derived from another species), the presence at least one mutated regulatory region (e.g., a promoter, a terminator, a riboswitch, a ribosome binding site), the presence of at least one non-native plasmid, the presence of at least one antibiotic resistance cassette, or a combination thereof. Genetic signatures between different strains may be identified by PCR amplification optionally followed by DNA sequencing of the genomic region(s) of interest or of the whole genome. In the case in which one strain (compared with another of the same species) has gained or lost antibiotic resistance or gained or lost a biosynthetic capability (such as an auxotrophic strain), strains may be differentiated by selection or counter-selection using an antibiotic or nutrient/metabolite, respectively.


The terms “subject” or “patient” refers to any mammal. A subject or a patient described as “in need thereof” refers to one in need of a treatment (or prevention) for a disease. Mammals (i.e., mammalian animals) include humans, laboratory animals (e.g., primates, rats, mice), livestock (e.g., cows, sheep, goats, pigs), and household pets (e.g., dogs, cats, rodents). The subject may be a human. The subject may be a non-human mammal including but not limited to of a dog, a cat, a cow, a horse, a pig, a donkey, a goat, a camel, a mouse, a rat, a guinea pig, a sheep, a llama, a monkey, a gorilla or a chimpanzee. The subject may be healthy, or may be suffering from a cancer at any developmental stage, wherein any of the stages are either caused by or opportunistically supported of a cancer associated or causative pathogen, or may be at risk of developing a cancer, or transmitting to others a cancer associated or cancer causative pathogen. In some embodiments, a subject has lung cancer, bladder cancer, prostate cancer, plasmacytoma, colorectal cancer, rectal cancer, Merkel Cell carcinoma, salivary gland carcinoma, ovarian cancer, and/or melanoma. The subject may have a tumor. The subject may have a tumor that shows enhanced macropinocytosis with the underlying genomics of this process including Ras activation. In other embodiments, the subject has another cancer. In some embodiments, the subject has undergone a cancer therapy.


As used herein, a “systemic effect” in a subject treated with a pharmaceutical composition containing bacteria or mEVs (e.g., a pharmaceutical agent comprising bacteria or mEVs) of the instant invention means a physiological effect occurring at one or more sites outside the gastrointestinal tract. Systemic effect(s) can result from immune modulation (e.g., via an increase and/or a reduction of one or more immune cell types or subtypes (e.g., CD8+ T cells) and/or one or more cytokines). Such systemic effect(s) may be the result of the modulation by bacteria or mEVs of the instant invention on immune or other cells (such as epithelial cells) in the gastrointestinal tract which then, directly or indirectly, result in the alteration of activity (activation and/or deactivation) of one or more biochemical pathways outside the gastrointestinal tract. The systemic effect may include treating or preventing a disease or condition in a subject.


As used herein, the term “treating” a disease in a subject or “treating” a subject having or suspected of having a disease refers to administering to the subject to a pharmaceutical treatment, e.g., the administration of one or more agents (e.g., pharmaceutical agent), such that at least one symptom of the disease is decreased or prevented from worsening. Thus, in one embodiment, “treating” refers inter alia to delaying progression, expediting remission, inducing remission, augmenting remission, speeding recovery, increasing efficacy of or decreasing resistance to alternative therapeutics, or a combination thereof.


As used herein, a “type” of bacteria may be distinguished from other bacteria by: genus, species, sub-species, strain or by any other taxonomic categorization, whether based on morphology, physiology, genotype, protein expression or other characteristics known in the art.


Bacteria

In certain aspects, the pharmaceutical agent of the solid dosage forms described herein comprises bacteria and/or microbial extracellular vesicles (mEVs) (such as smEVs and/or pmEVs). Within a pharmaceutical agent that contains bacteria and mEVs, the mEVs can be from the same bacterial origin (e.g., same strain) as the bacteria of the pharmaceutical agent. The pharmaceutical agent can contain bacteria and/or mEVs from one or more strains.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are modified to reduce toxicity or other adverse effects, to enhance delivery) (e.g., oral delivery) (e.g., by improving acid resistance, muco-adherence and/or penetration and/or resistance to bile acids, digestive enzymes, resistance to anti-microbial peptides and/or antibody neutralization), to target desired cell types (e.g., M-cells, goblet cells, enterocytes, dendritic cells, macrophages), to enhance their immunomodulatory and/or therapeutic effect of the bacteria and/or mEVs (e.g., either alone or in combination with another pharmaceutical agent), and/or to enhance immune activation or suppression by the bacteria and/or mEVs (such as smEVs and/or pmEVs) (e.g., through modified production of polysaccharides, pili, fimbriae, adhesins). In some embodiments, the engineered bacteria described herein are modified to improve bacteria and/or mEV (such as smEV and/or pmEV) manufacturing (e.g., higher oxygen tolerance, stability, improved freeze-thaw tolerance, shorter generation times). For example, in some embodiments, the engineered bacteria described include bacteria harboring one or more genetic changes, such change being an insertion, deletion, translocation, or substitution, or any combination thereof, of one or more nucleotides contained on the bacterial chromosome or endogenous plasmid and/or one or more foreign plasmids, wherein the genetic change may result in the overexpression and/or underexpression of one or more genes. The engineered bacteria may be produced using any technique known in the art, including but not limited to site-directed mutagenesis, transposon mutagenesis, knock-outs, knock-ins, polymerase chain reaction mutagenesis, chemical mutagenesis, ultraviolet light mutagenesis, transformation (chemically or by electroporation), phage transduction, directed evolution, or any combination thereof.


Examples of taxonomic groups (e.g., class, order, family, genus, species or strain) of bacteria that can be used as a source of bacteria and/or mEVs (such as smEVs and/or pmEVs) for a pharmaceutical agent described herein are provided herein (e.g., listed in Table 1, Table 2, and/or Table 3 and/or elsewhere in the specification (e.g., Table J)). In some embodiments, the bacterial strain is a bacterial strain having a genome that has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8% or 99.9% sequence identity to a strain listed herein. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are oncotrophic bacteria. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are immunomodulatory bacteria. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are immunostimulatory bacteria. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are immunosuppressive bacteria. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are immunomodulatory bacteria. In certain embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are generated from a combination of bacterial strains provided herein. In some embodiments, the combination is a combination of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45 or 50 bacterial strains. In some embodiments, the combination includes the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are from bacterial strains listed herein and/or bacterial strains having a genome that has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8% or 99.9% sequence identity to a strain listed herein (e.g., listed in Table 1, Table 2, and/or Table 3 and/or elsewhere in the specification (e.g., Table J)). In certain embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are generated from a bacterial strain provided herein. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are from a bacterial strain listed herein (e.g., listed in Table 1, Table 2, and/or Table 3 and/or elsewhere in the specification (e.g., Table J)) and/or a bacterial strain having a genome that has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8% or 99.9% sequence identity to a strain listed herein (e.g., listed in Table 1, Table 2, and/or Table 3 and/or elsewhere in the specification (e.g., Table J)).


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Gram negative bacteria.


In some embodiments, the Gram negative bacteria belong to the class Negativicutes. The Negativicutes represent a unique class of microorganisms as they are the only diderm members of the Firmicutes phylum. These anaerobic organisms can be found in the environment and are normal commensals of the oral cavity and GI tract of humans. Because these organisms have an outer membrane, the yields of EVs from this class were investigated. It was found that on a per cell basis these bacteria produce a high number of vesicles (10-150 EVs/cell). The EVs from these organisms are broadly stimulatory and highly potent in in vitro assays. Investigations into their therapeutic applications in several oncology and inflammation in vivo models have shown their therapeutic potential. The Negativicutes class includes the families Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, and Sporomusaceae. The Negativicutes class includes the genera Megasphaera, Selenomonas, Propionospora, and Acidaminococcus. Exemplary Negativicutes species include, but are not limited to, Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, and Propionospora sp.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Gram positive bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are aerobic bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are acidophile bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are alkaliphile bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are neutralophile bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are fastidious bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are nonfastidious bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained or the mEVs themselves are lyophilized.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained or the mEVs themselves are gamma irradiated (e.g., at 17.5 or 25 kGy).


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained or the mEVs themselves are UV irradiated.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained or the mEVs themselves are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained or the mEVs themselves are acid treated.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained or the mEVs themselves are oxygen sparged (e.g., at 0.1 vvm for two hours).


The phase of growth can affect the amount or properties of bacteria and/or mEVs produced by bacteria. For example, in the methods of mEVs preparation provided herein, mEVs can be isolated, e.g., from a culture, at the start of the log phase of growth, midway through the log phase, and/or once stationary phase growth has been reached.


In certain embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained from obligate anaerobic bacteria. Examples of obligate anaerobic bacteria include gram-negative rods (including the genera of Bacteroides, Prevotella, Porphyromonas, Fusobacterium, Bilophila and Sutterella spp.), gram-positive cocci (primarily Peptostreptococcus spp.), gram-positive spore-forming (Clostridium spp.), non-spore-forming bacilli (Actinomyces, Propionibacterium, Eubacterium, Lactobacillus and Bifidobacterium spp.), and gram-negative cocci (mainly Veillonella spp.). In some embodiments, the obligate anaerobic bacteria are of a genus selected from the group consisting of Agathobaculum, Atopobium, Blautia, Burkholderia, Dielma, Longicatena, Paraclostridium, Turicibacter, and Tyzzerella.


The Negativicutes class includes the families Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, and Sporomusaceae. The Negativicutes class includes the genera Megasphaera, Selenomonas, Propionospora, and Acidaminococcus. Exemplary Negativicutes species include, but are not limited to, Megasphaera sp., Selenomonas felix, Acidaminococcus intestini, and Propionospora sp.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Negativicutes class.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Veillonellaceae family.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Selenomonadaceae family.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Acidaminococcaceae family.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Sporomusaceae family.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Megasphaera genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Selenomonas genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Propionospora genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Acidaminococcus genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Megasphaera sp. bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Selenomonas felix bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Acidaminococcus intestini bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Propionospora sp. bacteria.


The Oscillospriraceae family within the Clostridia class of microorganisms are common commensal organisms of vertebrates.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Clostridia class.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Oscillospriraceae family.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Faecalibacterium genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Fournierella genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Harryflintia genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Agathobaculum genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are bacteria of a genus selected from the group consisting of Escherichia, Klebsiella, Lactobacillus, Shigella, and Staphylococcus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are a species selected from the group consisting of Blautia massiliensis, Paraclostridium benzoelyticum, Dielma fastidiosa, Longicatena caecimuris, Lactococcus lactis cremoris, Tyzzerella nexilis, Hungatella effluvia, Klebsiella quasipneumoniae subsp. Simihpneumoniae, Klebsiella oxytoca, and Veillonella tobetsuensis.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are a Prevotella bacteria selected from the group consisting of Prevotella albensis, Prevotella amnii, Prevotella bergensis, Prevotella bivia, Prevotella brevis, Prevotella bryantii, Prevotella buccae, Prevotella buccalis, Prevotella copri, Prevotella dentalis, Prevotella denticola, Prevotella disiens, Prevotella histicola, Prevotella intermedia, Prevotella maculosa, Prevotella marshii, Prevotella melaninogenica, Prevotella micans, Prevotella multiformis, Prevotella nigrescens, Prevotella oris, Prevotella oris, Prevotella oulorum, Prevotella pallens, Prevotella salivae, Prevotella stercorea, Prevotella tannerae, Prevotella timonensis, Prevotella jejuni, Prevotella aurantiaca, Prevotella baroniae, Prevotella colorans, Prevotella corporis, Prevotella dentasini, Prevotella enoeca, Prevotella falsenii, Prevotella fusca, Prevotella heparinolytica, Prevotella loescheii, Prevotella multisaccharivorax, Prevotella nanceiensis, Prevotella oryzae, Prevotella paludivivens, Prevotella pleuritidis, Prevotella ruminicola, Prevotella saccharolytica, Prevotella scopos, Prevotella shahii, Prevotella zoogleoformans, and Prevotella veroralis.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are a strain of bacteria comprising a genomic sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the genomic sequence of the strain of bacteria deposited with the ATCC Deposit number as provided in Table 3. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are a strain of bacteria comprising a 16S sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the 16S sequence of the strain of bacteria deposited with the ATCC Deposit number as provided in Table 3.


The Negativicutes class includes the families Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, and Sporomusaceae. The Negativicutes class includes the genera Megasphaera, Selenomonas, Propionospora, and Acidaminococcus. Exemplary Negativicutes species include, but are not limited to, Megasphaera sp., Selenomonas felix, Acidaminococcus intestini, and Propionospora sp.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Negativicutes class.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Veillonellaceae family.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Selenomonadaceae family.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Acidaminococcaceae family.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Sporomusaceae family.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Megasphaera genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Selenomonas genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Propionospora genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Acidaminococcus genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Megasphaera sp. bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Selenomonas felix bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Acidaminococcus intestini bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Propionospora sp. bacteria.


The Oscillospriraceae family within the Clostridia class of microorganisms are common commensal organisms of vertebrates.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Clostridia class.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Oscillospriraceae family.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Faecalibacterium genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Fournierella genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Harryflintia genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the Agathobaculum genus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are bacteria of order Bacteroidales. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the family Porphyromonoadaceae. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the family Prevotellaceae. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are bacteria of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are bacteria of the class Bacteroidia that stain Gram negative. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are bacteria of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are bacteria of the class Clostridia [phylum Firmicutes]. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the order Eubacteriales. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the family Oscillispiraceae. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the family Lachnospiraceae. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the family Peptostreptococcaceae. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the family Clostridiales family XIII/Incertae sedis 41. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Clostridia that stain Gram negative. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Clostridia that stain Gram positive. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Negativicutes [phylum Firmicutes]. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the order Veillonellales. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the family Veillonelloceae. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the order Selenomonadales. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are bacteria of the family Selenomonadaceae. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the family Sporomusaceae. In some embodiments, t the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are the EVs are from bacteria of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Synergistia [phylum Synergistota]. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the order Synergistales. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the family Synergistaceae. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Synergistia that stain Gram negative. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are from one strain of bacteria, e.g., a strain provided herein.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are from one strain of bacteria (e.g., a strain provided herein) or from more than one strain provided herein.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Lactococcus lactis cremoris bacteria, e.g., a strain comprising at least 90% or at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Lactococcus bacteria, e.g., Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Prevotella bacteria, e.g., a strain comprising at least 90% or at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Prevotella bacteria, e.g., Prevotella Strain B 50329 (NRRL accession number B 50329).


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Bifidobacterium bacteria, e.g., a strain comprising at least 90% or at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Bifidobacterium bacteria, e.g., Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Veillonella bacteria, e.g., a strain comprising at least 90% or at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Veillonella bacteria, e.g., Veillonella bacteria deposited as ATCC designation number PTA-125691.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.


In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.


In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bifidobacterium; Lactobacillus; or Olsenella.


In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.


In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.


In some embodiments, the bacteria of the pharmaceutical agent or from which the mEVs of the pharmaceutical agent are obtained are bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis, Faecalibacterium prausnitzii, Megasphaera massiliensis or Roseburia intestinalis.









TABLE 1







Bacteria by Class











Class
Order
Family
Genus
Species





Actinobacter
Actinomycetales
Mycobacteriaceae

Mycobacterium






Streptomycetaceae

Streptomyces


Streptomyces








lividans,








Streptomyces








coelicolor,








Streptomyces








sudanesis,








Streptomyces








somaliensis




Bifidobacteriales
Bifidobacteriaceae

Bifidobacterium


Bifidobacterium








adolescentis,








Bifidobacterium








animalis,








Bifidobacterium








bifidum,








Bifidobacterium








breve,








Bifidobacterium








lactis,








Bifidobacterium








longum,








Bifidobacterium








pseudocatenulatum




Coriobacteriales
Coriobacteriaceae

Collinsella


Collinsella








aerofaciens







Olsenella


Olsenellafaecalis




Propionibacteriales
Propionibacteraceae

Propionibacterium



Bacilli
Bacillales
Bacillales

Gemella


Gemella





incertaesedis


haemolysans,





family XI


Gemella








morbillorum





Listeraceae

Listeria


Listeria








monocytogenes,








Listeria welshimeri




Lactobacilluses
Enterococcaceae

Enterococcus


Enterococcus








durans,








Enterococcus








faecium,








Enterococcus








faecalis,








Enterococcus








gallinarum,








Enterococcus








villorum







Lactobacillus


Lactobacillus casei,








Lactobacillus








fermentum,








Lactococcus lactis








cremoris,








Lactobacillus








mucosae,








Lactobacillus








plantarum,








Lactobacillus








reuteri,








Lactobacillus








rhamnosus, L.








salvarius





Streptococcaceae

Lactococcus







Staphylococcus


Staphylococcus








aureus







Streptococcus


Streptococcus








agalactiae,








Streptococcus








aureus,








Streptococcus








australi,








Streptococcus








mutans,








Streptococcus








parasanguinis,








Streptococcus








pneumoniae,








Streptococcus








pyogenes,








Streptococcus








salivraius



Bacteriodes
Bacteroidales
Bacteriodaceae

Bacteriodes


Bacteroides caccae,








Bacteroides








cellulosilyticus,








Bacteroides








coprocola,








Bacteroides dorei,








Bacteroides fragilis,








Bacteroides ovatus,








Bacteroides








putredinis,








Bacteroides








salanitronis,








Bacteroides








thetaiotaomicron,








Bacteroides








vulgatus





Odoribacteraceae

Odoribacter


Odoribacter








splanchnicus





Porphyromonadaceae

Parabacteriodes


Parabacteriodes








distasonis,








Parabacteroides








goldsteinii, P








Parabacteriodes








merdae







Porphyromonas


Porphyromonas








gingivalis





Prevotellaceae

Prevotella


Prevotella








albensis,








Prevotella amnii,








Prevotella








aurantiaca,








Prevotella








baroniae,








Prevotella








bergensis,








Prevotella bivia,








Prevotella brevis,








Prevotella bryantii,








Prevotella buccae,








Prevotella








buccalis,








Prevotella








colorans,








Prevotella








corporis,








Prevotella copri,








Prevotella dentalis,








Prevotella








dentasini,








Prevotella








denticola,








Prevotella disiens,,








Prevotella enoeca,








Prevotella falsenii,








Prevotella fusca,








Prevotella








heparinolytica,








Prevotella








histicola,








Prevotella








intermedia,








Prevotella jejuni, ,








Prevotella








loescheii,








Prevotella








maculosa,








Prevotella marshii,








Prevotella








melaninogenica,








Prevotella micans,








Prevotella








multiformis,








Prevotella








multisaccharivorax,








Prevotella








nanceiensis,








Prevotella








nigrescens,








Prevotella oralis,








Prevotella oris, ,








Prevotella oryzae,








Prevotella








oulorum,








Prevotella pallens,








Prevotella








paludivivens,








Prevotella








pleuritidis








Prevotella








ruminicola,








Prevotella








saccharolytica,








Prevotella salivae,








Prevotella scopos,








Prevotella shahii,








Prevotella








stercorea,








Prevotella








tannerae,








Prevotella








timonensis,








Prevotella








veroralis,








Prevotella








zoogleoformans





Rikenellaceae

Alstipes


Alistipes communis,








Alistipes dispar, A.








finegoldii, Alistipes








indistinctus,








Alistipes ihumii,








Alistipes inops,,








Alistipes








massiliensis,,








Alistipes megaguti,








Alistipes obesi,








Alistipes








onderdonkii,








Alistipes








provencensis,








Alistipes putredinis,








Alistipes








senegalensis, ,








Alistipes shahii,








Alistipes timonensis



Betaproteoba
Burkholderiales
Alcaligenaceae

Paenalcaligenes


Paenalcaligenes



cteria




hominis







Bordella


Bordella pertussis





Burkholderiaceae

Burkholderia


Burkholderia mallei,








Burkholderia








pseudomallei







Ralstonia


Ralstonia








solanacearum





Neisseriaceae

Neisseria


Neisseria








meningitidis





Sutterellaceae

Sutterella


Sutterella








parvirubra,








Sutterella








stercoricanis,








Sutterella








wadsworthensis



Clostridia
Clostridiales
Catabacteriaceae

Catabacter


Catabacter








hongkongensis





Clostridiaceae

Aminiphila


Anaerosphaera








aminiphila







Christensenellaceae


C. massiliensis, C.








minuta,








C. timonensis







Hungatella


Hungatella effluvia





Eubacteriaceae

Eubacterium


Eubacterium








contortum,








Enterococcus








durans,








Eubacterium








eligens,








Eubacterium








faecium








Enterococcus








faecalis,








Enterococcus








gallinarum,








Eubacterium








hadrum,








Eubacterium hallii,








Eubacterium








limosum,








Eubacterium








ramulus,








Eubacterium








rectale,








Enterococcus








villorum





Lachnospiraceae

Anaerostipes


Anaerostipes








caccae,








Anaerostipes hadrus







Blautia


Blautia








hydrogenotrophica,








Blautia massiliensis,








Blautia stercoris,








Blautia wexlerae







Catonella


Catonella morbi







Coprococcus


Coprococcus catus,








Coprococcus comes,








Coprococcus








eutactus







Dialister


Dialister invisus,








Dialister








micraeophilus,








Dialister








succinatiphilus







Dorea


Dorea








formicigenerans,








Dorea longicatena,







Johnsonella


Johnsonella ignava







Oribacterium


Oribacterium








parvum,








Oribacterium sinus







Lachnobacterium







Lachnoclostridium







Lacrimispora


Lacrimispora








sacchaarolytica







Roseburia


Roseburia hominis,








seburia intestinalis







Tyzzerella


Tyzzerella nexilis





Oscillospiraceae

Oscillibacter


Oscillibacter








valericigenes







Harryflintia


Harryflinta








acetispora





Peptococcaceae




Peptostreptococcaceae

Paraclostridium


Paraclostridium








benzoelyticum







Peptostreptococcus


Peptostreptococcus








russellii





Ruminococcaceae


Agathobaculum sp.







Fournierella


Fournierella








masssiliensis







Ruminococcus


Ruminococcus








albus,








Ruminococcus








bromii, Ruminococcus








callidus,








Ruminococcus








gnavus,








Ruminococcus








inulinivorans,








Ruminococcus








obeum,








Ruminococcus








torques







Faecalibacterium


Faecalibacterium








prasusnitzii





Clostridiales family


Intestimonas





XIII/Incertae sedis


butyriciproducens



Fusobacteria
Fusobacteriales
Fusobacteriaceae

Fusobacterium


Fusobacterium








nucleatum,








Fusobacterium








naviforme





Leptotrichiaceae

Leptotrichia







Sneathia



Gammaprote
Enterobacterales
Enterobacteriaceae

Klebsiella


Klebsiella oxytoca,,



obacteria




Klebsiella








pneumoniae,








Klebsiella








quasipneumoniae







subsp.







Similipneumoniae,







Escherichia


Escherichia coli







strain Nissle 1917






(EcN)







Escherichia coli







strain ECOR12







Escherichia coli







strain ECOR63






Shigella



Negativicutes

Acidaminococcaceae

Acidaminococcus


Acidaminococcus








fermentans,








Acidaminococcus








intestine







Phascolarctobacterium


Phascolarctobacterium








faecium,








Phascolarctobacterium








succinatutens





Selenomonadaceae

Selenomonas


Selenomonas felix,








Selemonadales








incertae sedis,








Selenomonas








sputigena





Sporomusaceae

Selenomonadales





Veillonellaceae

Allisonella







Anaeroglobus


Anaeroglobus








germinatus







Caecibacter







Colibacter







Veillonella


Veillonella parvula







Megasphaera


Megasphera








elsedenii,








Megasphaera








massiliensis,








Megasphera








micronuciformis








Megasphaera sp







Massilibacillus


Massilibacillus








massiliensis







Propionispira







Negativicoccus


Negativicoccus








succinicivornas







Veillonella


Veillonella dispar,








Veillonella parvula,








Veillonella ratti,








Veillonella








tobetsuensis




Synergistales
Synergistaceae

Aminobacterium


Aminobacterium








mobile







Cloacibacillus


Cloacibacillus








evryensis







Rarimicrobium


Rarimicrobium








hominis



Verrucomicro
Verrucomicrobiales
Akkermansiaceae

Akkermansia


Akkermansia



bia




mucinophila

















TABLE 2







Exemplary Bacterial Strains









Public DB


OTU
Accession






Actinobacillus actinomycetemcomitans

AY362885



Actinobacillus minor

ACFT01000025



Actinobacillus pleuropneumoniae

NR_074857



Actinobacillus succinogenes

CP000746



Actinobacillus ureae

AEVG01000167



Actinobaculum massiliae

AF487679



Actinobaculum schaalii

AY957507



Actinobaculum sp. BM#101342

AY282578



Actinobaculum sp. P2P_19 P1

AY207066



Akkermansia muciniphila

CP001071



Alistipes finegoldii

NR_043064



Alistipes indistinctus

AB490804



Alistipes onderdonkii

NR_043318



Alistipes putredinis

ABFK02000017



Alistipes shahii

FP929032



Alistipes sp. HGB5

AENZ01000082



Alistipes sp. JC50

JF824804



Alistipes sp. RMA 9912

GQ140629



Anaerostipes caccae

ABAX03000023



Anaerostipes sp. 3_2_56FAA

ACWB01000002



Bacillus aeolius

NR_025557



Bacillus aerophilus

NR_042339



Bacillus aestuarii

GQ980243



Bacillus alcalophilus

X76436



Bacillus amyloliquefaciens

NR_075005



Bacillus anthracis

AAEN01000020



Bacillus atrophaeus

NR_075016



Bacillus badius

NR_036893



Bacillus cereus

ABDJ01000015



Bacillus circulans

AB271747



Bacillus clausii

FN397477



Bacillus coagulans

DQ297928



Bacillus firmus

NR_025842



Bacillus flexus

NR_024691



Bacillus fordii

NR_025786



Bacillus gelatini

NR_025595



Bacillus halmapalus

NR_026144



Bacillus halodurans

AY144582



Bacillus herbersteinensis

NR_042286



Bacillus horti

NR_036860



Bacillus idriensis

NR_043268



Bacillus lentus

NR_040792



Bacillus licheniformis

NC_006270



Bacillus megaterium

GU252124



Bacillus nealsonii

NR_044546



Bacillus niabensis

NR_043334



Bacillus niacini

NR_024695



Bacillus pocheonensis

NR_041377



Bacillus pumilus

NR_074977



Bacillus safensis

JQ624766



Bacillus simplex

NR_042136



Bacillus sonorensis

NR_025130



Bacillus sp. 10403023 MM10403188

CAET01000089



Bacillus sp. 2_A_57_CT2

ACWD01000095



Bacillus sp. 2008724126

GU252108



Bacillus sp. 2008724139

GU252111



Bacillus sp. 7_16AIA

FN397518



Bacillus sp. 9_3AIA

FN397519



Bacillus sp. AP8

JX101689



Bacillus sp. B27(2008)

EU362173



Bacillus sp. BT1B_CT2

ACWC01000034



Bacillus sp. GB1.1

FJ897765



Bacillus sp. GB9

FJ897766



Bacillus sp. HU19.1

FJ897769



Bacillus sp. HU29

FJ897771



Bacillus sp. HU33.1

FJ897772



Bacillus sp. JC6

JF824800



Bacillus sp. oral taxon F26

HM099642



Bacillus sp. oral taxon F28

HM099650



Bacillus sp. oral taxon F79

HM099654



Bacillus sp. SRC_DSF1

GU797283



Bacillus sp. SRC_DSF10

GU797292



Bacillus sp. SRC_DSF2

GU797284



Bacillus sp. SRC_DSF6

GU797288



Bacillus sp. tc09

HQ844242



Bacillus sp. zh168

FJ851424



Bacillus sphaericus

DQ286318



Bacillus sporothermodurans

NR_026010



Bacillus subtilis

EU627588



Bacillus thermoamylovorans

NR_029151



Bacillus weihenstephanensis

NR_074926


Bacteroidales bacterium ph8
JN837494


Bacteroidales genomosp. P1
AY341819


Bacteroidales genomosp. P2 oral clone MB1_G13
DQ003613


Bacteroidales genomosp. P3 oral clone MB1_G34
DQ003615


Bacteroidales genomosp. P4 oral clone MB2_G17
DQ003617


Bacteroidales genomosp. P5 oral clone MB2_P04
DQ003619


Bacteroidales genomosp. P6 oral clone MB3_C19
DQ003634


Bacteroidales genomosp. P7 oral clone MB3_P19
DQ003623


Bacteroidales genomosp. P8 oral clone MB4_G15
DQ003626



Bacteroides acidifaciens

NR_028607



Bacteroides barnesiae

NR_041446



Bacteroides caccae

EU136686



Bacteroides cellulosilyticus

ACCH01000108



Bacteroides clarus

AFBM01000011



Bacteroides coagulans

AB547639



Bacteroides coprocola

ABIY02000050



Bacteroides coprophilus

ACBW01000012



Bacteroides dorei

ABWZ01000093



Bacteroides eggerthii

ACWG01000065



Bacteroides faecis

GQ496624



Bacteroides finegoldii

AB222699



Bacteroides fluxus

AFBN01000029



Bacteroides fragilis

AP006841



Bacteroides galacturonicus

DQ497994



Bacteroides helcogenes

CP002352



Bacteroides heparinolyticus

JN867284



Bacteroides intestinalis

ABJL02000006



Bacteroides massiliensis

AB200226



Bacteroides nordii

NR_043017



Bacteroides oleiciplenus

AB547644



Bacteroides ovatus

ACWH01000036



Bacteroides pectinophilus

ABVQ01000036



Bacteroides plebeius

AB200218



Bacteroides pyogenes

NR_041280



Bacteroides salanitronis

CP002530



Bacteroides salyersiae

EU136690



Bacteroides sp. 1_1_14

ACRP01000155



Bacteroides sp. 1_1_30

ADCL01000128



Bacteroides sp. 1_1_6

ACIC01000215



Bacteroides sp. 2_1_22

ACPQ01000117



Bacteroides sp. 2_1_56FAA

ACWI01000065



Bacteroides sp. 2_2_4

ABZZ01000168



Bacteroides sp. 20_3

ACRQ01000064



Bacteroides sp. 3_1_19

ADCJ01000062



Bacteroides sp. 3_1_23

ACRS01000081



Bacteroides sp. 3_1_33FAA

ACPS01000085



Bacteroides sp. 3_1_40A

ACRT01000136



Bacteroides sp. 3_2_5

ACIB01000079



Bacteroides sp. 315_5

FJ848547



Bacteroides sp. 31SF15

AJ583248



Bacteroides sp. 31SF18

AJ583249



Bacteroides sp. 35AE31

AJ583244



Bacteroides sp. 35AE37

AJ583245



Bacteroides sp. 35BE34

AJ583246



Bacteroides sp. 35BE35

AJ583247



Bacteroides sp. 4_1_36

ACTC01000133



Bacteroides sp. 4_3_47FAA

ACDR02000029



Bacteroides sp. 9_1_42FAA

ACAA01000096



Bacteroides sp. AR20

AF139524



Bacteroides sp. AR29

AF139525



Bacteroides sp. B2

EU722733



Bacteroides sp. D1

ACAB02000030



Bacteroides sp. D2

ACGA01000077



Bacteroides sp. D20

ACPT01000052



Bacteroides sp. D22

ADCK01000151



Bacteroides sp. F_4

AB470322



Bacteroides sp. NB_8

AB117565



Bacteroides sp. WH2

AY895180



Bacteroides sp. XB12B

AM230648



Bacteroides sp. XB44A

AM230649



Bacteroides stercoris

ABFZ02000022



Bacteroides thetaiotaomicron

NR_074277



Bacteroides uniformis

AB050110



Bacteroides ureolyticus

GQ167666



Bacteroides vulgatus

CP000139



Bacteroides xylanisolvens

ADKP01000087


Bacteroidetes bacterium oral taxon D27
HM099638


Bacteroidetes bacterium oral taxon F31
HM099643


Bacteroidetes bacterium oral taxon F44
HM099649



Barnesiella intestinihominis

AB370251


Bifidobacteriaceae genomosp. C1
AY278612



Bifidobacterium adolescentis

AAXD02000018



Bifidobacterium angulatum

ABYS02000004



Bifidobacterium animalis

CP001606



Bifidobacterium bifidum

ABQP01000027



Bifidobacterium breve

CP002743



Bifidobacterium catenulatum

ABXY01000019



Bifidobacterium dentium

CP001750



Bifidobacterium gallicum

ABXB03000004



Bifidobacterium infantis

AY151398



Bifidobacterium kashiwanohense

AB491757



Bifidobacterium longum

ABQQ01000041



Bifidobacterium pseudocatenulatum

ABXX02000002



Bifidobacterium pseudolongum

NR_043442



Bifidobacterium scardovii

AJ307005



Bifidobacterium sp. HM2

AB425276



Bifidobacterium sp. HMLN12

JF519685



Bifidobacterium sp. M45

HM626176



Bifidobacterium sp. MSX5B

HQ616382



Bifidobacterium sp. TM_7

AB218972



Bifidobacterium thermophilum

DQ340557



Bifidobacterium urinalis

AJ278695



Blautia coccoides

AB571656



Blautia glucerasea

AB588023



Blautia glucerasei

AB439724



Blautia hansenii

ABYU02000037



Blautia hydrogenotrophica

ACBZ01000217



Blautia luti

AB691576



Blautia producta

AB600998



Blautia schinkii

NR_026312



Blautia sp. M25

HM626178



Blautia stercoris

HM626177



Blautia wexlerae

EF036467



Bordetella bronchiseptica

NR_025949



Bordetella holmesii

AB683187



Bordetella parapertussis

NR_025950



Bordetella pertussis

BX640418



Borrelia afzelii

ABCU01000001



Borrelia burgdorferi

ABGI01000001



Borrelia crocidurae

DQ057990



Borrelia duttonii

NC_011229



Borrelia garinii

ABJV01000001



Borrelia hermsii

AY597657



Borrelia hispanica

DQ057988



Borrelia persica

HM161645



Borrelia recurrentis

AF107367



Borrelia sp. NE49

AJ224142



Borrelia spielmanii

ABKB01000002



Borrelia turicatae

NC_008710



Borrelia valaisiana

ABCY01000002



Brucella ovis

NC_009504



Brucella sp. 83_13

ACBQ01000040



Brucella sp. BO1

EU053207



Brucella suis

ACBK01000034



Burkholderia ambifaria

AAUZ01000009



Burkholderia cenocepacia

AAHI01000060



Burkholderia cepacia

NR_041719



Burkholderia mallei

CP000547



Burkholderia multivorans

NC_010086



Burkholderia oklahomensis

DQ108388



Burkholderia pseudomallei

CP001408



Burkholderia rhizoxinica

HQ005410



Burkholderia sp. 383

CP000151



Burkholderia xenovorans

U86373


Burkholderiales bacterium 1_1_47
ADCQ01000066



Butyrivibrio crossotus

ABWN01000012



Butyrivibrio fibrisolvens

U41172



Chlamydia muridarum

AE002160



Chlamydia psittaci

NR_036864



Chlamydia trachomatis

U68443


Chlamydiales bacterium NS11
JN606074



Citrobacter amalonaticus

FR870441



Citrobacter braakii

NR_028687



Citrobacter farmeri

AF025371



Citrobacter freundii

NR_028894



Citrobacter gillenii

AF025367



Citrobacter koseri

NC_009792



Citrobacter murliniae

AF025369



Citrobacter rodentium

NR_074903



Citrobacter sedlakii

AF025364



Citrobacter sp. 30_2

ACDJ01000053



Citrobacter sp. KMSI_3

GQ468398



Citrobacter werkmanii

AF025373



Citrobacter youngae

ABWL02000011



Cloacibacillus evryensis

GQ258966


Clostridiaceae bacterium END_2
EF451053


Clostridiaceae bacterium JC13
JF824807



Clostridiales bacterium 1_7_47FAA

ABQR01000074



Clostridiales bacterium 9400853

HM587320



Clostridiales bacterium 9403326

HM587324



Clostridiales bacterium oral clone P4PA_66 P1

AY207065



Clostridiales bacterium oral taxon 093

GQ422712



Clostridiales bacterium oral taxon F32

HM099644



Clostridiales bacterium ph2

JN837487



Clostridiales bacterium SY8519

AB477431



Clostridiales genomosp. BVAB3

CP001850



Clostridiales sp. SM4_1

FP929060



Clostridiales sp. SS3_4

AY305316



Clostridiales sp. SSC_2

FP929061



Clostridium acetobutylicum

NR_074511



Clostridium aerotolerans

X76163



Clostridium aldenense

NR_043680



Clostridium aldrichii

NR_026099



Clostridium algidicarnis

NR_041746



Clostridium algidixylanolyticum

NR_028726



Clostridium aminovalericum

NR_029245



Clostridium amygdalinum

AY353957



Clostridium argentinense

NR_029232



Clostridium asparagiforme

ACCJ01000522



Clostridium baratii

NR_029229



Clostridium bartlettii

ABEZ02000012



Clostridium beijerinckii

NR_074434



Clostridium bifermentans

X73437



Clostridium bolteae

ABCC02000039



Clostridium botulinum

NC_010723



Clostridium butyricum

ABDT01000017



Clostridium cadaveris

AB542932



Clostridium carboxidivorans

FR733710



Clostridium carnis

NR_044716



Clostridium celatum

X77844



Clostridium celerecrescens

JQ246092



Clostridium cellulosi

NR_044624



Clostridium chauvoei

EU106372



Clostridium citroniae

ADLJ01000059



Clostridium clariflavum

NR_041235



Clostridium clostridiiformes

M59089



Clostridium clostridioforme

NR_044715



Clostridium coccoides

EF025906



Clostridium cochlearium

NR_044717



Clostridium cocleatum

NR_026495



Clostridium colicanis

FJ957863



Clostridium colinum

NR_026151



Clostridium difficile

NC_013315



Clostridium disporicum

NR_026491



Clostridium estertheticum

NR_042153



Clostridium fallax

NR_044714



Clostridium favososporum

X76749



Clostridium felsineum

AF270502



Clostridium frigidicarnis

NR_024919



Clostridium gasigenes

NR_024945



Clostridium ghonii

AB542933



Clostridium glycolicum

FJ384385



Clostridium glycyrrhizinilyticum

AB233029



Clostridium haemolyticum

NR_024749



Clostridium hathewayi

AY552788



Clostridium hiranonis

AB023970



Clostridium histolyticum

HF558362



Clostridium hylemonae

AB023973



Clostridium indolis

AF028351



Clostridium innocuum

M23732



Clostridium irregulare

NR_029249



Clostridium isatidis

NR_026347



Clostridium kluyveri

NR_074165



Clostridium lactatifermentans

NR_025651



Clostridium lavalense

EF564277



Clostridium leptum

AJ305238



Clostridium limosum

FR870444



Clostridium magnum

X77835



Clostridium malenominatum

FR749893



Clostridium mayombei

FR733682



Clostridium methylpentosum

ACEC01000059



Clostridium nexile

X73443



Clostridium novyi

NR_074343



Clostridium orbiscindens

Y18187



Clostridium oroticum

FR749922



Clostridium paraputrificum

AB536771



Clostridium perfringens

ABDW01000023



Clostridium phytofermentans

NR_074652



Clostridium piliforme

D14639



Clostridium putrefaciens

NR_024995



Clostridium quinii

NR_026149



Clostridium ramosum

M23731



Clostridium rectum

NR_029271



Clostridium saccharogumia

DQ100445



Clostridium saccharolyticum

CP002109



Clostridium sardiniense

NR_041006



Clostridium sartagoforme

NR_026490



Clostridium scindens

AF262238



Clostridium septicum

NR_026020



Clostridium sordellii

AB448946



Clostridium sp. 7_2_43FAA

ACDK01000101



Clostridium sp. D5

ADBG01000142



Clostridium sp. HGF2

AENW01000022



Clostridium sp. HPB_46

AY862516



Clostridium sp. JC122

CAEV01000127



Clostridium sp. L2_50

AAYW02000018



Clostridium sp. LMG 16094

X95274



Clostridium sp. M62_1

ACFX02000046



Clostridium sp. MLG055

AF304435



Clostridium sp. MT4 E

FJ159523



Clostridium sp. NMBHI_1

JN093130



Clostridium sp. NML 04A032

EU815224



Clostridium sp. SS2_1

ABGC03000041



Clostridium sp. SY8519

AP012212



Clostridium sp. TM_40

AB249652



Clostridium sp. YIT 12069

AB491207



Clostridium sp. YIT 12070

AB491208



Clostridium sphenoides

X73449



Clostridium spiroforme

X73441



Clostridium sporogenes

ABKW02000003



Clostridium sporosphaeroides

NR_044835



Clostridium stercorarium

NR_025100



Clostridium sticklandii

L04167



Clostridium straminisolvens

NR_024829



Clostridium subterminale

NR_041795



Clostridium sulfidigenes

NR_044161



Clostridium symbiosum

ADLQ01000114



Clostridium tertium

Y18174



Clostridium tetani

NC_004557



Clostridium thermocellum

NR_074629



Clostridium tyrobutyricum

NR_044718



Clostridium viride

NR_026204



Clostridium xylanolyticum

NR_037068



Collinsella aerofaciens

AAVN02000007



Collinsella intestinalis

ABXH02000037



Collinsella stercoris

ABXJ01000150



Collinsella tanakaei

AB490807



Coprobacillus cateniformis

AB030218



Coprobacillus sp. 29_1

ADKX01000057



Coprobacillus sp. D7

ACDT01000199



Coprococcus catus

EU266552



Coprococcus comes

ABVR01000038



Coprococcus eutactus

EF031543



Coprococcus sp. ART55_1

AY350746



Dialister invisus

ACIM02000001



Dialister micraerophilus

AFBB01000028



Dialister microaerophilus

AENT01000008



Dialister pneumosintes

HM596297



Dialister propionicifaciens

NR_043231



Dialister sp. oral taxon 502

GQ422739



Dialister succinatiphilus

AB370249



Dorea formicigenerans

AAXA02000006



Dorea longicatena

AJ132842



Enhydrobacter aerosaccus

ACYI01000081



Enterobacter aerogenes

AJ251468



Enterobacter asburiae

NR_024640



Enterobacter cancerogenus

Z96078



Enterobacter cloacae

FP929040



Enterobacter cowanii

NR_025566



Enterobacter hormaechei

AFHR01000079



Enterobacter sp. 247BMC

HQ122932



Enterobacter sp. 638

NR_074777



Enterobacter sp. JC163

JN657217



Enterobacter sp. SCSS

HM007811



Enterobacter sp. TSE38

HM156134


Enterobacteriaceae bacterium 9_2_54FAA
ADCU01000033


Enterobacteriaceae bacterium CF01Ent_1
AJ489826


Enterobacteriaceae bacterium Smarlab 3302238
AY538694



Enterococcus avium

AF133535



Enterococcus caccae

AY943820



Enterococcus casseliflavus

AEWT01000047



Enterococcus durans

AJ276354



Enterococcus faecalis

AE016830



Enterococcus faecium

AM157434



Enterococcus gallinarum

AB269767



Enterococcus gilvus

AY033814



Enterococcus hawaiiensis

AY321377



Enterococcus hirae

AF061011



Enterococcus italicus

AEPV01000109



Enterococcus mundtii

NR_024906



Enterococcus raffinosus

FN600541



Enterococcus sp. BV2CASA2

JN809766



Enterococcus sp. CCRI_16620

GU457263



Enterococcus sp. F95

FJ463817



Enterococcus sp. RfL6

AJ133478



Enterococcus thailandicus

AY321376


Erysipelotrichaceae bacterium 3_1_53
ACTJ01000113


Erysipelotrichaceae bacterium 5_2_54FAA



Escherichia albertii

ABKX01000012



Escherichia coli

NC_008563



Escherichia fergusonii

CU928158



Escherichia hermannii

HQ407266



Escherichia sp. 1_1_43

ACID01000033



Escherichia sp. 4_1_40B

ACDM02000056



Escherichia sp. B4

EU722735



Escherichia vulneris

NR_041927


Eubacteriaceae bacterium P4P_50 P4
AY207060



Eubacterium barkeri

NR_044661



Eubacterium biforme

ABYT01000002



Eubacterium brachy

U13038



Eubacterium budayi

NR_024682



Eubacterium callanderi

NR_026330



Eubacterium cellulosolvens

AY178842



Eubacterium contortum

FR749946



Eubacterium coprostanoligenes

HM037995



Eubacterium cylindroides

FP929041



Eubacterium desmolans

NR_044644



Eubacterium dolichum

L34682



Eubacterium eligens

CP001104



Eubacterium fissicatena

FR749935



Eubacterium hadrum

FR749933



Eubacterium hallii

L34621



Eubacterium infirmum

U13039



Eubacterium limosum

CP002273



Eubacterium moniliforme

HF558373



Eubacterium multiforme

NR_024683



Eubacterium nitritogenes

NR_024684



Eubacterium nodatum

U13041



Eubacterium ramulus

AJ011522



Eubacterium rectale

FP929042



Eubacterium ruminantium

NR_024661



Eubacterium saburreum

AB525414



Eubacterium saphenum

NR_026031



Eubacterium siraeum

ABCA03000054



Eubacterium sp. 3_1_31

ACTL01000045



Eubacterium sp. AS15b

HQ616364



Eubacterium sp. OBRC9

HQ616354



Eubacterium sp. oral clone GI038

AY349374



Eubacterium sp. oral clone IR009

AY349376



Eubacterium sp. oral clone JH012

AY349373



Eubacterium sp. oral clone JI012

AY349379



Eubacterium sp. oral clone JN088

AY349377



Eubacterium sp. oral clone JS001

AY349378



Eubacterium sp. oral clone OH3A

AY947497



Eubacterium sp. WAL 14571

FJ687606



Eubacterium tenue

M59118



Eubacterium tortuosum

NR_044648



Eubacterium ventriosum

L34421



Eubacterium xylanophilum

L34628



Eubacterium yurii

AEES01000073



Fusobacterium canifelinum

AY162222



Fusobacterium genomosp. C1

AY278616



Fusobacterium genomosp. C2

AY278617



Fusobacterium gonidiaformans

ACET01000043



Fusobacterium mortiferum

ACDB02000034



Fusobacterium naviforme

HQ223106



Fusobacterium necrogenes

X55408



Fusobacterium necrophorum

AM905356



Fusobacterium nucleatum

ADVK01000034



Fusobacterium periodonticum

ACJY01000002



Fusobacterium russii

NR_044687



Fusobacterium sp. 1_1_41FAA

ADGG01000053



Fusobacterium sp. 11_3_2

ACUO01000052



Fusobacterium sp. 12_1B

AGWJ01000070



Fusobacterium sp. 2_1_31

ACDC02000018



Fusobacterium sp. 3_1_27

ADGF01000045



Fusobacterium sp. 3_1_33

ACQE01000178



Fusobacterium sp. 3_1_36A2

ACPU01000044



Fusobacterium sp. 3_1_5R

ACDD01000078



Fusobacterium sp. AC18

HQ616357



Fusobacterium sp. ACB2

HQ616358



Fusobacterium sp. AS2

HQ616361



Fusobacterium sp. CM1

HQ616371



Fusobacterium sp. CM21

HQ616375



Fusobacterium sp. CM22

HQ616376



Fusobacterium sp. D12

ACDG02000036



Fusobacterium sp. oral clone ASCF06

AY923141



Fusobacterium sp. oral clone ASCF11

AY953256



Fusobacterium ulcerans

ACDH01000090



Fusobacterium varium

ACIE01000009



Gemella haemolysans

ACDZ02000012



Gemella morbillorum

NR_025904



Gemella morbillorum

ACRX01000010



Gemella sanguinis

ACRY01000057



Gemella sp. oral clone ASCE02

AY923133



Gemella sp. oral clone ASCF04

AY923139



Gemella sp. oral clone ASCF12

AY923143



Gemella sp. WAL 1945J

EU427463



Klebsiella oxytoca

AY292871



Klebsiella pneumoniae

CP000647



Klebsiella sp. AS10

HQ616362



Klebsiella sp. Co9935

DQ068764



Klebsiella sp. enrichment culture

HM195210


clone SRC_DSD25



Klebsiella sp. OBRC7

HQ616353



Klebsiella sp. SP_BA

FJ999767



Klebsiella sp. SRC_DSD1

GU797254



Klebsiella sp. SRC_DSD11

GU797263



Klebsiella sp. SRC_DSD12

GU797264



Klebsiella sp. SRC_DSD15

GU797267



Klebsiella sp. SRC_DSD2

GU797253



Klebsiella sp. SRC_DSD6

GU797258



Klebsiella variicola

CP001891



Lachnobacterium bovis

GU324407



Lachnospira multipara

FR733699



Lachnospira pectinoschiza

L14675


Lachnospiraceae bacterium 1_1_57FAA
ACTM01000065


Lachnospiraceae bacterium 1_4_56FAA
ACTN01000028


Lachnospiraceae bacterium 2_1_46FAA
ADLB01000035


Lachnospiraceae bacterium 2_1_58FAA
ACTO01000052


Lachnospiraceae bacterium 3_1_57FAA_CT1
ACTP01000124


Lachnospiraceae bacterium 4_1_37FAA
ADCR01000030


Lachnospiraceae bacterium 5_1_57FAA
ACTR01000020


Lachnospiraceae bacterium 5_1_63FAA
ACTS01000081


Lachnospiraceae bacterium 6_1_63FAA
ACTV01000014


Lachnospiraceae bacterium 8_1_57FAA
ACWQ01000079


Lachnospiraceae bacterium 9_1_43BFAA
ACTX01000023


Lachnospiraceae bacterium A4
DQ789118


Lachnospiraceae bacterium DJF VP30
EU728771


Lachnospiraceae bacterium ICM62
HQ616401


Lachnospiraceae bacterium MSX33
HQ616384


Lachnospiraceae bacterium oral taxon 107
ADDS01000069


Lachnospiraceae bacterium oral taxon F15
HM099641


Lachnospiraceae genomosp. C1
AY278618



Lactobacillus acidipiscis

NR_024718



Lactobacillus acidophilus

CP000033



Lactobacillus alimentarius

NR_044701



Lactobacillus amylolyticus

ADNY01000006



Lactobacillus amylovorus

CP002338



Lactobacillus antri

ACLL01000037



Lactobacillus brevis

EU194349



Lactobacillus buchneri

ACGH01000101



Lactobacillus casei

CP000423



Lactobacillus catenaformis

M23729



Lactobacillus coleohominis

ACOH01000030



Lactobacillus coryniformis

NR_044705



Lactobacillus crispatus

ACOG01000151



Lactobacillus curvatus

NR_042437



Lactobacillus delbrueckii

CP002341



Lactobacillus dextrinicus

NR_036861



Lactobacillus farciminis

NR_044707



Lactobacillus fermentum

CP002033



Lactobacillus gasseri

ACOZ01000018



Lactobacillus gastricus

AICN01000060



Lactobacillus genomosp. C1

AY278619



Lactobacillus genomosp. C2

AY278620



Lactobacillus helveticus

ACLM01000202



Lactobacillus hilgardii

ACGP01000200



Lactobacillus hominis

FR681902



Lactobacillus iners

AEKJ01000002



Lactobacillus jensenii

ACQD01000066



Lactobacillus johnsonii

AE017198



Lactobacillus kalixensis

NR_029083



Lactobacillus kefiranofaciens

NR_042440



Lactobacillus kefiri

NR_042230



Lactobacillus kimchii

NR_025045



Lactobacillus leichmannii

JX986966



Lactobacillus mucosae

FR693800



Lactobacillus murinus

NR_042231



Lactobacillus nodensis

NR_041629



Lactobacillus oeni

NR_043095



Lactobacillus oris

AEKL01000077



Lactobacillus parabrevis

NR_042456



Lactobacillus parabuchneri

NR_041294



Lactobacillus paracasei

ABQV01000067



Lactobacillus parakefiri

NR_029039



Lactobacillus pentosus

JN813103



Lactobacillus perolens

NR_029360



Lactobacillus plantarum

ACGZ02000033



Lactobacillus pontis

HM218420



Lactobacillus reuteri

ACGW02000012



Lactobacillus rhamnosus

ABWJ01000068



Lactobacillus rogosae

GU269544



Lactobacillus ruminis

ACGS02000043



Lactobacillus sakei

DQ989236



Lactobacillus salivarius

AEBA01000145



Lactobacillus saniviri

AB602569



Lactobacillus senioris

AB602570



Lactobacillus sp. 66c

FR681900



Lactobacillus sp. BT6

HQ616370



Lactobacillus sp. KLDS 1.0701

EU600905



Lactobacillus sp. KLDS 1.0702

EU600906



Lactobacillus sp. KLDS 1.0703

EU600907



Lactobacillus sp. KLDS 1.0704

EU600908



Lactobacillus sp. KLDS 1.0705

EU600909



Lactobacillus sp. KLDS 1.0707

EU600911



Lactobacillus sp. KLDS 1.0709

EU600913



Lactobacillus sp. KLDS 1.0711

EU600915



Lactobacillus sp. KLDS 1.0712

EU600916



Lactobacillus sp. KLDS 1.0713

EU600917



Lactobacillus sp. KLDS 1.0716

EU600921



Lactobacillus sp. KLDS 1.0718

EU600922



Lactobacillus sp. KLDS 1.0719

EU600923



Lactobacillus sp. oral clone HT002

AY349382



Lactobacillus sp. oral clone HT070

AY349383



Lactobacillus sp. oral taxon 052

GQ422710



Lactobacillus tucceti

NR_042194



Lactobacillus ultunensis

ACGU01000081



Lactobacillus vaginalis

ACGV01000168



Lactobacillus vini

NR_042196



Lactobacillus vitulinus

NR_041305



Lactobacillus zeae

NR_037122



Lactococcus garvieae

AF061005



Lactococcus lactis

CP002365



Lactococcus raffinolactis

NR_044359



Listeria grayi

ACCR02000003



Listeria innocua

JF967625



Listeria ivanovii

X56151



Listeria monocytogenes

CP002003



Listeria welshimeri

AM263198



Megasphaera elsdenii

AY038996



Megasphaera genomosp. C1

AY278622



Megasphaera genomosp. type_1

ADGP01000010



Megasphaera micronuciformis

AECS01000020



Megasphaera sp. BLPYG_07

HM990964



Megasphaera sp. UPII 199_6

AFIJ01000040



Microbacterium gubbeenense

NR_025098



Microbacterium lacticum

EU714351



Mitsuokella jalaludinii

NR_028840



Mitsuokella multacida

ABWK02000005



Mitsuokella sp. oral taxon 521

GU413658



Mitsuokella sp. oral taxon G68

GU432166



Mycobacterium abscessus

AGQU01000002



Mycobacterium africanum

AF480605



Mycobacterium alsiensis

AJ938169



Mycobacterium avium

CP000479



Mycobacterium chelonae

AB548610



Mycobacterium colombiense

AM062764



Mycobacterium elephantis

AF385898



Mycobacterium gordonae

GU142930



Mycobacterium intracellulare

GQ153276



Mycobacterium kansasii

AF480601



Mycobacterium lacus

NR_025175



Mycobacterium leprae

FM211192



Mycobacterium lepromatosis

EU203590



Mycobacterium mageritense

FR798914



Mycobacterium mantenii

FJ042897



Mycobacterium marinum

NC_010612



Mycobacterium microti

NR_025234



Mycobacterium neoaurum

AF268445



Mycobacterium parascrofulaceum

ADNV01000350



Mycobacterium paraterrae

EU919229



Mycobacterium phlei

GU142920



Mycobacterium seoulense

DQ536403



Mycobacterium smegmatis

CP000480



Mycobacterium sp. 1761

EU703150



Mycobacterium sp. 1776

EU703152



Mycobacterium sp. 1781

EU703147



Mycobacterium sp. 1791

EU703148



Mycobacterium sp. 1797

EU703149



Mycobacterium sp. AQIGA4

HM210417



Mycobacterium sp. B10_07.09.0206

HQ174245



Mycobacterium sp. GN_10546

FJ497243



Mycobacterium sp. GN_10827

FJ497247



Mycobacterium sp. GN_11124

FJ652846



Mycobacterium sp. GN_9188

FJ497240



Mycobacterium sp. GR_2007_210

FJ555538



Mycobacterium sp. HE5

AJ012738



Mycobacterium sp. NLA001000736

HM627011



Mycobacterium sp. W

DQ437715



Mycobacterium tuberculosis

CP001658



Mycobacterium ulcerans

AB548725



Mycobacterium vulneris

EU834055



Mycoplasma agalactiae

AF010477



Mycoplasma amphoriforme

AY531656



Mycoplasma arthritidis

NC_011025



Mycoplasma bovoculi

NR_025987



Mycoplasma faucium

NR_024983



Mycoplasma fermentans

CP002458



Mycoplasma flocculare

X62699



Mycoplasma genitalium

L43967



Mycoplasma hominis

AF443616



Mycoplasma orale

AY796060



Mycoplasma ovipneumoniae

NR_025989



Mycoplasma penetrans

NC_004432



Mycoplasma pneumoniae

NC_000912



Mycoplasma putrefaciens

U26055



Mycoplasma salivarium

M24661


Mycoplasmataceae genomosp. P1 oral
DQ003614


clone MB1_G23



Neisseria bacilliformis

AFAY01000058



Neisseria cinerea

ACDY01000037



Neisseria elongata

ADBF01000003



Neisseria flavescens

ACQV01000025



Neisseria genomosp. P2 oral clone MB5_P15

DQ003630



Neisseria gonorrhoeae

CP002440



Neisseria lactamica

ACEQ01000095



Neisseria macacae

AFQE01000146



Neisseria meningitidis

NC_003112



Neisseria mucosa

ACDX01000110



Neisseria pharyngis

AJ239281



Neisseria polysaccharea

ADBE01000137



Neisseria sicca

ACKO02000016



Neisseria sp. KEM232

GQ203291



Neisseria sp. oral clone AP132

AY005027



Neisseria sp. oral clone JC012

AY349388



Neisseria sp. oral strain B33KA

AY005028



Neisseria sp. oral taxon 014

ADEA01000039



Neisseria sp. SMC_A9199

FJ763637



Neisseria sp. TM10_1

DQ279352



Neisseria subflava

ACEO01000067



Odoribacter laneus

AB490805



Odoribacter splanchnicus

CP002544



Oscillibacter sp. G2

HM626173



Oscillibacter valericigenes

NR_074793



Oscillospira guilliermondii

AB040495



Paenibacillus barcinonensis

NR_042272



Paenibacillus barengoltzii

NR_042756



Paenibacillus chibensis

NR_040885



Paenibacillus cookii

NR_025372



Paenibacillus durus

NR_037017



Paenibacillus glucanolyticus

D78470



Paenibacillus lactis

NR_025739



Paenibacillus lautus

NR_040882



Paenibacillus pabuli

NR_040853



Paenibacillus polymyxa

NR_037006



Paenibacillus popilliae

NR_040888



Paenibacillus sp. CIP 101062

HM212646



Parabacteroides distasonis

CP000140



Parabacteroides goldsteinii

AY974070



Parabacteroides gordonii

AB470344



Parabacteroides johnsonii

ABYH01000014



Parabacteroides merdae

EU136685



Parabacteroidessp. D13

ACPW01000017



Parabacteroidessp. NS31_3

JN029805



Peptococcus niger

NR_029221



Peptococcus sp. oral clone JM048

AY349389



Peptococcus sp. oral taxon 167

GQ422727



Peptoniphilus asaccharolyticus

D14145



Peptoniphilus duerdenii

EU526290



Peptoniphilus harei

NR_026358



Peptoniphilus indolicus

AY153431



Peptoniphilus ivorii

Y07840



Peptoniphilus lacrimalis

ADDO01000050



Peptoniphilus sp. gpac007

AM176517



Peptoniphilus sp. gpac018A

AM176519



Peptoniphilus sp. gpac077

AM176527



Peptoniphilus sp. gpac148

AM176535



Peptoniphilus sp. JC140

JF824803



Peptoniphilus sp. oral taxon 386

ADCS01000031



Peptoniphilus sp. oral taxon 836

AEAA01000090


Peptostreptococcaceae bacterium ph1
JN837495



Peptostreptococcus anaerobius

AY326462



Peptostreptococcus micros

AM176538



Peptostreptococcus sp. 9succ1

X90471



Peptostreptococcus sp. oral clone AP24

AB175072



Peptostreptococcus sp. oral clone FJ023

AY349390



Peptostreptococcus sp. P4P_31 P3

AY207059



Peptostreptococcus stomatis

ADGQ01000048


Porphyromonadaceae bacterium NML 060648
EF184292



Porphyromonas asaccharolytica

AENO01000048



Porphyromonas endodontalis

ACNN01000021



Porphyromonas gingivalis

AE015924



Porphyromonas levii

NR_025907



Porphyromonas macacae

NR_025908



Porphyromonas somerae

AB547667



Porphyromonas sp. oral clone BB134

AY005068



Porphyromonas sp. oral clone F016

AY005069



Porphyromonas sp. oral clone P2PB_52 P1

AY207054



Porphyromonas sp. oral clone P4GB_100 P2

AY207057



Porphyromonas sp. UQD 301

EU012301



Porphyromonas uenonis

ACLR01000152



Prevotella albensis

NR_025300



Prevotella amnii

AB547670



Prevotella bergensis

ACKS01000100



Prevotella bivia

ADFO01000096



Prevotella brevis

NR_041954



Prevotella buccae

ACRB01000001



Prevotella buccalis

JN867261



Prevotella copri

ACBX02000014



Prevotella corporis

L16465



Prevotella dentalis

AB547678



Prevotella denticola

CP002589



Prevotella disiens

AEDO01000026



Prevotella genomosp. C1

AY278624



Prevotella genomosp. C2

AY278625



Prevotella genomosp. P7 oral clone MB2_P31

DQ003620



Prevotella genomosp. P8 oral clone MB3_P13

DQ003622



Prevotella genomosp. P9 oral clone MB7_G16

DQ003633



Prevotella heparinolytica

GQ422742



Prevotella histicola

JN867315



Prevotella intermedia

AF414829



Prevotella loescheii

JN867231



Prevotella maculosa

AGEK01000035



Prevotella marshii

AEEI01000070



Prevotella melaninogenica

CP002122



Prevotella micans

AGWK01000061



Prevotella multiformis

AEWX01000054



Prevotella multisaccharivorax

AFJE01000016



Prevotella nanceiensis

JN867228



Prevotella nigrescens

AFPX01000069



Prevotella oralis

AEPE01000021



Prevotella oris

ADDV01000091



Prevotella oulorum

L16472



Prevotella pallens

AFPY01000135



Prevotella ruminicola

CP002006



Prevotella salivae

AB108826



Prevotella sp. BI_42

AJ581354



Prevotella sp. CM38

HQ610181



Prevotella sp. ICM1

HQ616385



Prevotella sp. ICM55

HQ616399



Prevotella sp. JCM 6330

AB547699



Prevotella sp. oral clone AA020

AY005057



Prevotella sp. oral clone ASCG10

AY923148



Prevotella sp. oral clone ASCG12

DQ272511



Prevotella sp. oral clone AU069

AY005062



Prevotella sp. oral clone CY006

AY005063



Prevotella sp. oral clone DA058

AY005065



Prevotella sp. oral clone FL019

AY349392



Prevotella sp. oral clone FU048

AY349393



Prevotella sp. oral clone FW035

AY349394



Prevotella sp. oral clone GI030

AY349395



Prevotella sp. oral clone GI032

AY349396



Prevotella sp. oral clone GI059

AY349397



Prevotella sp. oral clone GU027

AY349398



Prevotella sp. oral clone HF050

AY349399



Prevotella sp. oral clone ID019

AY349400



Prevotella sp. oral clone IDR_CEC_0055

AY550997



Prevotella sp. oral clone IK053

AY349401



Prevotella sp. oral clone IK062

AY349402



Prevotella sp. oral clone P4PB_83 P2

AY207050



Prevotella sp. oral taxon 292

GQ422735



Prevotella sp. oral taxon 299

ACWZ01000026



Prevotella sp. oral taxon 300

GU409549



Prevotella sp. oral taxon 302

ACZK01000043



Prevotella sp. oral taxon 310

GQ422737



Prevotella sp. oral taxon 317

ACQH01000158



Prevotella sp. oral taxon 472

ACZS01000106



Prevotella sp. oral taxon 781

GQ422744



Prevotella sp. oral taxon 782

GQ422745



Prevotella sp. oral taxon F68

HM099652



Prevotella sp. oral taxon G60

GU432133



Prevotella sp. oral taxon G70

GU432179



Prevotella sp. oral taxon G71

GU432180



Prevotella sp. SEQ053

JN867222



Prevotella sp. SEQ065

JN867234



Prevotella sp. SEQ072

JN867238



Prevotella sp. SEQ116

JN867246



Prevotella sp. SG12

GU561343



Prevotella sp. sp24

AB003384



Prevotella sp. sp34

AB003385



Prevotella stercorea

AB244774



Prevotella tannerae

ACIJ02000018



Prevotella timonensis

ADEF01000012



Prevotella veroralis

ACVA01000027


Prevotellaceae bacterium P4P_62 P1
AY207061


Propionibacteriaceae bacterium NML 02_0265
EF599122



Propionibacterium acidipropionici

NC_019395



Propionibacterium acnes

ADJM01000010



Propionibacterium avidum

AJ003055



Propionibacterium freudenreichii

NR_036972



Propionibacterium granulosum

FJ785716



Propionibacterium jensenii

NR_042269



Propionibacterium propionicum

NR_025277



Propionibacterium sp. 434_HC2

AFIL01000035



Propionibacterium sp. H456

AB177643



Propionibacterium sp. LG

AY354921



Propionibacterium sp. oral taxon 192

GQ422728



Propionibacterium sp. S555a

AB264622



Propionibacterium thoenii

NR_042270



Pseudomonas aeruginosa

AABQ07000001



Pseudomonas fluorescens

AY622220



Pseudomonas gessardii

FJ943496



Pseudomonas mendocina

AAUL01000021



Pseudomonas monteilii

NR_024910



Pseudomonas poae

GU188951



Pseudomonas pseudoalcaligenes

NR_037000



Pseudomonas putida

AF094741



Pseudomonas sp. 2_1_26

ACWU01000257



Pseudomonas sp. G1229

DQ910482



Pseudomonas sp. NP522b

EU723211



Pseudomonas stutzeri

AM905854



Pseudomonas tolaasii

AF320988



Pseudomonas viridiflava

NR_042764



Ralstonia pickettii

NC_010682



Ralstonia sp. 5_7_47FAA

ACUF01000076



Roseburia cecicola

GU233441



Roseburia faecalis

AY804149



Roseburia faecis

AY305310



Roseburia hominis

AJ270482



Roseburia intestinalis

FP929050



Roseburia inulinivorans

AJ270473



Roseburia sp. 11SE37

FM954975



Roseburia sp. 11SE38

FM954976



Rothia aeria

DQ673320



Rothia dentocariosa

ADDW01000024



Rothia mucilaginosa

ACVO01000020



Rothia nasimurium

NR_025310



Rothia sp. oral taxon 188

GU470892



Ruminobacter amylophilus

NR_026450


Ruminococcaceae bacterium D16
ADDX01000083



Ruminococcus albus

AY445600



Ruminococcus bromii

EU266549



Ruminococcus callidus

NR_029160



Ruminococcus champanellensis

FP929052



Ruminococcus flavefaciens

NR_025931



Ruminococcus gnavus

X94967



Ruminococcus hansenii

M59114



Ruminococcus lactaris

ABOU02000049



Ruminococcus obeum

AY169419



Ruminococcus sp. 18P13

AJ515913



Ruminococcus sp. 5_1_39BFAA

ACII01000172



Ruminococcus sp. 9SE51

FM954974



Ruminococcus sp. ID8

AY960564



Ruminococcus sp. K_1

AB222208



Ruminococcus torques

AAVP02000002



Salmonella bongori

NR_041699



Salmonella enterica

NC_011149



Salmonella enterica

NC_011205



Salmonella enterica

DQ344532



Salmonella enterica

ABEH02000004



Salmonella enterica

ABAK02000001



Salmonella enterica

NC_011080



Salmonella enterica

EU118094



Salmonella enterica

NC_011094



Salmonella enterica

AE014613



Salmonella enterica

ABFH02000001



Salmonella enterica

ABEM01000001



Salmonella enterica

ABAM02000001



Salmonella typhimurium

DQ344533



Salmonella typhimurium

AF170176



Selenomonas artemidis

HM596274



Selenomonas dianae

GQ422719



Selenomonas flueggei

AF287803



Selenomonas genomosp. C1

AY278627



Selenomonas genomosp. C2

AY278628



Selenomonas genomosp. P5

AY341820



Selenomonas genomosp. P6 oral clone MB3_C41

DQ003636



Selenomonas genomosp. P7 oral clone MB5_C08

DQ003627



Selenomonas genomosp. P8 oral clone MB5_P06

DQ003628



Selenomonas infelix

AF287802



Selenomonas noxia

GU470909



Selenomonas ruminantium

NR_075026



Selenomonas sp. FOBRC9

HQ616378



Selenomonas sp. oral clone FT050

AY349403



Selenomonas sp. oral clone GI064

AY349404



Selenomonas sp. oral clone GT010

AY349405



Selenomonas sp. oral clone HU051

AY349406



Selenomonas sp. oral clone IK004

AY349407



Selenomonas sp. oral clone IQ048

AY349408



Selenomonas sp. oral clone JI021

AY349409



Selenomonas sp. oral clone JS031

AY349410



Selenomonas sp. oral clone OH4A

AY947498



Selenomonas sp. oral clone P2PA_80 P4

AY207052



Selenomonas sp. oral taxon 137

AENV01000007



Selenomonas sp. oral taxon 149

AEEJ01000007



Selenomonas sputigena

ACKP02000033



Serratia fonticola

NR_025339



Serratia liquefaciens

NR_042062



Serratia marcescens

GU826157



Serratia odorifera

ADBY01000001



Serratia proteamaculans

AAUN01000015



Shigella boydii

AAKA01000007



Shigella dysenteriae

NC_007606



Shigella flexneri

AE005674



Shigella sonnei

NC_007384



Sphingobacterium faecium

NR_025537



Sphingobacterium mizutaii

JF708889



Sphingobacterium multivorum

NR_040953



Sphingobacterium spiritivorum

ACHA02000013



Sphingomonas echinoides

NR_024700



Sphingomonas sp. oral clone FI012

AY349411



Sphingomonas sp. oral clone FZ016

AY349412



Sphingomonas sp. oral taxon A09

HM099639



Sphingomonas sp. oral taxon F71

HM099645


Staphylococcaceae bacterium NML 92_0017
AY841362



Staphylococcus aureus

CP002643



Staphylococcus auricularis

JQ624774



Staphylococcus capitis

ACFR01000029



Staphylococcus caprae

ACRH01000033



Staphylococcus carnosus

NR_075003



Staphylococcus cohnii

JN175375



Staphylococcus condimenti

NR_029345



Staphylococcus epidermidis

ACHE01000056



Staphylococcus equorum

NR_027520



Staphylococcus fleurettii

NR_041326



Staphylococcus haemolyticus

NC_007168



Staphylococcus hominis

AM157418



Staphylococcus lugdunensis

AEQA01000024



Staphylococcus pasteuri

FJ189773



Staphylococcus pseudintermedius

CP002439



Staphylococcus saccharolyticus

NR_029158



Staphylococcus saprophyticus

NC_007350



Staphylococcus sciuri

NR_025520



Staphylococcus sp. clone bottae7

AF467424



Staphylococcus sp. H292

AB177642



Staphylococcus sp. H780

AB177644



Staphylococcus succinus

NR_028667



Staphylococcus vitulinus

NR_024670



Staphylococcus warneri

ACPZ01000009



Staphylococcus xylosus

AY395016



Streptobacillus moniliformis

NR_027615



Streptococcus agalactiae

AAJO01000130



Streptococcus alactolyticus

NR_041781



Streptococcus anginosus

AECT01000011



Streptococcus australis

AEQR01000024



Streptococcus bovis

AEEL01000030



Streptococcus canis

AJ413203



Streptococcus constellatus

AY277942



Streptococcus cristatus

AEVC01000028



Streptococcus downei

AEKN01000002



Streptococcus dysgalactiae

AP010935



Streptococcus equi

CP001129



Streptococcus equinus

AEVB01000043



Streptococcus gallolyticus

FR824043



Streptococcus genomosp. C1

AY278629



Streptococcus genomosp. C2

AY278630



Streptococcus genomosp. C3

AY278631



Streptococcus genomosp. C4

AY278632



Streptococcus genomosp. C5

AY278633



Streptococcus genomosp. C6

AY278634



Streptococcus genomosp. C7

AY278635



Streptococcus genomosp. C8

AY278609



Streptococcus gordonii

NC_009785



Streptococcus infantarius

ABJK02000017



Streptococcus infantis

AFNN01000024



Streptococcus intermedius

NR_028736



Streptococcus lutetiensis

NR_037096



Streptococcus massiliensis

AY769997



Streptococcus milleri

X81023



Streptococcus mitis

AM157420



Streptococcus mutans

AP010655



Streptococcus oligofermentans

AY099095



Streptococcus oralis

ADMV01000001



Streptococcus parasanguinis

AEKM01000012



Streptococcus pasteurianus

AP012054



Streptococcus peroris

AEVF01000016



Streptococcus pneumoniae

AE008537



Streptococcus porcinus

EF121439



Streptococcus pseudopneumoniae

FJ827123



Streptococcus pseudoporcinus

AENS01000003



Streptococcus pyogenes

AE006496



Streptococcus ratti

X58304



Streptococcus salivarius

AGBV01000001



Streptococcus sanguinis

NR_074974



Streptococcus sinensis

AF432857



Streptococcus sp. 16362

JN590019



Streptococcus sp. 2_1_36FAA

ACOI01000028



Streptococcus sp. 2285_97

AJ131965



Streptococcus sp. 69130

X78825



Streptococcus sp. AC15

HQ616356



Streptococcus sp. ACS2

HQ616360



Streptococcus sp. AS20

HQ616366



Streptococcus sp. BS35a

HQ616369



Streptococcus sp. C150

ACRI01000045



Streptococcus sp. CM6

HQ616372



Streptococcus sp. CM7

HQ616373



Streptococcus sp. ICM10

HQ616389



Streptococcus sp. ICM12

HQ616390



Streptococcus sp. ICM2

HQ616386



Streptococcus sp. ICM4

HQ616387



Streptococcus sp. ICM45

HQ616394



Streptococcus sp. M143

ACRK01000025



Streptococcus sp. M334

ACRL01000052



Streptococcus sp. OBRC6

HQ616352



Streptococcus sp. oral clone ASB02

AY923121



Streptococcus sp. oral clone ASCA03

DQ272504



Streptococcus sp. oral clone ASCA04

AY923116



Streptococcus sp. oral clone ASCA09

AY923119



Streptococcus sp. oral clone ASCB04

AY923123



Streptococcus sp. oral clone ASCB06

AY923124



Streptococcus sp. oral clone ASCC04

AY923127



Streptococcus sp. oral clone ASCC05

AY923128



Streptococcus sp. oral clone ASCC12

DQ272507



Streptococcus sp. oral clone ASCD01

AY923129



Streptococcus sp. oral clone ASCD09

AY923130



Streptococcus sp. oral clone ASCD10

DQ272509



Streptococcus sp. oral clone ASCE03

AY923134



Streptococcus sp. oral clone ASCE04

AY953253



Streptococcus sp. oral clone ASCE05

DQ272510



Streptococcus sp. oral clone ASCE06

AY923135



Streptococcus sp. oral clone ASCE09

AY923136



Streptococcus sp. oral clone ASCE10

AY923137



Streptococcus sp. oral clone ASCE12

AY923138



Streptococcus sp. oral clone ASCF05

AY923140



Streptococcus sp. oral clone ASCF07

AY953255



Streptococcus sp. oral clone ASCF09

AY923142



Streptococcus sp. oral clone ASCG04

AY923145



Streptococcus sp. oral clone BW009

AY005042



Streptococcus sp. oral clone CH016

AY005044



Streptococcus sp. oral clone GK051

AY349413



Streptococcus sp. oral clone GM006

AY349414



Streptococcus sp. oral clone P2PA_41 P2

AY207051



Streptococcus sp. oral clone P4PA_30 P4

AY207064



Streptococcus sp. oral taxon 071

AEEP01000019



Streptococcus sp. oral taxon G59

GU432132



Streptococcus sp. oral taxon G62

GU432146



Streptococcus sp. oral taxon G63

GU432150



Streptococcus sp. SHV515

Y07601



Streptococcus suis

FM252032



Streptococcus thermophilus

CP000419



Streptococcus uberis

HQ391900



Streptococcus urinalis

DQ303194



Streptococcus vestibularis

AEKO01000008



Streptococcus viridans

AF076036



Sutterella morbirenis

AJ832129



Sutterella parvirubra

AB300989



Sutterella sanguinus

AJ748647



Sutterella sp. YIT 12072

AB491210



Sutterella stercoricanis

NR_025600



Sutterella wadsworthensis

ADMF01000048



Synergistes genomosp. C1

AY278615



Synergistes sp. RMA 14551

DQ412722


Synergistetes bacterium ADV897
GQ258968


Synergistetes bacterium LBVCM1157
GQ258969


Synergistetes bacterium oral taxon 362
GU410752


Synergistetes bacterium oral taxon D48
GU430992



Turicibacter sanguinis

AF349724



Veillonella atypica

AEDS01000059



Veillonella dispar

ACIK02000021



Veillonella genomosp. P1 oral clone MB5_P17

DQ003631



Veillonella montpellierensis

AF473836



Veillonella parvula

ADFU01000009



Veillonella sp. 3_1_44

ADCV01000019



Veillonella sp. 6_1_27

ADCW01000016



Veillonella sp. ACP1

HQ616359



Veillonella sp. AS16

HQ616365



Veillonella sp. BS32b

HQ616368



Veillonella sp. ICM51a

HQ616396



Veillonella sp. MSA12

HQ616381



Veillonella sp. NVG 100cf

EF108443



Veillonella sp. OK11

JN695650



Veillonella sp. oral clone ASCA08

AY923118



Veillonella sp. oral clone ASCB03

AY923122



Veillonella sp. oral clone ASCG01

AY923144



Veillonella sp. oral clone ASCG02

AY953257



Veillonella sp. oral clone OH1A

AY947495



Veillonella sp. oral taxon 158

AENU01000007


Veillonellaceae bacterium oral taxon 131
GU402916


Veillonellaceae bacterium oral taxon 155
GU470897



Vibrio cholerae

AAUR01000095



Vibrio fluvialis

X76335



Vibrio furnissii

CP002377



Vibrio mimicus

ADAF01000001



Vibrio parahaemolyticus

AAWQ01000116



Vibrio sp. RC341

ACZT01000024



Vibrio vulnificus

AE016796



Yersinia aldovae

AJ871363



Yersinia aleksiciae

AJ627597



Yersinia bercovieri

AF366377



Yersinia enterocolitica

FR729477



Yersinia frederiksenii

AF366379



Yersinia intermedia

AF366380



Yersinia kristensenii

ACCA01000078



Yersinia mollaretii

NR_027546



Yersinia pestis

AE013632



Yersinia pseudotuberculosis

NC_009708



Yersinia rohdei

ACCD01000071
















TABLE 3







Exemplary Bacterial Strains










Strain
Deposit Number








Parabacteroides goldsteinii

PTA-126574




Bifidobacterium animalis ssp. lactis Strain A

PTA-125097




Blautia Massiliensis Strain A

PTA-125134




Prevotella Strain B

NRRL accession




Number B 50329




Prevotella Histicola

PTA-126140




Blautia Strain A

PTA-125346




Lactococcus lactis cremoris Strain A

PTA-125368




Lactobacillus salivarius

PTA-125893




Ruminococcus gnavus strain

PTA-125706




Tyzzerella nexilis strain

PTA-125707




Paraclostridium benzoelyticum

PTA-125894




Ruminococcus gnavus (also referred to as

PTA-126695




Mediterraneibacter gnavus)





Veillonella parvula

PTA-125710




Veillonella atypica Strain A

PTA-125709




Veillonella atypica Strain B

PTA-125711




Veillonella parvula Strain A

PTA-125691




Veillonella parvula Strain B

PTA-125711




Veillonella tobetsuensis Strain A

PTA-125708




Agathobaculum sp.

PTA-125892




Turicibacter sanguinis

PTA-125889




Klebsiella quasipneumoniae subsp.

PTA-125891




similipneumoniae





Klebsiella oxytoca

PTA-125890




Megasphaera Sp. Strain A

PTA-126770




Megasphaera Sp.

PTA-126837




Harryflintia acetispora

PTA-126694




Fournierella massiliensis

PTA-126696











Modified Bacteria and mEVs


In some aspects, the bacteria and/or mEVs (such as smEVs and/or pmEVs) described herein are modified such that they comprise, are linked to, and/or are bound by a therapeutic moiety.


In some embodiments, the therapeutic moiety is a cancer-specific moiety. In some embodiments, the cancer-specific moiety has binding specificity for a cancer cell (e.g., has binding specificity for a cancer-specific antigen). In some embodiments, the cancer-specific moiety comprises an antibody or antigen binding fragment thereof. In some embodiments, the cancer-specific moiety comprises a T cell receptor or a chimeric antigen receptor (CAR). In some embodiments, the cancer-specific moiety comprises a ligand for a receptor expressed on the surface of a cancer cell or a receptor-binding fragment thereof. In some embodiments, the cancer-specific moiety is a bipartite fusion protein that has two parts: a first part that binds to and/or is linked to the bacterium and a second part that is capable of binding to a cancer cell (e.g., by having binding specificity for a cancer-specific antigen). In some embodiments, the first part is a fragment of or a full-length peptidoglycan recognition protein, such as PGRP. In some embodiments the first part has binding specificity for the mEV (e.g., by having binding specificity for a bacterial antigen). In some embodiments, the first and/or second part comprises an antibody or antigen binding fragment thereof. In some embodiments, the first and/or second part comprises a T cell receptor or a chimeric antigen receptor (CAR). In some embodiments, the first and/or second part comprises a ligand for a receptor expressed on the surface of a cancer cell or a receptor-binding fragment thereof. In certain embodiments, co-administration of the cancer-specific moiety with the pharmaceutical agent (either in combination or in separate administrations) increases the targeting of the pharmaceutical agent to the cancer cells.


In some embodiments, the bacteria and/or mEVs described herein can be modified such that they comprise, are linked to, and/or are bound by a magnetic and/or paramagnetic moiety (e.g., a magnetic bead). In some embodiments, the magnetic and/or paramagnetic moiety is comprised by and/or directly linked to the bacteria. In some embodiments, the magnetic and/or paramagnetic moiety is linked to and/or a part of a bacteria- or an mEV-binding moiety that binds to the bacteria or mEV. In some embodiments, the bacteria- or mEV-binding moiety is a fragment of or a full-length peptidoglycan recognition protein, such as PGRP. In some embodiments the bacteria- or mEV-binding moiety has binding specificity for the bacteria or mEV (e.g., by having binding specificity for a bacterial antigen). In some embodiments, the bacteria- or mEV-binding moiety comprises an antibody or antigen binding fragment thereof. In some embodiments, the bacteria- or mEV-binding moiety comprises a T cell receptor or a chimeric antigen receptor (CAR). In some embodiments, the bacteria- or mEV-binding moiety comprises a ligand for a receptor expressed on the surface of a cancer cell or a receptor-binding fragment thereof. In certain embodiments, co-administration of the magnetic and/or paramagnetic moiety with the bacteria or mEVs (either together or in separate administrations) can be used to increase the targeting of the mEVs (e.g., to cancer cells and/or a part of a subject where cancer cells are present.


Production of Processed Microbial Extracellular Vesicles (pmEVs)


In certain aspects, the pmEVs described herein can be prepared using any method known in the art.


In some embodiments, the pmEVs are prepared without a pmEV purification step. For example, in some embodiments, bacteria from which the pmEVs described herein are released are killed using a method that leaves the bacterial pmEVs intact, and the resulting bacterial components, including the pmEVs, are used in the methods and compositions described herein. In some embodiments, the bacteria are killed using an antibiotic (e.g., using an antibiotic described herein). In some embodiments, the bacteria are killed using UV irradiation.


In some embodiments, the pmEVs described herein are purified from one or more other bacterial components. Methods for purifying pmEVs from bacteria (and optionally, other bacterial components) are known in the art. In some embodiments, pmEVs are prepared from bacterial cultures using methods described in Thein, et al. (J. Proteome Res. 9(12):6135-6147 (2010)) or Sandrini, et al. (Bio-protocol 4(21): e1287 (2014)), each of which is hereby incorporated by reference in its entirety. In some embodiments, the bacteria are cultured to high optical density and then centrifuged to pellet bacteria (e.g., at 10,000-15,000×g for 10-15 min at room temperature or 4° C.). In some embodiments, the supernatants are discarded and cell pellets are frozen at −80° C. In some embodiments, cell pellets are thawed on ice and resuspended in 100 mM Tris-HCl, pH 7.5 supplemented with 1 mg/mL DNase I. In some embodiments, cells are lysed using an Emulsiflex C-3 (Avestin, Inc.) under conditions recommended by the manufacturer. In some embodiments, debris and unlysed cells are pelleted by centrifugation at 10,000×g for 15 min at 4° C. In some embodiments, supernatants are then centrifuged at 120,000×g for 1 hour at 4° C. In some embodiments, pellets are resuspended in ice-cold 100 mM sodium carbonate, pH 11, incubated with agitation for 1 hr at 4° C., and then centrifuged at 120,000×g for 1 hour at 4° C. In some embodiments, pellets are resuspended in 100 mM Tris-HCl, pH 7.5, re-centrifuged at 120,000×g for 20 min at 4° C., and then resuspended in 0.1 M Tris-HCl, pH 7.5 or in PBS. In some embodiments, samples are stored at −20° C.


In certain aspects, pmEVs are obtained by methods adapted from Sandrini et al, 2014. In some embodiments, bacterial cultures are centrifuged at 10,000-15,500×g for 10-15 min at room temp or at 4° C. In some embodiments, cell pellets are frozen at −80° C. and supernatants are discarded. In some embodiments, cell pellets are thawed on ice and resuspended in 10 mM Tris-HCl, pH 8.0, 1 mM EDTA supplemented with 0.1 mg/mL lysozyme. In some embodiments, samples are incubated with mixing at room temp or at 37° C. for 30 min. In some embodiments, samples are re-frozen at −80° C. and thawed again on ice. In some embodiments, DNase I is added to a final concentration of 1.6 mg/mL and MgCl2 to a final concentration of 100 mM. In some embodiments, samples are sonicated using a QSonica Q500 sonicator with 7 cycles of 30 sec on and 30 sec off. In some embodiments, debris and unlysed cells are pelleted by centrifugation at 10,000×g for 15 min. at 4° C. In some embodiments, supernatants are then centrifuged at 110,000×g for 15 min at 4° C. In some embodiments, pellets are resuspended in 10 mM Tris-HCl, pH 8.0, 2% Triton X-100 and incubated 30-60 min with mixing at room temperature. In some embodiments, samples are centrifuged at 110,000×g for 15 min at 4° C. In some embodiments, pellets are resuspended in PBS and stored at −20° C.


In certain aspects, a method of forming (e.g., preparing) isolated bacterial pmEVs, described herein, comprises the steps of: (a) centrifuging a bacterial culture, thereby forming a first pellet and a first supernatant, wherein the first pellet comprises cells; (b) discarding the first supernatant; (c) resuspending the first pellet in a solution; (d) lysing the cells; (e) centrifuging the lysed cells, thereby forming a second pellet and a second supernatant; (f) discarding the second pellet and centrifuging the second supernatant, thereby forming a third pellet and a third supernatant; (g) discarding the third supernatant and resuspending the third pellet in a second solution, thereby forming the isolated bacterial pmEVs.


In some embodiments, the method further comprises the steps of: (h) centrifuging the solution of step (g), thereby forming a fourth pellet and a fourth supernatant; (i) discarding the fourth supernatant and resuspending the fourth pellet in a third solution. In some embodiments, the method further comprises the steps of: (j) centrifuging the solution of step (i), thereby forming a fifth pellet and a fifth supernatant; and (k) discarding the fifth supernatant and resuspending the fifth pellet in a fourth solution.


In some embodiments, the centrifugation of step (a) is at 10,000×g. In some embodiments the centrifugation of step (a) is for 10-15 minutes. In some embodiments, the centrifugation of step (a) is at 4° C. or room temperature. In some embodiments, step (b) further comprises freezing the first pellet at −80° C. In some embodiments, the solution in step (c) is 100 mM Tris-HCl, pH 7.5 supplemented with 1 mg/ml DNaseI. In some embodiments, the solution in step (c) is 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, supplemented with 0.1 mg/ml lysozyme. In some embodiments, step (c) further comprises incubating for 30 minutes at 37° C. or room temperature. In some embodiments, step (c) further comprises freezing the first pellet at −80° C. In some embodiments, step (c) further comprises adding DNase I to a final concentration of 1.6 mg/ml. In some embodiments, step (c) further comprises adding MgCl2 to a final concentration of 100 mM. In some embodiments, the cells are lysed in step (d) via homogenization. In some embodiments, the cells are lysed in step (d) via emulsiflex C3. In some embodiments, the cells are lysed in step (d) via sonication. In some embodiments, the cells are sonicated in 7 cycles, wherein each cycle comprises 30 seconds of sonication and 30 seconds without sonication. In some embodiments, the centrifugation of step (e) is at 10,000×g. In some embodiments, the centrifugation of step (e) is for 15 minutes. In some embodiments, the centrifugation of step (e) is at 4° C. or room temperature.


In some embodiments, the centrifugation of step (f) is at 120,000×g. In some embodiments, the centrifugation of step (f) is at 110,000×g. In some embodiments, the centrifugation of step (f) is for 1 hour. In some embodiments, the centrifugation of step (f) is for 15 minutes. In some embodiments, the centrifugation of step (f) is at 4° C. or room temperature. In some embodiments, the second solution in step (g) is 100 mM sodium carbonate, pH 11. In some embodiments, the second solution in step (g) is 10 mM Tris-HCl pH 8.0, 2% triton X-100. In some embodiments, step (g) further comprises incubating the solution for 1 hour at 4° C. In some embodiments, step (g) further comprises incubating the solution for 30-60 minutes at room temperature. In some embodiments, the centrifugation of step (h) is at 120,000×g. In some embodiments, the centrifugation of step (h) is at 110,000×g. In some embodiments, the centrifugation of step (h) is for 1 hour. In some embodiments, the centrifugation of step (h) is for 15 minutes. In some embodiments, the centrifugation of step (h) is at 4° C. or room temperature. In some embodiments, the third solution in step (i) is 100 mM Tris-HCl, pH 7.5. In some embodiments, the third solution in step (i) is PBS. In some embodiments, the centrifugation of step (j) is at 120,000×g. In some embodiments, the centrifugation of step (j) is for 20 minutes. In some embodiments, the centrifugation of step (j) is at 4° C. or room temperature. In some embodiments, the fourth solution in step (k) is 100 mM Tris-HCl, pH 7.5 or PBS.


pmEVs obtained by methods provided herein may be further purified by size based column chromatography, by affinity chromatography, and by gradient ultracentrifugation, using methods that may include, but are not limited to, use of a sucrose gradient or Optiprep gradient. Briefly, using a sucrose gradient method, if ammonium sulfate precipitation or ultracentrifugation were used to concentrate the filtered supernatants, pellets are resuspended in 60% sucrose, 30 mM Tris, pH 8.0. If filtration was used to concentrate the filtered supernatant, the concentrate is buffer exchanged into 60% sucrose, 30 mM Tris, pH 8.0, using an Amicon Ultra column. Samples are applied to a 35-60% discontinuous sucrose gradient and centrifuged at 200,000×g for 3-24 hours at 4° C. Briefly, using an Optiprep gradient method, if ammonium sulfate precipitation or ultracentrifugation were used to concentrate the filtered supernatants, pellets are resuspended in 35% Optiprep in PBS. In some embodiments, if filtration was used to concentrate the filtered supernatant, the concentrate is diluted using 60% Optiprep to a final concentration of 35% Optiprep. Samples are applied to a 35-60% discontinuous sucrose gradient and centrifuged at 200,000×g for 3-24 hours at 4° C.


In some embodiments, to confirm sterility and isolation of the pmEV preparations, pmEVs are serially diluted onto agar medium used for routine culture of the bacteria being tested, and incubated using routine conditions. Non-sterile preparations are passed through a 0.22 um filter to exclude intact cells. To further increase purity, isolated pmEVs may be DNase or proteinase K treated.


In some embodiments, the sterility of the pmEV preparations can be confirmed by plating a portion of the pmEVs onto agar medium used for standard culture of the bacteria used in the generation of the pmEVs and incubating using standard conditions.


In some embodiments select pmEVs are isolated and enriched by chromatography and binding surface moieties on pmEVs. In other embodiments, select pmEVs are isolated and/or enriched by fluorescent cell sorting by methods using affinity reagents, chemical dyes, recombinant proteins or other methods known to one skilled in the art.


The pmEVs can be analyzed, e.g., as described in Jeppesen, et al. Cell 177:428 (2019).


In some embodiments, pmEVs are lyophilized.


In some embodiments, pmEVs are gamma irradiated (e.g., at 17.5 or 25 kGy).


In some embodiments, pmEVs are UV irradiated.


In some embodiments, pmEVs are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, pmEVs are acid treated.


In some embodiments, pmEVs are oxygen sparged (e.g., at 0.1 vvm for two hours).


The phase of growth can affect the amount or properties of bacteria. In the methods of pmEV preparation provided herein, pmEVs can be isolated, e.g., from a culture, at the start of the log phase of growth, midway through the log phase, and/or once stationary phase growth has been reached.


Production of Secreted Microbial Extracellular Vesicles (smEVs)


In certain aspects, the smEVs described herein can be prepared using any method known in the art.


In some embodiments, the smEVs are prepared without an smEV purification step. For example, in some embodiments, bacteria described herein are killed using a method that leaves the smEVs intact and the resulting bacterial components, including the smEVs, are used in the methods and compositions described herein. In some embodiments, the bacteria are killed using an antibiotic (e.g., using an antibiotic described herein). In some embodiments, the bacteria are killed using UV irradiation. In some embodiments, the bacteria are heat-killed.


In some embodiments, the smEVs described herein are purified from one or more other bacterial components. Methods for purifying smEVs from bacteria are known in the art. In some embodiments, smEVs are prepared from bacterial cultures using methods described in S. Bin Park, et al. PLoS ONE. 6(3):e17629 (2011) or G. Norheim, et al. PLoS ONE. 10(9): e0134353 (2015) or Jeppesen, et al. Cell 177:428 (2019), each of which is hereby incorporated by reference in its entirety. In some embodiments, the bacteria are cultured to high optical density and then centrifuged to pellet bacteria (e.g., at 10,000×g for 30 min at 4° C., at 15,500×g for 15 min at 4° C.). In some embodiments, the culture supernatants are then passed through filters to exclude intact bacterial cells (e.g., a 0.22 μm filter). In some embodiments, the supernatants are then subjected to tangential flow filtration, during which the supernatant is concentrated, species smaller than 100 kDa are removed, and the media is partially exchanged with PBS. In some embodiments, filtered supernatants are centrifuged to pellet bacterial smEVs (e.g., at 100,000-150,000×g for 1-3 hours at 4° C., at 200,000×g for 1-3 hours at 4° C.). In some embodiments, the smEVs are further purified by resuspending the resulting smEV pellets (e.g., in PBS), and applying the resuspended smEVs to an Optiprep (iodixanol) gradient or gradient (e.g., a 30-60% discontinuous gradient, a 0-45% discontinuous gradient), followed by centrifugation (e.g., at 200,000×g for 4-20 hours at 4° C.). smEV bands can be collected, diluted with PBS, and centrifuged to pellet the smEVs (e.g., at 150,000×g for 3 hours at 4° C., at 200,000×g for 1 hour at 4° C.). The purified smEVs can be stored, for example, at −80° C. or −20° C. until use. In some embodiments, the smEVs are further purified by treatment with DNase and/or proteinase K.


For example, in some embodiments, cultures of bacteria can be centrifuged at 11,000×g for 20-40 min at 4° C. to pellet bacteria. Culture supernatants may be passed through a 0.22 μm filter to exclude intact bacterial cells. Filtered supernatants may then be concentrated using methods that may include, but are not limited to, ammonium sulfate precipitation, ultracentrifugation, or filtration. For example, for ammonium sulfate precipitation, 1.5-3 M ammonium sulfate can be added to filtered supernatant slowly, while stirring at 4° C. Precipitations can be incubated at 4° C. for 8-48 hours and then centrifuged at 11,000×g for 20-40 min at 4° C. The resulting pellets contain bacteria smEVs and other debris. Using ultracentrifugation, filtered supernatants can be centrifuged at 100,000-200,000×g for 1-16 hours at 4° C. The pellet of this centrifugation contains bacteria smEVs and other debris such as large protein complexes. In some embodiments, using a filtration technique, such as through the use of an Amicon Ultra spin filter or by tangential flow filtration, supernatants can be filtered so as to retain species of molecular weight>50 or 100 kDa.


Alternatively, smEVs can be obtained from bacteria cultures continuously during growth, or at selected time points during growth, for example, by connecting a bioreactor to an alternating tangential flow (ATF) system (e.g., XCell ATF from Repligen). The ATF system retains intact cells (>0.22 um) in the bioreactor, and allows smaller components (e.g., smEVs, free proteins) to pass through a filter for collection. For example, the system may be configured so that the <0.22 um filtrate is then passed through a second filter of 100 kDa, allowing species such as smEVs between 0.22 um and 100 kDa to be collected, and species smaller than 100 kDa to be pumped back into the bioreactor. Alternatively, the system may be configured to allow for medium in the bioreactor to be replenished and/or modified during growth of the culture. smEVs collected by this method may be further purified and/or concentrated by ultracentrifugation or filtration as described above for filtered supernatants.


smEVs obtained by methods provided herein may be further purified by size-based column chromatography, by affinity chromatography, by ion-exchange chromatography, and by gradient ultracentrifugation, using methods that may include, but are not limited to, use of a sucrose gradient or Optiprep gradient. Briefly, using a sucrose gradient method, if ammonium sulfate precipitation or ultracentrifugation were used to concentrate the filtered supernatants, pellets are resuspended in 60% sucrose, 30 mM Tris, pH 8.0. If filtration was used to concentrate the filtered supernatant, the concentrate is buffer exchanged into 60% sucrose, 30 mM Tris, pH 8.0, using an Amicon Ultra column. Samples are applied to a 35-60% discontinuous sucrose gradient and centrifuged at 200,000×g for 3-24 hours at 4° C. Briefly, using an Optiprep gradient method, if ammonium sulfate precipitation or ultracentrifugation were used to concentrate the filtered supernatants, pellets are resuspended in PBS and 3 volumes of 60% Optiprep are added to the sample. In some embodiments, if filtration was used to concentrate the filtered supernatant, the concentrate is diluted using 60% Optiprep to a final concentration of 35% Optiprep. Samples are applied to a 0-45% discontinuous Optiprep gradient and centrifuged at 200,000×g for 3-24 hours at 4° C., e.g., 4-24 hours at 4° C.


In some embodiments, to confirm sterility and isolation of the smEV preparations, smEVs are serially diluted onto agar medium used for routine culture of the bacteria being tested, and incubated using routine conditions. Non-sterile preparations are passed through a 0.22 um filter to exclude intact cells. To further increase purity, isolated smEVs may be DNase or proteinase K treated.


In some embodiments, for preparation of smEVs used for in vivo injections, purified smEVs are processed as described previously (G. Norheim, et al. PLoS ONE. 10(9): e0134353 (2015)). Briefly, after sucrose gradient centrifugation, bands containing smEVs are resuspended to a final concentration of 50 μg/mL in a solution containing 3% sucrose or other solution suitable for in vivo injection known to one skilled in the art. This solution may also contain adjuvant, for example aluminum hydroxide at a concentration of 0-0.5% (w/v). In some embodiments, for preparation of smEVs used for in vivo injections, smEVs in PBS are sterile-filtered to <0.22 um.


In certain embodiments, to make samples compatible with further testing (e.g., to remove sucrose prior to TEM imaging or in vitro assays), samples are buffer exchanged into PBS or 30 mM Tris, pH 8.0 using filtration (e.g., Amicon Ultra columns), dialysis, or ultracentrifugation (200,000×g, ≥3 hours, 4° C.) and resuspension.


In some embodiments, the sterility of the smEV preparations can be confirmed by plating a portion of the smEVs onto agar medium used for standard culture of the bacteria used in the generation of the smEVs and incubating using standard conditions.


In some embodiments, select smEVs are isolated and enriched by chromatography and binding surface moieties on smEVs. In other embodiments, select smEVs are isolated and/or enriched by fluorescent cell sorting by methods using affinity reagents, chemical dyes, recombinant proteins or other methods known to one skilled in the art.


The smEVs can be analyzed, e.g., as described in Jeppesen, et al. Cell 177:428 (2019).


In some embodiments, smEVs are lyophilized.


In some embodiments, smEVs are gamma irradiated (e.g., at 17.5 or 25 kGy).


In some embodiments, smEVs are UV irradiated.


In some embodiments, smEVs are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).


In some embodiments, smEVs s are acid treated.


In some embodiments, smEVs are oxygen sparged (e.g., at 0.1 vvm for two hours).


The phase of growth can affect the amount or properties of bacteria and/or smEVs produced by bacteria. For example, in the methods of smEV preparation provided herein, smEVs can be isolated, e.g., from a culture, at the start of the log phase of growth, midway through the log phase, and/or once stationary phase growth has been reached.


The growth environment (e.g., culture conditions) can affect the amount of smEVs produced by bacteria. For example, the yield of smEVs can be increased by an smEV inducer, as provided in Table 4.









TABLE 4







Culture Techniques to Increase smEV Production









smEV inducement
smEV inducer
Acts on





Temperature





Heat
stress response



RT to 37° C. temp change
simulates infection



37 to 40° C. temp change
febrile infection


ROS



Plumbagin
oxidative stress response



Cumene hydroperoxide
oxidative stress response



Hydrogen Peroxide
oxidative stress response


Antibiotics



Ciprofloxacin
bacterial SOS response



Gentamycin
protein synthesis



Polymyxin B
outer membrane



D-cylcloserine
cell wall


Osmolyte



NaCl
osmotic stress


Metal Ion Stress



Iron Chelation
iron levels



EDTA
removes divalent cations



Low Hemin
iron levels


Media additives or removal



Lactate
growth



Amino acid deprivation
stress



Hexadecane
stress



Glucose
growth



Sodium bicarbonate
ToxT induction



PQS
vesiculator (from bacteria)



Diamines + DFMO
membrane anchoring



High nutrients
(negativicutes only)



Low nutrients
enhanced growth


Other mechanisms



Oxygen
oxygen stress in anaerobe



No Cysteine
oxygen stress in anaerobe



Inducing biofilm or



floculation



Diauxic Growth



Phage



Urea









In the methods of smEVs preparation provided herein, the method can optionally include exposing a culture of bacteria to an smEV inducer prior to isolating smEVs from the bacterial culture. The culture of bacteria can be exposed to an smEV inducer at the start of the log phase of growth, midway through the log phase, and/or once stationary phase growth has been reached.


Solid Dosage Form Compositions

In certain embodiments, provided herein are solid dosage forms comprising a pharmaceutical agent that contains bacteria and/or mEVs (such as smEVs and/or pmEVs). In some embodiments, the pharmaceutical agent can optionally contain one or more additional components, such as a cryoprotectant. The pharmaceutical agent can be lyophilized (e.g., resulting in a powder). The pharmaceutical agent can be combined with one or more excipients (e.g., pharmaceutically acceptable excipients) in the solid dosage form. In some embodiments, the pharmaceutical agent can be (or be present in) a medicinal product, medical food, a food product, or a dietary supplement.


In certain embodiments, provided herein are solid dosage forms comprising a pharmaceutical agent that contains bacteria. The bacteria can be live bacteria (e.g., powder or biomass thereof); non-live (dead) bacteria (e.g., powder or biomass thereof); non replicating bacteria (e.g., powder or biomass thereof); gamma irradiated bacteria (e.g., powder or biomass thereof); and/or lyophilized bacteria (e.g., powder or biomass thereof).


In certain embodiments, provided herein are solid dosage forms comprising a pharmaceutical agent that contains mEVs. The mEVs can be from culture media (e.g., culture supernatant). The mEVs can be from live bacteria (e.g., powder or biomass thereof); the mEVs can be from non-live (dead) bacteria (e.g., powder or biomass thereof); the mEVs can be from non replicating bacteria (e.g., powder or biomass thereof); the mEVs can be from gamma irradiated bacteria (e.g., powder or biomass thereof); and/or the mEVs can be from lyophilized bacteria (e.g., powder or biomass thereof).


In some embodiments, the pharmaceutical agent comprises mEVs substantially or entirely free of bacteria (e.g., whole bacteria) (e.g., live bacteria, dead (e.g., killed) bacteria, non-replicating bacteria, attenuated bacteria. In some embodiments, the pharmaceutical agents comprise both mEVs and bacteria (e.g., whole bacteria) (e.g., live bacteria, killed bacteria, attenuated bacteria). In some embodiments, the pharmaceutical agents comprise bacteria and/or mEVs from one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) of the bacteria strains or species listed herein. In some embodiments, the pharmaceutical agents comprise bacteria and/or mEVs from one of the bacteria strains or species listed herein. In some embodiments, the pharmaceutical agents comprise lyophilized bacteria and/or mEVs. In some embodiments, the pharmaceutical agent comprises gamma irradiated bacteria and/or mEVs. The mEVs (such as smEVs and/or pmEVs) can be gamma irradiated after the mEVs are isolated (e.g., prepared).


In some embodiments, to quantify the numbers of mEVs (such as smEVs and/or pmEVs) and/or bacteria present in a sample, electron microscopy (e.g., EM of ultrathin frozen sections) can be used to visualize the mEVs (such as smEVs and/or pmEVs) and/or bacteria and count their relative numbers. Alternatively, nanoparticle tracking analysis (NTA), Coulter counting, or dynamic light scattering (DLS) or a combination of these techniques can be used. NTA and the Coulter counter count particles and show their sizes. DLS gives the size distribution of particles, but not the concentration. Bacteria frequently have diameters of 1-2 um (microns). The full range is 0.2-20 um. Combined results from Coulter counting and NTA can reveal the numbers of bacteria and/or mEVs (such as smEVs and/or pmEVs) in a given sample. Coulter counting reveals the numbers of particles with diameters of 0.7-10 um. For most bacterial and/or mEV (such as smEV and/or pmEV) samples, the Coulter counter alone can reveal the number of bacteria and/or mEVs (such as smEVs and/or pmEVs) in a sample. pmEVs are 20-600 nm in diameter. For NTA, a Nanosight instrument can be obtained from Malvern Pananlytical. For example, the NS300 can visualize and measure particles in suspension in the size range 10-2000 nm. NTA allows for counting of the numbers of particles that are, for example, 50-1000 nm in diameter. DLS reveals the distribution of particles of different diameters within an approximate range of 1 nm-3 um.


mEVs can be characterized by analytical methods known in the art (e.g., Jeppesen, et al. Cell 177:428 (2019)).


In some embodiments, the bacteria and/or mEVs may be quantified based on particle count. For example, particle count of a bacteria and/or mEV preparation can be measured using NTA.


In some embodiments, the bacteria and/or mEVs may be quantified based on the amount of protein, lipid, or carbohydrate. For example, total protein content of a bacteria and/or preparation can be measured using the Bradford assay or BCA.


In some embodiments, mEVs are isolated away from one or more other bacterial components of the source bacteria or bacterial culture. In some embodiments, bacteria are isolated away from one or more other bacterial components of the source bacterial culture. In some embodiments, the pharmaceutical agent further comprises other bacterial components.


In certain embodiments, the mEV preparation obtained from the source bacteria may be fractionated into subpopulations based on the physical properties (e.g., sized, density, protein content, binding affinity) of the subpopulations. One or more of the mEV subpopulations can then be incorporated into the pharmaceutical agents of the invention.


In certain aspects, provided herein are solid dosage forms comprising pharmaceutical agents that comprise bacteria and/or mEVs (such as smEVs and/or pmEVs) useful for the treatment and/or prevention of disease (e.g., a cancer, an autoimmune disease, an inflammatory disease, or a metabolic disease), as well as methods of making and/or identifying such bacteria and/or mEVs, and methods of using pharmaceutical agents and solid dosage forms thereof (e.g., for the treatment of a cancer, an autoimmune disease, an inflammatory disease, or a metabolic disease, either alone or in combination with other therapeutics). In some embodiments, the pharmaceutical agents comprise both mEVs (such as smEVs and/or pmEVs) and bacteria (e.g., whole bacteria) (e.g., live bacteria, dead (e.g., killed) bacteria, non-replicating bacteria, attenuated bacteria). In some embodiments, the pharmaceutical agents comprise bacteria in the absence of mEVs (such as smEVs and/or pmEVs). In some embodiments, the pharmaceutical agents comprise mEVs (such as smEVs and/or pmEVs) in the absence of bacteria. In some embodiments, the pharmaceutical agents comprise mEVs (such as smEVs and/or pmEVs) and/or bacteria from one or more of the bacteria strains or species listed herein. In some embodiments, the pharmaceutical agents comprise mEVs (such as smEVs and/or pmEVs) and/or bacteria from one of the bacteria strains or species listed herein.


In certain aspects, provided are pharmaceutical agents for administration to a subject (e.g., human subject). In some embodiments, the pharmaceutical agents are combined with additional active and/or inactive materials in order to produce a final product, which may be in single dosage unit or in a multi-dose format. In some embodiments, the pharmaceutical agent is combined with an adjuvant such as an immuno-adjuvant (e.g., a STING agonist, a TLR agonist, or a NOD agonist).


In some embodiments, the solid dosage form comprises at least one carbohydrate.


In some embodiments, the solid dosage form comprises at least one lipid. In some embodiments, the lipid comprises at least one fatty acid selected from lauric acid (12:0), myristic acid (14:0), palmitic acid (16:0), palmitoleic acid (16:1), margaric acid (17:0), heptadecenoic acid (17:1), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2), linolenic acid (18:3), octadecatetraenoic acid (18:4), arachidic acid (20:0), eicosenoic acid (20:1), eicosadienoic acid (20:2), eicosatetraenoic acid (20:4), eicosapentaenoic acid (20:5) (EPA), docosanoic acid (22:0), docosenoic acid (22:1), docosapentaenoic acid (22:5), docosahexaenoic acid (22:6) (DHA), and tetracosanoic acid (24:0).


In some embodiments, the solid dosage form comprises at least one supplemental mineral or mineral source. Examples of minerals include, without limitation: chloride, sodium, calcium, iron, chromium, copper, iodine, zinc, magnesium, manganese, molybdenum, phosphorus, potassium, and selenium. Suitable forms of any of the foregoing minerals include soluble mineral salts, slightly soluble mineral salts, insoluble mineral salts, chelated minerals, mineral complexes, non-reactive minerals such as carbonyl minerals, and reduced minerals, and combinations thereof.


In some embodiments, the solid dosage form comprises at least one vitamin. The at least one vitamin can be fat-soluble or water-soluble vitamins. Suitable vitamins include but are not limited to vitamin C, vitamin A, vitamin E, vitamin B12, vitamin K, riboflavin, niacin, vitamin D, vitamin B6, folic acid, pyridoxine, thiamine, pantothenic acid, and biotin. Suitable forms of any of the foregoing are salts of the vitamin, derivatives of the vitamin, compounds having the same or similar activity of the vitamin, and metabolites of the vitamin.


In some embodiments, the solid dosage form comprises an excipient. Non-limiting examples of suitable excipients include a buffering agent, a preservative, a stabilizer, a binder, a compaction agent, a lubricant, a dispersion enhancer, a disintegration agent, a flavoring agent, a sweetener, and a coloring agent.


Suitable excipients that can be included in the solid dosage form can be one or more pharmaceutically acceptable excipients known in the art. For example, see Rowe, Sheskey, and Quinn, eds., Handbook of Pharmaceutical Excipients, sixth ed.; 2009; Pharmaceutical Press and American Pharmacists Association.


Solid Dosage Forms

The solid dosage form described herein can be, e.g., a tablet or a minitablet. Further, a plurality of minitablets can be in (e.g., loaded into) a capsule.


In certain embodiments, the solid dosage form comprises a capsule. In some embodiments, the capsule is a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule. In some embodiments, the capsule is a size 0 capsule. As used herein, the size of the capsule refers to the size of the tablet prior to application of an enteric coating. In some embodiments, the capsule is banded after loading (and prior to enterically coating the capsule). In some embodiments, the capsule is banded with an HPMC-based banding solution.


In some embodiments, the solid dosage form comprises a tablet (>4 mm) (e.g., 5 mm-17 mm). For example, the tablet is a 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm, 11 mm, 12 mm, 13 mm, 14 mm, 15 mm, 16 mm, 17 mm, or 18 mm tablet. The size refers to the diameter of the tablet, as is known in the art. As used herein, the size of the tablet refers to the size of the tablet prior to application of an enteric coating.


In some embodiments, the solid dosage form comprises a minitablet. The minitablet can be in the size range of 1 mm-4 mm range. E.g., the minitablet can be a 1 mm minitablet, 1.5 mm minitablet, 2 mm minitablet, 3 mm minitablet, or 4 mm minitablet. The size refers to the diameter of the minitablet, as is known in the art. As used herein, the size of the minitablet refers to the size of the minitablet prior to application of an enteric coating.


The minitablets can be in a capsule. The capsule can be a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule. The capsule that contains the minitablets can comprise HPMC (hydroxyl propyl methyl cellulose) or gelatin. The minitablets can be inside a capsule: the number of minitablets inside a capsule will depend on the size of the capsule and the size of the minitablets. As an example, a size 0 capsule can contain 31-35 (an average of 33) minitablets that are 3 mm minitablets. In some embodiments, the capsule is banded after loading. In some embodiments, the capsule is banded with an HPMC-based banding solution.


Coating:

The solid dosage form (e.g., capsule, tablet or minitablet) described herein can be enterically coated, e.g., with one enteric coating layer or with two layers of enteric coating, e.g., an inner enteric coating and an outer enteric coating. The inner enteric coating and outer enteric coating are not identical (e.g., the inner enteric coating and outer enteric coating do not contain the same components in the same amounts). The enteric coating allows for release of the pharmaceutical agent, e.g., in the small intestine.


Release of the pharmaceutical agent in the small intestine allows the pharmaceutical agent to target and affect cells (e.g., epithelial cells and/or immune cells) located at these specific locations, e.g., which can cause a local effect in the gastrointestinal tract and/or cause a systemic effect (e.g., an effect outside of the gastrointestinal tract).


EUDRAGIT is the brand name for a diverse range of polymethacrylate-based copolymers. It includes anionic, cationic, and neutral copolymers based on methacrylic acid and methacrylic/acrylic esters or their derivatives.


Examples of other materials that can be used in the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) include cellulose acetate phthalate (CAP), cellulose acetate trimellitate (CAT), poly(vinyl acetate phthalate) (PVAP), hydroxypropyl methylcellulose phthalate (HPMCP), fatty acids, waxes, shellac (esters of aleurtic acid), plastics, plant fibers, zein, Aqua-Zein® (an aqueous zein formulation containing no alcohol), amylose starch, starch derivatives, dextrins, methyl acrylate-methacrylic acid copolymers, cellulose acetate succinate, hydroxypropyl methyl cellulose acetate succinate (hypromellose acetate succinate), methyl methacrylate-methacrylic acid copolymers, and/or sodium alginate.


The enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) can include a methacrylic acid ethyl acrylate (MAE) copolymer (1:1).


The one enteric coating can include methacrylic acid ethyl acrylate (MAE) copolymer (1:1) (such as Kollicoat MAE 100P).


The one enteric coating can include a Eudragit coplymer, e.g., a Eudragit L (e.g., Eudragit L 100-55; Eudragit L 30 D-55), a Eudragit S, a Eudragit RL, a Eudragit RS, a Eudragit E, or a Eudragit FS (e.g., Eudragit FS 30 D).


Other examples of materials that can be used in the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) include those described in, e.g., U.S. Pat. Nos. 6,312,728; 6,623,759; 4,775,536; 5,047,258; 5,292,522; 6,555,124; 6,638,534; U.S. 2006/0210631; U.S. 2008/200482; U.S. 2005/0271778; U.S. 2004/0028737; WO 2005/044240.


See also, e.g., U.S. Pat. No. 9,233,074, which provides pH dependent, enteric polymers that can be used with the solid dosage forms provided herein, including methacrylic acid copolymers, polyvinylacetate phthalate, hydroxypropylmethyl cellulose acetate succinate, hydroxypropylmethyl cellulose phthalate and cellulose acetate phthalate; suitable methacrylic acid copolymers include: poly(methacrylic acid, methyl methacrylate) 1:1 sold, for example, under the Eudragit L100 trade name; poly(methacrylic acid, ethyl acrylate) 1:1 sold, for example, under the Eudragit L100-55 trade name; partially-neutralized poly(methacrylic acid, ethyl acrylate) 1:1 sold, for example, under the Kollicoat MAE-10OP trade name; and poly(methacrylic acid, methyl methacrylate) 1:2 sold, for example, under the Eudragit S100 trade name.


In some embodiments, the solid dosage form comprises a sub-coat, e.g., under the enteric coating (e.g., one enteric coating). The sub-coat can be used, e.g., to visually mask the appearance of the pharmaceutical agent.


Dose

The dose of the pharmaceutical agent (e.g., for human subjects) is the dose per capsule or tablet or per total number of minitablets used in a capsule.


In embodiments where dose is determined by total cell count, total cell count can be determined by Coulter counter.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×107 to about 2×1012 (e.g about 3×1010 or about 1.5×1011 or about 1.5×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×1010 to about 2×1012 (e.g., about 1.6×1011 or about 8×1011 or about 9.6×1011 about 12.8×1011 or about 1.6×1012) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×109, about 3×109, about 5×109, about 1.5×1010, about 3×1010, about 5×1010, about 1.5×1011, about 1.5×1012, or about 2×1012 cells, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×105 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises mEVs and the dose of mEVs is about 1×1010 to about 7×1013 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


In some embodiments, wherein the pharmaceutical agent comprises mEVs, the dose of mEVs is about 2×106 to about 2×1016 particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.


The solid dosage form allows higher efficacy if used at the same dose as in powder form; and/or allows a reduced dose (e.g., 1/10 lower dose) for similar efficacy as when the pharmaceutical agent is used in powder form.


In some embodiments, wherein the pharmaceutical agent comprises bacteria, the dose can be approximately 1/10 dose for similar efficacy as when the pharmaceutical agent is used in powder form and the dose can be about 3×109 or about 1.5×1010 cells per dose.


The solid dosage form can allow higher efficacy if used at the same dose of the pharmaceutical agent as in a powder formulation.


In some embodiments, the pharmaceutical agent dose can be a milligram (mg) dose determined by weight the pharmaceutical agent. The dose of the pharmaceutical agent is per capsule or tablet or per total number of minitablets, e.g., in a capsule.


For example, to administer a 1× dose of the pharmaceutical agent of about 400 mg, about 200 mg of the pharmaceutical agent is present per capsule and two capsules are administered, resulting in a dose of about 400 mg. The two capsules can be administered, for example, 1× or 2× daily.


As another example, to obtain similar efficacy as a powder form of the pharmaceutical agent, the dose of pharmaceutical agent can be reduced by 1/10 when prepared as a solid dosage form described herein (e.g., by enterically coating a tablet or minitablet containing the pharmaceutical agent.


For example, for a minitablet: about 0.1 to about 3.5 mg (0.1, 0.35, 1.0, 3.5 mg) of the pharmaceutical agent can be contained per minitablet. The minitablets can be inside a capsule: the number of minitablets inside a capsule will depend on the size of the capsule and the size of the minitablets. For example, an average of 33 (range of 31-35) 3 mm minitablets fit inside a size 0 capsule. As an example, 0.1-3.5 mg of the pharmaceutical agent per minitablet, the dose range will be 3.3 mg-115.5 mg (for 33 minitablets in size 0 capsule) per capsule (3.1 mg-108.5 mg for 31 minitablets in size 0 capsule) (3.5 mg-122.5 mg for 35 minitablets in size 0 capsule). Multiple capsules and/or larger capsule(s) can be administered to increase the administered dose and/or can be administered one or more times per day to increase the administered dose.


In some embodiments, the dose can be about 3 mg to about 125 mg of the pharmaceutical agent, per capsule or tablet or per total number of minitablets, e.g., in a capsule.


In some embodiments, the dose can be about 35 mg to about 1200 mg (e.g., about 35 mg, about 125 mg, about 350 mg, or about 1200 mg) of the pharmaceutical agent.


In some embodiments, the dose of the pharmaceutical agent can be about 30 mg to about 3500 mg (about 25, about 50, about 75, about 100, about 150, about 250, about 300, about 350, about 400, about 500, about 600, about 750, about 1000, about 1250, about 1300, about 2000, about 2500, about 3000, or about 3500 mg).


A human dose can be calculated appropriately based on allometric scaling of a dose administered to a model organism (e.g., mouse).


In some embodiments, one or two tablets capsules can be administered one or two times a day.


The pharmaceutical agent contains the bacteria and/or mEVs and can also contain one or more additional components, such as cryoprotectants, stabilizers, etc.


In some embodiments, the mg (by weight) dose of the pharmaceutical agent is, e.g., about 1 mg to about 500 mg per capsule, or per tablet, or per total number of minitablets, e.g., used in a capsule.


Methods of Use

The solid dosage forms described herein allow, e.g., for oral administration of a pharmaceutical agent contained therein.


The solid dosage forms described herein can provide an increase in therapeutic efficacy and/or physiological effect as compared to other dosage forms (e.g., non-enterically coated dosage forms (e.g., non-minitablet non-enterically coated dosage forms, or non-tablet non-enterically coated dosage forms) or a suspension of biomass or powder).


The solid dosage forms described herein can provide release in the small intestine of the pharmaceutical agent contained in the solid dosage form.


The solid dosage forms described herein can provide release of the pharmaceutical agent in the small intestine, e.g., to deliver the pharmaceutical agent that can act on immune cells and/or epithelial cells in the small intestine, e.g., to cause a systemic effect (e.g., an effect outside of the gastrointestinal tract) and/or a local effect in the gastrointestinal tract.


The solid dosage forms described herein can provide increased efficacy and/or physiological effect (as measured by a systemic effect (e.g., outside of the gastrointestinal tract) of the pharmaceutical agent, e.g., in ear thickness in a DTH model for inflammation; tumor size in cancer model), e.g., as compared to oral gavage of the same dose of pharmaceutical agent.


The solid dosage forms described herein can be used in the treatment and/or prevention of a cancer, inflammation, autoimmunity, or a metabolic condition.


Methods of using a solid dosage form (e.g., for oral administration) (e.g., for pharmaceutical use) comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), and wherein the solid dosage form is enterically coated are described herein.


The methods and administered solid dosage forms described herein allow, e.g., for oral administration of a pharmaceutical agent contained therein. The solid dosage form can be administered to a subject is a fed or fasting state. The solid dosage form can be administered, e.g., on an empty stomach (e.g., one hour before eating or two hours after eating). The solid dosage form can be administered one hour before eating. The solid dosage form can be administered two hours after eating.


The methods and administered solid dosage forms described herein can provide an increase in therapeutic efficacy and/or physiological effect as compared to other dosage forms (e.g., non-enterically coated dosage forms (e.g., non-minitablet non-enterically coated dosage forms, or non-tablet non-enterically coated dosage forms) or a suspension of biomass or powder).


The methods and administered solid dosage forms described herein can provide release in the small intestine of the pharmaceutical agent contained in the solid dosage form.


The methods and administered solid dosage forms described herein can provide release of the pharmaceutical agent in the small intestine, e.g., to deliver the pharmaceutical agent that can act on immune cells and/or epithelial cells in the small intestine, e.g., to cause a systemic effect (e.g., an effect outside of the gastrointestinal tract) and/or a local effect in the gastrointestinal tract.


The methods and administered solid dosage forms described herein can provide increased efficacy and/or physiological effect (as measured by a systemic effect (e.g., outside of the gastrointestinal tract) of the pharmaceutical agent, e.g., in ear thickness in a DTH model for inflammation; tumor size in cancer model), e.g., as compared to oral gavage of the same dose of pharmaceutical agent.


The methods and administered solid dosage forms described herein can be used in the treatment and/or prevention of a cancer, inflammation, autoimmunity, dysbiosis, or a metabolic condition.


A solid dosage form for use in the treatment and/or prevention of a cancer, inflammation, autoimmunity, dysbiosis, or a metabolic condition is provided herein.


Use of a solid dosage form for the preparation of a medicament for the treatment and/or prevention of a cancer, inflammation, autoimmunity, dysbiosis, or a metabolic condition is provided herein.


Method of Making Solid Dosage Forms

The disclosure also provides methods of making a solid dosage form (e.g., for oral administration) (e.g., for pharmaceutical use) that comprises a pharmaceutical agent. The pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs). The pharmaceutical agent can also contain one or more additional components (e.g., a cryoprotectant). The solid dosage form is enterically coated.


A method of making the solid dosage form can include:

    • Loading the pharmaceutical agent into a capsule; and
    • Coating the capsule with one or two layers of enteric coating (e.g., with an enteric coating or inner enteric coating and outer enteric coating as described herein), thereby preparing an enterically coated capsule, and thereby preparing the solid dosage form;
    • Optionally combining the pharmaceutical agent with a pharmaceutically acceptable excipient prior to loading into the capsule; and/or
    • Optionally banding the capsule after loading the capsule (e.g., optionally banding the capsule after loading the capsule and prior to enterically coating the capsule).


A method of making the solid dosage form can include:

    • Compressing a pharmaceutical agent described herein into a minitablet; and
    • Coating the minitablet with one or two layers of enteric coating (e.g., with an enteric coating or inner enteric coating and outer enteric coating as described herein), thereby preparing an enterically coated minitablet;
    • Optionally filling a capsule with a plurality of enterically coated minitablets, thereby preparing the solid dosage form.


A method of making the solid dosage form can include:

    • Compressing a pharmaceutical agent described herein into a tablet; and
    • Coating the tablet with one or two layers of enteric coating (e.g., with an enteric coating or inner enteric coating and outer enteric coating as described herein), thereby preparing enterically coated tablet, and thereby preparing the solid dosage form.


A method of making the solid dosage form can include a method for preparing an enterically coated capsule comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) loading the pharmaceutical agent into a capsule; and
    • b) enterically coating the capsule (e.g., with an enteric coating or inner enteric coating and outer enteric coating as described herein), thereby preparing the enterically coated capsule (thereby preparing the solid dosage form).


A method of making the solid dosage form can include a method for preparing an enterically coated capsule comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;
    • b) loading the pharmaceutical agent and pharmaceutically acceptable excipient into a capsule; and
    • c) enterically coating the capsule (e.g., with an enteric coating or inner enteric coating and outer enteric coating as described herein), thereby preparing the enterically coated capsule (thereby preparing the solid dosage form).


A method of making the solid dosage form can include a method for preparing an enterically coated capsule comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) loading the pharmaceutical agent into a capsule;
    • b) banding the capsule; and
    • c) enterically coating the capsule (e.g., with an enteric coating or inner enteric coating and outer enteric coating as described herein), thereby preparing the enterically coated capsule (thereby preparing the solid dosage form).


A method of making the solid dosage form can include a method for preparing an enterically coated capsule comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;
    • b) loading the pharmaceutical agent and pharmaceutically acceptable excipient into a capsule;
    • c) banding the capsule; and
    • d) enterically coating the capsule (e.g., with an enteric coating or inner enteric coating and outer enteric coating as described herein), thereby preparing the enterically coated capsule (thereby preparing the solid dosage form).


A method of making the solid dosage form can include a method for preparing an enterically coated tablet comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;
    • b) compressing the pharmaceutical agent and pharmaceutically acceptable excipient, thereby forming a tablet; and
    • c) enterically coating the tablet (e.g., with an enteric coating or inner enteric coating and outer enteric coating as described herein), thereby preparing the enterically coated tablet (thereby preparing the solid dosage form).


A method of making the solid dosage form can include a method for preparing an enterically coated minitablet comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;
    • b) compressing the pharmaceutical agent and pharmaceutically acceptable excipient, thereby forming a minitablet; and
    • c) enterically coating the minitablet (e.g., with an enteric coating or inner enteric coating and outer enteric coating as described herein), thereby preparing the enterically coated minitablet (thereby preparing the solid dosage form). Optionally, the minitablet is loaded into a capsule.


A method of making the solid dosage form can include a method for preparing a capsule comprising enterically coated minitablets comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising:

    • a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;
    • b) compressing the pharmaceutical agent and pharmaceutically acceptable excipient, thereby forming a minitablet;
    • c) enterically coating the minitablet (e.g., with an enteric coating or inner enteric coating and outer enteric coating as described herein), and
    • d) loading the capsule with enterically coated minitablets,
    • thereby preparing the capsule (thereby preparing the solid dosage form).


Additional Aspects of the Solid Dosage Forms

The solid dosage forms, e.g., as described herein, comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), and wherein the solid dosage form is enterically coated, can provide a therapeutically effective amount of the pharmaceutical agent to a subject, e.g., a human.


The solid dosage forms, e.g., as described herein, comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), and wherein the solid dosage form is enterically coated, can provide a non-natural amount of the therapeutically effective components (e.g., present in the pharmaceutical agent) to a subject, e.g., a human.


The solid dosage forms, e.g., as described herein, comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), and wherein the solid dosage form is enterically coated, can provide an unnatural quantity of the therapeutically effective components (e.g., present in the pharmaceutical agent) to a subject, e.g., a human.


The solid dosage forms, e.g., as described herein, comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the therapeutic agent comprises bacteria and/or microbial extracellular vesicles (mEVs), and wherein the solid dosage form is enterically coated, can bring about one or more changes to a subject, e.g., human, e.g., to treat or prevent a disease or a health disorder.


The solid dosage forms, e.g., as described herein, comprising a pharmaceutical agent (e.g., a therapeutically effective amount thereof), wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), and wherein the solid dosage form is enterically coated, has potential for significant utility, e.g., to affect a subject, e.g., a human, e.g., to treat or prevent a disease or a health disorder.


Other Content of Solid Dosage Forms

The solid dosage forms described herein (e.g., enterically coated tablets or minitablets) can be used to deliver an additional pharmaceutical agent (e.g., in place of, or in addition to, a pharmaceutical agent that comprises bacteria and/or mEVs (e.g., as defined herein)), such as a small molecule, vitamin or mineral supplement, or dietary supplement, to the small intestine.


Additional pharmaceutical agents that contain a small molecule that can be prepared in a solid dosage form described herein include one or more of the following small molecules: analgesics, anti-inflammatories, anaesthetics, anticonvulsants, antidiabetic agents, antihistamines, anti-infectives, antineoplastics, antiparkinsonian agents, antirheumatic agents, appetite stimulants, appetite suppressants, blood modifiers, bone metabolism modifiers, cardiovascular agents, central nervous system depressants, central nervous system stimulants, decongestants, dopamine receptor agonists, electrolytes, gastrointestinal agents, immunomodulators, muscle relaxants, narcotics, parasympathomimetics, sympathomimetics, sedatives, and hypnotics; pirenzepine, misoprostol, ursodeoxycholic acid, Alosetron, Cilansetron, Mosapride, Prucalopride, Tegaserod, Metoclopramide, Bromopride, Clebopride, Domperidone, Alizapride, Cinitapride, Cisapride, Codeine, Morphine, loperamide, diphenoxylate, methylnaltrexone bromide, Valerian, and mannitol; Antispasmodics selected from the group consisting of atropine sulphate, dicycloverine hydrochloride, hyoscine butylbromine, propantheline bromide, alverine citrate, and mebeverine hydrochloride; Motility stimulants selected from the group consisting of metoclorpramide and domperidone; H2-Receptor antagonists selected from the group consisting of Cimetidine, famotidinenizatidine, and ranitidine; Antimuscarinics; Chelates selected from the group consisting of Tripotassium dicitratbismuthate and sucralfate; Prostaglandin analogues; Aminosalicylates selected from the group consisting of balsazide sodium, mesalazine, olsalazine, and sulphasalazine; Corticosteroids selected from the group consisting of beclometasone dipropionate, budenoside, hydrocortisone, and prednisolone; Affecting immune response selected from the group consisting of ciclosporin, mercaptopurine, methotrexate, adalimumab, and infliximab; Stimulant Laxatives selected from the group consisting of bisacodyl, dantron, docusate, and sodium picosulfate; Drugs affecting biliary composition and flow; Bile acids sequestrants selected from the group consisting of colestyramine, Oxyphencyclimine, Camylofin, Mebeverine, Trimebutine, Rociverine, Dicycloverine, Dihexyverine, Difemerine, Piperidolate, Benzilone, Mepenzolate, Pipenzolate, Glycopyrronium, Oxyphenonium, Penthienate, Methantheline, Propantheline, Otilonium bromide, Tridihexethyl, Isopropamide, Hexocyclium, Poldine, Bevonium, Diphemanil, Tiemonium iodide, Prifinium bromide, Timepidium bromide, Fenpiverinium, Papaverine, Drotaverine, Moxaverine, 5-HT3 antagonists, 5-HT4 agonists, Fenpiprane, Diisopromine, Chlorbenzoxamine, Pinaverium, Fenoverine, Idanpramine, Proxazole, Alverine, Trepibutone, Isometheptene, Caroverine, Phloroglucinol, Silicones, Trimethyldiphenylpropylamine, Atropine, Hyoscyamine, Scopolamine, Butylscopolamine, Methylscopolamine, Methylatropine, Fentonium, Cimetropium bromide, and primarily dopamine antagonists; Proton pump inhibitors selected from the group consisting of Omeprazole, lansoprazole, pantoprazole, esomeprazole, and rabeprazole sodium; Opioids and opioid receptor antagonists; Analgesics selected from the group consisting of Acetaminophen, Diclofenac, Diflunisal, Etodolac, Fenoprofen, Flurbiprofen, Ibuprofen, Indomethacin, Ketoprofen, Ketorolac, Meclofenamate, Mefenamic Acid, Meloxicam, Nabumetone, Naproxen, Oxaprozin, Phenylbutazone, Piroxicam, Sulindac, Tolmetin, Celecoxib, Buprenorphine, Butorphanol, Codeine, Hydrocodone, Hydromorphone, Levorphanol, Meperidine, Methadone, Morphine, Nalbuphine, Oxycodone, Oxymorphone, Pentazocine, Propoxyphene, and Tramadol; Sleep drugs selected from the group consisting of Nitrazepam, Flurazepam, Loprazolam, Lormetazepam, Temazepam, Zaleplon, Zolpidem, Zopiclone, Chloral Hydrate, Triclofos, Clomethiazole, Quazepam, triazolam, Estazolam, Clonazepam, Alprazolam, Eszopiclone, Rozerem, Trazodone, Amitriptyline, Doxepin, Benzodiazepine drugs, melatonin, diphenhydramine, and herbal remedies; Cardiac glycosides selected from the group consisting of Digoxin and digitoxin; Phosphodiesterase inhibitors selected from the group consisting of enoximone and milrinone; Thiazides and related diuretics selected from the group consisting of bendroflumethiazide, chlortalidone, cyclopenthiazide, inapamide, metolazone, and xipamide; Diuretics selected from the group consisting of furosemide, bumetanide, and torasemide; Potassium sparing diuretics and aldosterone antagonists selected from the group consisting of amiloride hydrochloride, triamterene, weplerenone, and spironolactone; Osmotic diuretics; Drugs for arrhythmias selected from the group consisting of adenosine, amiodarone hydrochloride, disopyramide, flecainide acetate, propafenone hydrochloride, and lidocaine hydrochloride; Beta adrenoreceptor blocking drugs selected from the group consisting of propranolol, atenolol, acebutolol, bisoprolol fumarate, carvedilol, celiprolol, esmolol, lebatolol, metoprolol tartrate, nadolol, nebivolol, oxprenolol, pindolol, solatol, and timolol; Hypertension drugs selected from the group consisting of ambrisentan, bosentan, diazoxide, hydralazine, iloprost, minoxidil, sildenafil, sitaxentan, sodium nitroprusside, clonidine, methyldopa, moxonidine, guanethidine monosulphate, doxazosin, indoramin, prazosin, terazosin, phenoxybenzamine, and phentolamine mesilate; Drugs affecting the renin-angiotensin system selected from the group consisting of Captropril, Cilazapril, Enalapril Maleate, Fosinopril, Imidapril, Lisinopril, Moexipril, Perindopril Erbumine, Quinapril, Ramipril, Trandolapril, Candesartan Cilexetil, Eprosartan, Irbesartan, Losartan, Olmesartan Medoxomil, Telmisartan, Valsartan, and Aliskiren; Nitrates, calcium channel Blockers, and antianginal drugs selected from the group consisting of Glyceryl trinitrate, Isosorbide Dinitrate, Isosorbide Mononitrate, Amlodipine, Diltiazem, Felodipine, Isradipine, Lacidipine, Lercanidipine, Nicardipine, Nifedipine, Nimodipine, Verapamil, Ivabradine, Nicorandil, and Ranolazine; Peripheral vasodilators and related drugs selected from the group consisting of Cilostazol, Inositol Nicotinate, Moxisylyte, Naftidrofuryl Oxalate, and Pentoxifylline; Sympathomimetics selected from the group consisting of Dopamine, Dopexamine, Ephedrine, Metaraminol, Noradrenaline Acid Tartrate, Norephidrine Bitartrate, and Phenylephidrine; Anticoagulants and protamine selected from the group consisting of Heparin, Bemiparin, Dalteparin, Enoxaparin, Tinzaparin, Danaparoid, Bivalirudin, Lepirudin, Epoprostenol, Fondaprinux, Warfarin, Acenocoumarol, Phenindione, Dabigatran Etexilate, Rivaroxaban, and Protamine Sulphate; Antiplatelet drugs selected from the group consisting of Abciximab, Asprin, Clopidogrel, Dipyridamole, Eptifibatide, Prasugrel, and Tirofiban; Fibrinolytic and antifibrinolytic drugs selected from the group consisting of Alteplase, Reteplase, Streptokinase, Tenecteplase, Urokinase, Etamsylate, and Tranexamic Acid; Lipid regulating drugs selected from the group consisting of Atorvastatin, Fluvastatin, Pravastatin, Rosuvastatin, Simvastatin, Colesevam, Colestyramine, Colestipol, Ezetimibe, Bezafibrate, Ciprofibrate, Fenofibrate, Gemfibrozyl, Acipmox, Nictotinic Acid, Omega three fatty acid compounds, Ethanolamine Oleate, and Sodium Tetradecyl Suphate; CNS Drugs selected from the group consisting of Benperidol, Chlorpromazine, Flupentixol, Haloperidol, Levomepromazine, Pericyazine, Perphenazine, Pimozide, Prochlorperazine, Promazine, Sulpiride, Trifluoperazine, Zuclopenthixol, Amisulpride, Aripiprazole, Clozapine, Olanzapine, Paliperidone, Quetiapine, Riperidone, Sertindole, Zotepine, Flupentixol, Fluphenazine, Olanzapine Embonate, Pipotiazine Palmitate, Risperidone, Zuclopenthixol Decanoate, Carbamazepine, Valproate, Valproic acid, Lithium Carbonate, Lithium Citrate, Amitriptyline, Clomipramine, Dosulepin, Imipramine, Lofepramine, Nortriptyline, Trimipramine, mianserin, Trazodone, Phenelzine, Isocarboxazid, Tranylcypromine, Moclobemide, Citalopram, Escitalopram, Fluoxetine, Fluvoxamine, Paroxetine, Sertraline, Agomelatine, Duloxetine, Flupentixol, Mirtazapine, Reboxetine, Trytophan, Venflaxine, Atomoxetine, Dexametamine, Methylphenidate, Modafinil, Eslicarbazepine, Ocarbazepene, Ethosuximide, Gabapentin, Pregabalin, Lacosamide, Lamotrigine, Levetiracetam, Phenobarbital, Primidone, Phenytoin, Rufinamide, Tiagabine, Topiramate, Vigabatrin, Zonisamide, ropinirole, Rotigotine, Co-Beneldopa, Levodopa, Co-Careldopa, Rasagiline, Selegiline, Entacapone, Tolcapone, Amantidine, Orphenadrine, Procyclidine, Trihexyphenidyl, Haloperidol, Piracetam, Riluzole, Tetrabenazine, Acamprosate, Disulfiram, Bupropion, Vareniciline, Buprenorphine, Lofexidine, Donepezil, Galantamine, Memantine, and Rivastigimine; Anti-Infectives selected from the group consisting of Benzylpenicillin, Phenoxymethylpenicillin, Flucloxacillin, Temocillin, Amoxicillin, Ampicillin, Co-Amoxiclav, Co-Fluampicil, Piperacillin, Ticarcillin, Pivmecillinam, Cephalosporins, Cefaclor, Cefadroxil, Cefalexin, Cefixime, Cefotaxime, Cefradine, Ceftazidime, Cefuroxime, Ertapenem, Imipenem, Meropenem, Aztreonam, Tetracycline, Demeclocycline, Doxocycline, Lymecycline, Minocycline, Oxytetracycline, Tigecycline, Gentamicin, Amikacin, Neomycin, Tobramycin, Erythromycin, Azithromycin, Clarithromycin, Telithromycin, Clindamycin, Chloramphenicol, Fusidic Acid, Vancomycin, Teicoplanin, Daptomycin, Linezolid, Quinupristin, Colistin, Co-Trimoxazole, Sulpadiazine, Trimethoprim, Capreomycin, Cycloserine, Ethambutol, Isoniazid, Pyrazinamide, Rifabutin, Rifampicin, Streptomycin, Dapsone, Clofazimine, Metronidazole, Tinidazole, Ciproflaxacin, Levoflaxacin, Moxifloxacin, Nalidixic Acid, Norflaxine, Orflaxacin, Nitrofurantoin, Methenamine Hippurate, Amphotericin, Anidulafungin, Caspofungin, Fluconazole, Flucytosine, Griseofluvin, Itraconzole, Ketoconazole, Micafungin, Nystatin, Posaconazole, Terbinafine, Voriconazole, Abacavir, Didanosine, Emtricitabine, Lamivudine, Stavudine, Tenofovir Disoproxil, Zidovudine, Atazanavir, Darunavir, Fosamprenavir, Indinavir, Lopinair, Nelfinavir, Ritonavir, Saquinavir, Tipranavir, Efavirenz, Etravirine, Nevarapine, Enfuvirtide, Maraviroc, Raltegravir, Aciclovir, Famciclovir, Inosine Pranobex, Valaciclovir, Cidofovir, Gangciclovir, Foscarnet, Valgangciclovir, Adefovir Dipivoxil, Entecavir, Telbivudine, Amantadine, Oseltamivir, Zanamivir, Palivizumab, Ribavirin, Artemether, Chloroquine, Mefloquine, Primaquine, Proguanil, Pyrimethamine, Quinine, Doxycyclin, Diloxanide Furoate, Metronidaziole, Tinidazole, Mepacrine, Sodium Stibogluconate, Atovaquone, Pentamidine Isetionate, Mebendazole, and Piperazine; and other drugs selected from the group consisting of Benztropine, procyclidine, biperiden, Amantadine, Bromocriptine, Pergolide, Entacapone, Tolcapone, Selegeline, Pramipexole, budesonide, formoterol, quetiapine fumarate, olanzapine, pioglitazone, montelukast, Zoledromic Acid, valsartan, latanoprost, Irbesartan, Clopidogrel, Atomoxetine, Dexamfetamine, Methylphenidate, Modafinil, Bleomycin, Dactinomycin, Daunorubicin, Idarubicin, Mitomycin, Mitoxantrone, Azacitidine, Capecitabine, Cladribine, Clofarabine, Cytarabine, Fludarabine, Flourouracil, Gemcitabine, mercaptopurine, methotrexate, Nelarabine, Pemetrexed, Raltitrexed, Thioguanine, Apomorphine, Betamethasone, Cortisone, Deflazacort, Dexamethosone, Hydrocortisone, Methylprednisolone, Prednisolone, Triamcinolone, Ciclosporine, Sirolimus, Tacrolimus, Interferon Alpha, and Interferon Beta.


Additional pharmaceutical agents that contain a vitamin and/or mineral supplement that can be prepared in a solid dosage form described herein include one or more of the following a vitamin and/or mineral supplements: Vitamin A, Biotin, Vitamin B1 (Thiamin), Vitamin B12, Vitamin B6, Calcium, Choline, Chromium, Copper, Vitamin C, Vitamin D (e.g., Vitamin D3), Vitamin E, Fluoride, Folate, Iodine, Iron, Vitamin K, Magnesium, Manganese, Niacin, Pantothenic Acid, Phosphorus, Potassium, Riboflavin, Selenium, Thiamin, and/or Zinc.


Additional pharmaceutical agents that contain a dietary supplement (e.g., a vitamin, a mineral, an herb, an amino acid, an oil, and/or an enzyme) that can be prepared in a solid dosage form described herein include one or more of the following dietary supplements: acacia rigidula, BMPEA, DMAA, DMBA, DMHA, methylsynephrine, phenibut, picamilon, caffeine, tianeptine, vinpocetine, fish oil, flaxseed oil, omega-3, omega-6, omega-9, eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and/or alpha-linolenic acid (ALA).


The dose of the additional pharmaceutical agent in the solid dosage form (e.g., wherein the dose is per capsule or tablet or total per total number of minitablets used in a capsule) can be a dose described herein for a pharmaceutical agent that comprises bacteria and/or mEVs.


The dose of the additional pharmaceutical agent in the solid dosage form (e.g., wherein the dose is per capsule or tablet or total per total number of minitablets used in a capsule) can be, e.g., about 0.001 mg to about 10 mg fixed dose (e.g., about 0.05 mg to about 10 mg; about 0.1 mg to about 10 mg; about 0.1 mg to about 5 mg; about 0.5 mg to about 5 mg; about 1 mg, about 2 mg, about 3 mg, about 4 mg, or about 5 mg).


The dose of the additional pharmaceutical agent in the solid dosage form (e.g., wherein the dose is per capsule or tablet or total per total number of minitablets used in a capsule) can be, particularly for a supplement, e.g., about 1 mg to about 2000 mg (e.g., about 25 mg; about 50 mg; about 100 mg; about 250 mg; about 500 mg; about 750 mg; about 1000 mg; about 1500 mg; or about 2000 mg) or about 10 IU to about 5000 IU (international units) (e.g., about 25 IU; about 50 IU; about 100 IU; about 250 IU; about 500 IU; about 750 IU; about 1000 IU; about 1500 IU; about 2000 IU; about 3000 IU; about 4000 IU; or about 5000 IU).


Additional Pharmaceutical agents for Combination Use


In certain aspects, the methods provided herein include the administration to a subject of a solid dosage form described herein either alone or in combination with an additional pharmaceutical agent. In some embodiments, the additional pharmaceutical agent is an immunosuppressant, an anti-inflammatory agent, a steroid, and/or a cancer therapeutic.


In some embodiments, the solid dosage form is administered to the subject before the additional pharmaceutical agent is administered (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hours before or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 days before). In some embodiments, the solid dosage form is administered to the subject after the additional pharmaceutical agent is administered (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hours after or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 days after). In some embodiments, the solid dosage form and the additional pharmaceutical agent are administered to the subject simultaneously or nearly simultaneously (e.g., administrations occur within an hour of each other).


In some embodiments, an antibiotic is administered to the subject before the solid dosage form is administered to the subject (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hours before or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 days before). In some embodiments, an antibiotic is administered to the subject after the solid dosage form is administered to the subject (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hours before or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 days after). In some embodiments, the solid dosage form and the antibiotic are administered to the subject simultaneously or nearly simultaneously (e.g., administrations occur within an hour of each other).


In some embodiments, the additional pharmaceutical agent is a cancer therapeutic. In some embodiments, the cancer therapeutic is a chemotherapeutic agent. Examples of such chemotherapeutic agents include, but are not limited to, alkylating agents such as thiotepa and cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1); eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gammall and calicheamicin omegall; dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antibiotic chromophores, aclacinomysins, actinomycin, authrarnycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elformithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; podophyllinic acid; 2-ethylhydrazide; procarbazine; PSK polysaccharide complex); razoxane; rhizoxin; sizofuran; spirogermanium; tenuazonic acid; triaziquone; 2,2′,2″-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside (“Ara-C”); cyclophosphamide; thiotepa; taxoids, e.g., paclitaxel and doxetaxel; chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum coordination complexes such as cisplatin, oxaliplatin and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine; vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (e.g., CPT-11); topoisomerase inhibitor RFS 2000; difluoromethylomithine (DMFO); retinoids such as retinoic acid; capecitabine; and pharmaceutically acceptable salts, acids or derivatives of any of the above.


In some embodiments, the cancer therapeutic is a cancer immunotherapy agent. Immunotherapy refers to a treatment that uses a subject's immune system to treat cancer, e.g., checkpoint inhibitors, cancer vaccines, cytokines, cell therapy, CAR-T cells, and dendritic cell therapy. Non-limiting examples of immunotherapies are checkpoint inhibitors include Nivolumab (BMS, anti-PD-1), Pembrolizumab (Merck, anti-PD-1), Ipilimumab (BMS, anti-CTLA-4), MEDI4736 (AstraZeneca, anti-PD-L1), and MPDL3280A (Roche, anti-PD-L1). Other immunotherapies may be tumor vaccines, such as Gardail, Cervarix, BCG, sipulencel-T, Gp100:209-217, AGS-003, DCVax-L, Algenpantucel-L, Tergenpantucel-L, TG4010, ProstAtak, Prostvac-V/R-TRICOM, Rindopepimul, E75 peptide acetate, IMA901, POL-103A, Belagenpumatucel-L, GSK1572932A, MDX-1279, GV1001, and Tecemotide. The immunotherapy agent may be administered via injection (e.g., intravenously, intratumorally, subcutaneously, or into lymph nodes), but may also be administered orally, topically, or via aerosol. Immunotherapies may comprise adjuvants such as cytokines.


In some embodiments, the immunotherapy agent is an immune checkpoint inhibitor. Immune checkpoint inhibition broadly refers to inhibiting the checkpoints that cancer cells can produce to prevent or downregulate an immune response. Examples of immune checkpoint proteins include, but are not limited to, CTLA4, PD-1, PD-L1, PD-L2, A2AR, B7-H3, B7-H4, BTLA, KIR, LAG3, TIM-3 or VISTA. Immune checkpoint inhibitors can be antibodies or antigen binding fragments thereof that bind to and inhibit an immune checkpoint protein. Examples of immune checkpoint inhibitors include, but are not limited to, nivolumab, pembrolizumab, pidilizumab, AMP-224, AMP-514, STI-A1110, TSR-042, RG-7446, BMS-936559, MEDI-4736, MSB-0020718C, AUR-012 and STI-A1010.


In some embodiments, the methods provided herein include the administration of a pharmaceutical composition described herein in combination with one or more additional pharmaceutical agents. In some embodiments, the methods disclosed herein include the administration of two immunotherapy agents (e.g., immune checkpoint inhibitor). For example, the methods provided herein include the administration of a pharmaceutical composition described herein in combination with a PD-1 inhibitor (such as pemrolizumab or nivolumab or pidilizumab) or a CLTA-4 inhibitor (such as ipilimumab) or a PD-L1 inhibitor.


In some embodiments, the immunotherapy agent is an antibody or antigen binding fragment thereof that, for example, binds to a cancer-associated antigen. Examples of cancer-associated antigens include, but are not limited to, adipophilin, AIM-2, ALDH1A1, alpha-actinin-4, alpha-fetoprotein (“AFP”), ARTC1, B-RAF, BAGE-1, BCLX (L), BCR-ABL fusion protein b3a2, beta-catenin, BING-4, CA-125, CALCA, carcinoembryonic antigen (“CEA”), CASP-5, CASP-8, CD274, CD45, Cdc27, CDK12, CDK4, CDKN2A, CEA, CLPP, COA-1, CPSF, CSNK1A1, CTAG1, CTAG2, cyclin D1, Cyclin-A1, dek-can fusion protein, DKK1, EFTUD2, Elongation factor 2, ENAH (hMena), Ep-CAM, EpCAM, EphA3, epithelial tumor antigen (“ETA”), ETV6-AML1 fusion protein, EZH2, FGF5, FLT3-ITD, FN1, G250/MN/CAIX, GAGE-1,2,8, GAGE-3,4,5,6,7, GAS7, glypican-3, GnTV, gp100/Pme117, GPNMB, HAUS3, Hepsin, HER-2/neu, HERV-K-MEL, HLA-A11, HLA-A2, HLA-DOB, hsp70-2, IDO1, IGF2B3, IL13Ralpha2, Intestinal carboxyl esterase, K-ras, Kallikrein 4, KIF20A, KK-LC-1, KKLC1, KM-HN-1, KMHN1 also known as CCDC110, LAGE-1, LDLR-fucosyltransferaseAS fusion protein, Lengsin, M-CSF, MAGE-A1, MAGE-A10, MAGE-A12, MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A6, MAGE-A9, MAGE-C1, MAGE-C2, malic enzyme, mammaglobin-A, MART2, MATN, MC1R, MCSP, mdm-2, ME1, Melan-A/MART-1, Meloe, Midkine, MMP-2, MMP-7, MUC1, MUC5AC, mucin, MUM-1, MUM-2, MUM-3, Myosin, Myosin class I, N-raw, NA88-A, neo-PAP, NFYC, NY-BR-1, NY-ESO-1/LAGE-2, OA1, OGT, OS-9, P polypeptide, p53, PAP, PAX5, PBF, pml-RARalpha fusion protein, polymorphic epithelial mucin (“PEM”), PPP1R3B, PRAME, PRDX5, PSA, PSMA, PTPRK, RAB38/NY-MEL-1, RAGE-1, RBAF600, RGS5, RhoC, RNF43, RU2AS, SAGE, secernin 1, SIRT2, SNRPD1, SOX10, Sp17, SPA17, SSX-2, SSX-4, STEAP1, survivin, SYT-SSX1 or -SSX2 fusion protein, TAG-1, TAG-2, Telomerase, TGF-betaRll, TPBG, TRAG-3, Triosephosphate isomerase, TRP-1/gp75, TRP-2, TRP2-INT2, tyrosinase, tyrosinase (“TYR”), VEGF, WT1, XAGE-1b/GAGED2a. In some embodiments, the antigen is a neo-antigen.


In some embodiments, the immunotherapy agent is a cancer vaccine and/or a component of a cancer vaccine (e.g., an antigenic peptide and/or protein). The cancer vaccine can be a protein vaccine, a nucleic acid vaccine or a combination thereof. For example, in some embodiments, the cancer vaccine comprises a polypeptide comprising an epitope of a cancer-associated antigen. In some embodiments, the cancer vaccine comprises a nucleic acid (e.g., DNA or RNA, such as mRNA) that encodes an epitope of a cancer-associated antigen. Examples of cancer-associated antigens include, but are not limited to, adipophilin, AIM-2, ALDH1A1, alpha-actinin-4, alpha-fetoprotein (“AFP”), ARTC1, B-RAF, BAGE-1, BCLX (L), BCR-ABL fusion protein b3a2, beta-catenin, BING-4, CA-125, CALCA, carcinoembryonic antigen (“CEA”), CASP-5, CASP-8, CD274, CD45, Cdc27, CDK12, CDK4, CDKN2A, CEA, CLPP, COA-1, CPSF, CSNK1A1, CTAG1, CTAG2, cyclin D1, Cyclin-A1, dek-can fusion protein, DKK1, EFTUD2, Elongation factor 2, ENAH (hMena), Ep-CAM, EpCAM, EphA3, epithelial tumor antigen (“ETA”), ETV6-AML1 fusion protein, EZH2, FGF5, FLT3-ITD, FN1, G250/MN/CAIX, GAGE-1,2,8, GAGE-3,4,5,6,7, GAS7, glypican-3, GnTV, gp100/Pme117, GPNMB, HAUS3, Hepsin, HER-2/neu, HERV-K-MEL, HLA-A11, HLA-A2, HLA-DOB, hsp70-2, IDO1, IGF2B3, IL13Ralpha2, Intestinal carboxyl esterase, K-ras, Kallikrein 4, KIF20A, KK-LC-1, KKLC1, KM-HN-1, KMHN1 also known as CCDCl10, LAGE-1, LDLR-fucosyltransferaseAS fusion protein, Lengsin, M-CSF, MAGE-A1, MAGE-A10, MAGE-A12, MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A6, MAGE-A9, MAGE-C1, MAGE-C2, malic enzyme, mammaglobin-A, MART2, MATN, MC1R, MCSP, mdm-2, ME1, Melan-A/MART-1, Meloe, Midkine, MMP-2, MMP-7, MUC1, MUC5AC, mucin, MUM-1, MUM-2, MUM-3, Myosin, Myosin class I, N-raw, NA88-A, neo-PAP, NFYC, NY-BR-1, NY-ESO-1/LAGE-2, OA1, OGT, OS-9, P polypeptide, p53, PAP, PAX5, PBF, pml-RARalpha fusion protein, polymorphic epithelial mucin (“PEM”), PPP1R3B, PRAME, PRDX5, PSA, PSMA, PTPRK, RAB38/NY-MEL-1, RAGE-1, RBAF600, RGS5, RhoC, RNF43, RU2AS, SAGE, secernin 1, SIRT2, SNRPD1, SOX10, Sp17, SPA17, SSX-2, SSX-4, STEAP1, survivin, SYT-SSX1 or -SSX2 fusion protein, TAG-1, TAG-2, Telomerase, TGF-betaRll, TPBG, TRAG-3, Triosephosphate isomerase, TRP-1/gp75, TRP-2, TRP2-INT2, tyrosinase, tyrosinase (“TYR”), VEGF, WT1, XAGE-lb/GAGED2a. In some embodiments, the antigen is a neo-antigen. In some embodiments, the cancer vaccine is administered with an adjuvant. Examples of adjuvants include, but are not limited to, an immune modulatory protein, Adjuvant 65, α-GalCer, aluminum phosphate, aluminum hydroxide, calcium phosphate, β-Glucan Peptide, CpG ODN DNA, GPI-0100, lipid A, lipopolysaccharide, Lipovant, Montanide, N-acetyl-muramyl-L-alanyl-D-isoglutamine, Pam3CSK4, quil A, cholera toxin (CT) and heat-labile toxin from enterotoxigenic Escherichia coli (LT) including derivatives of these (CTB, mmCT, CTA1-DD, LTB, LTK63, LTR72, dmLT) and trehalose dimycolate.


In some embodiments, the immunotherapy agent is an immune modulating protein to the subject. In some embodiments, the immune modulatory protein is a cytokine or chemokine. Examples of immune modulating proteins include, but are not limited to, B lymphocyte chemoattractant (“BLC”), C-C motif chemokine 11 (“Eotaxin-1”), Eosinophil chemotactic protein 2 (“Eotaxin-2”), Granulocyte colony-stimulating factor (“G-CSF”), Granulocyte macrophage colony-stimulating factor (“GM-CSF”), 1-309, Intercellular Adhesion Molecule 1 (“ICAM-1”), Interferon alpha (“IFN-alpha”), Interferon beta (“IFN-beta”) Interferon gamma (“IFN-gamma”), Interlukin-1 alpha (“IL-1 alpha”), Interlukin-1 beta (“IL-1 beta”), Interleukin 1 receptor antagonist (“IL-1 ra”), Interleukin-2 (“IL-2”), Interleukin-4 (“IL-4”), Interleukin-5 (“IL-5”), Interleukin-6 (“IL-6”), Interleukin-6 soluble receptor (“IL-6 sR”), Interleukin-7 (“IL-7”), Interleukin-8 (“IL-8”), Interleukin-10 (“IL-10”), Interleukin-11 (“IL-11”), Subunit beta of Interleukin-12 (“IL-12 p40” or “IL-12 p′70”), Interleukin-13 (“IL-13”), Interleukin-15 (“IL-15”), Interleukin-16 (“IL-16”), Interleukin-17A-F (“IL-17A-F”), Interleukin-18 (“IL-18”), Interleukin-21 (“IL-21”), Interleukin-22 (“IL-22”), Interleukin-23 (“IL-23”), Interleukin-33 (“IL-33”), Chemokine (C-C motif) Ligand 2 (“MCP-1”), Macrophage colony-stimulating factor (“M-CSF”), Monokine induced by gamma interferon (“MIG”), Chemokine (C-C motif) ligand 2 (“MIP-1 alpha”), Chemokine (C-C motif) ligand 4 (“MIP-1 beta”), Macrophage inflammatory protein-1-delta (“MIP-1 delta”), Platelet-derived growth factor subunit B (“PDGF-BB”), Chemokine (C-C motif) ligand 5, Regulated on Activation, Normal T cell Expressed and Secreted (“RANTES”), TIMP metallopeptidase inhibitor 1 (“TIMP-1”), TIMP metallopeptidase inhibitor 2 (“TIMP-2”), Tumor necrosis factor, lymphotoxin-alpha (“TNF alpha”), Tumor necrosis factor, lymphotoxin-beta (“TNF beta”), Soluble TNF receptor type 1 (“sTNFRI”), sTNFRIIAR, Brain-derived neurotrophic factor (“BDNF”), Basic fibroblast growth factor (“bFGF”), Bone morphogenetic protein 4 (“BMP-4”), Bone morphogenetic protein 5 (“BMP-5”), Bone morphogenetic protein 7 (“BMP-7”), Nerve growth factor (“b-NGF”), Epidermal growth factor (“EGF”), Epidermal growth factor receptor (“EGFR”), Endocrine-gland-derived vascular endothelial growth factor (“EG-VEGF”), Fibroblast growth factor 4 (“FGF-4”), Keratinocyte growth factor (“FGF-7”), Growth differentiation factor 15 (“GDF-15”), Glial cell-derived neurotrophic factor (“GDNF”), Growth Hormone, Heparin-binding EGF-like growth factor (“HB-EGF”), Hepatocyte growth factor (“HGF”), Insulin-like growth factor binding protein 1 (“IGFBP-1”), Insulin-like growth factor binding protein 2 (“IGFBP-2”), Insulin-like growth factor binding protein 3 (“IGFBP-3”), Insulin-like growth factor binding protein 4 (“IGFBP-4”), Insulin-like growth factor binding protein 6 (“IGFBP-6”), Insulin-like growth factor 1 (“IGF-1”), Insulin, Macrophage colony-stimulating factor (“M-CSF R”), Nerve growth factor receptor (“NGF R”), Neurotrophin-3 (“NT-3”), Neurotrophin-4 (“NT-4”), Osteoclastogenesis inhibitory factor (“Osteoprotegerin”), Platelet-derived growth factor receptors (“PDGF-AA”), Phosphatidylinositol-glycan biosynthesis (“PIGF”), Skp, Cullin, F-box containing comples (“SCF”), Stem cell factor receptor (“SCF R”), Transforming growth factor alpha (“TGFalpha”), Transforming growth factor beta-1 (“TGF beta 1”), Transforming growth factor beta-3 (“TGF beta 3”), Vascular endothelial growth factor (“VEGF”), Vascular endothelial growth factor receptor 2 (“VEGFR2”), Vascular endothelial growth factor receptor 3 (“VEGFR3”), VEGF-D 6Ckine, Tyrosine-protein kinase receptor UFO (“Axl”), Betacellulin (“BTC”), Mucosae-associated epithelial chemokine (“CCL28”), Chemokine (C-C motif) ligand 27 (“CTACK”), Chemokine (C-X-C motif) ligand 16 (“CXCL16”), C-X-C motif chemokine 5 (“ENA-78”), Chemokine (C-C motif) ligand 26 (“Eotaxin-3”), Granulocyte chemotactic protein 2 (“GCP-2”), GRO, Chemokine (C-C motif) ligand 14 (“HCC-1”), Chemokine (C-C motif) ligand 16 (“HCC-4”), Interleukin-9 (“IL-9”), Interleukin-17 F (“IL-17F”), Interleukin-18-binding protein (“IL-18 BPa”), Interleukin-28 A (“IL-28A”), Interleukin 29 (“IL-29”), Interleukin 31 (“IL-31”), C-X-C motif chemokine 10 (“IP-10”), Chemokine receptor CXCR3 (“I-TAC”), Leukemia inhibitory factor (“LIF”), Light, Chemokine (C motif) ligand (“Lymphotactin”), Monocyte chemoattractant protein 2 (“MCP-2”), Monocyte chemoattractant protein 3 (“MCP-3”), Monocyte chemoattractant protein 4 (“MCP-4”), Macrophage-derived chemokine (“MDC”), Macrophage migration inhibitory factor (“MIF”), Chemokine (C-C motif) ligand 20 (“MIP-3 alpha”), C-C motif chemokine 19 (“MIP-3 beta”), Chemokine (C-C motif) ligand 23 (“MPIF-1”), Macrophage stimulating protein alpha chain (“MSPalpha”), Nucleosome assembly protein 1-like 4 (“NAP-2”), Secreted phosphoprotein 1 (“Osteopontin”), Pulmonary and activation-regulated cytokine (“PARC”), Platelet factor 4 (“PF4”), Stroma cell-derived factor-1 alpha (“SDF-1 alpha”), Chemokine (C-C motif) ligand 17 (“TARC”), Thymus-expressed chemokine (“TECK”), Thymic stromal lymphopoietin (“TSLP 4-IBB”), CD 166 antigen (“ALCAM”), Cluster of Differentiation 80 (“B7-1”), Tumor necrosis factor receptor superfamily member 17 (“BCMA”), Cluster of Differentiation 14 (“CD14”), Cluster of Differentiation 30 (“CD30”), Cluster of Differentiation 40 (“CD40 Ligand”), Carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) (“CEACAM-1”), Death Receptor 6 (“DR6”), Deoxythymidine kinase (“Dtk”), Type 1 membrane glycoprotein (“Endoglin”), Receptor tyrosine-protein kinase erbB-3 (“ErbB3”), Endothelial-leukocyte adhesion molecule 1 (“E-Selectin”), Apoptosis antigen 1 (“Fas”), Fms-like tyrosine kinase 3 (“Flt-3L”), Tumor necrosis factor receptor superfamily member 1 (“GITR”), Tumor necrosis factor receptor superfamily member 14 (“HVEM”), Intercellular adhesion molecule 3 (“ICAM-3”), IL-1 R4, IL-1 RI, IL-10 Rbeta, IL-17R, IL-2Rgamma, IL-21R, Lysosome membrane protein 2 (“LIMPII”), Neutrophil gelatinase-associated lipocalin (“Lipocalin-2”), CD62L (“L-Selectin”), Lymphatic endothelium (“LYVE-1”), MHC class I polypeptide-related sequence A (“MICA”), MHC class I polypeptide-related sequence B (“MICB”), NRG1-betal, Beta-type platelet-derived growth factor receptor (“PDGF Rbeta”), Platelet endothelial cell adhesion molecule (“PECAM-1”), RAGE, Hepatitis A virus cellular receptor 1 (“TIM-1”), Tumor necrosis factor receptor superfamily member IOC (“TRAIL R3”), Trappin protein transglutaminase binding domain (“Trappin-2”), Urokinase receptor (“uPAR”), Vascular cell adhesion protein 1 (“VCAM-1”), XEDARActivin A, Agouti-related protein (“AgRP”), Ribonuclease 5 (“Angiogenin”), Angiopoietin 1, Angiostatin, Catheprin S, CD40, Cryptic family protein IB (“Cripto-1”), DAN, Dickkopf-related protein 1 (“DKK-1”), E-Cadherin, Epithelial cell adhesion molecule (“EpCAM”), Fas Ligand (FasL or CD95L), Fcg RIIB/C, FoUistatin, Galectin-7, Intercellular adhesion molecule 2 (“ICAM-2”), IL-13 R1, IL-13R2, IL-17B, IL-2 Ra, IL-2 Rb, IL-23, LAP, Neuronal cell adhesion molecule (“NrCAM”), Plasminogen activator inhibitor-1 (“PAI-1”), Platelet derived growth factor receptors (“PDGF-AB”), Resistin, stromal cell-derived factor 1 (“SDF-1 beta”), sgp130, Secreted frizzled-related protein 2 (“ShhN”), Sialic acid-binding immunoglobulin-type lectins (“Siglec-5”), ST2, Transforming growth factor-beta 2 (“TGF beta 2”), Tie-2, Thrombopoietin (“TPO”), Tumor necrosis factor receptor superfamily member 10D (“TRAIL R4”), Triggering receptor expressed on myeloid cells 1 (“TREM-1”), Vascular endothelial growth factor C (“VEGF-C”), VEGFR1Adiponectin, Adipsin (“AND”), Alpha-fetoprotein (“AFP”), Angiopoietin-like 4 (“ANGPTL4”), Beta-2-microglobulin (“B2M”), Basal cell adhesion molecule (“BCAM”), Carbohydrate antigen 125 (“CA125”), Cancer Antigen 15-3 (“CA15-3”), Carcinoembryonic antigen (“CEA”), cAMP receptor protein (“CRP”), Human Epidermal Growth Factor Receptor 2 (“ErbB2”), Follistatin, Follicle-stimulating hormone (“FSH”), Chemokine (C-X-C motif) ligand 1 (“GRO alpha”), human chorionic gonadotropin (“beta HCG”), Insulin-like growth factor 1 receptor (“IGF-1 sR”), IL-1 sRII, IL-3, IL-18 Rb, IL-21, Leptin, Matrix metalloproteinase-1 (“MMP-1”), Matrix metalloproteinase-2 (“MMP-2”), Matrix metalloproteinase-3 (“MMP-3”), Matrix metalloproteinase-8 (“MMP-8”), Matrix metalloproteinase-9 (“MMP-9”), Matrix metalloproteinase-10 (“MMP-10”), Matrix metalloproteinase-13 (“MMP-13”), Neural Cell Adhesion Molecule (“NCAM-1”), Entactin (“Nidogen-1”), Neuron specific enolase (“NSE”), Oncostatin M (“OSM”), Procalcitonin, Prolactin, Prostate specific antigen (“PSA”), Sialic acid-binding Ig-like lectin 9 (“Siglec-9”), ADAM 17 endopeptidase (“TACE”), Thyroglobulin, Metalloproteinase inhibitor 4 (“TIMP-4”), TSH2B4, Disintegrin and metalloproteinase domain-containing protein 9 (“ADAM-9”), Angiopoietin 2, Tumor necrosis factor ligand superfamily member 13/Acidic leucine-rich nuclear phosphoprotein 32 family member B (“APRIL”), Bone morphogenetic protein 2 (“BMP-2”), Bone morphogenetic protein 9 (“BMP-9”), Complement component 5a (“C5a”), Cathepsin L, CD200, CD97, Chemerin, Tumor necrosis factor receptor superfamily member 6B (“DcR3”), Fatty acid-binding protein 2 (“FABP2”), Fibroblast activation protein, alpha (“FAP”), Fibroblast growth factor 19 (“FGF-19”), Galectin-3, Hepatocyte growth factor receptor (“HGF R”), IFN-gammalpha/beta R2, Insulin-like growth factor 2 (“IGF-2”), Insulin-like growth factor 2 receptor (“IGF-2 R”), Interleukin-1 receptor 6 (“IL-1R6”), Interleukin 24 (“IL-24”), Interleukin 33 (“IL-33”, Kallikrein 14, Asparaginyl endopeptidase (“Legumain”), Oxidized low-density lipoprotein receptor 1 (“LOX-1”), Mannose-binding lectin (“MBL”), Neprilysin (“NEP”), Notch homolog 1, translocation-associated (Drosophila) (“Notch-1”), Nephroblastoma overexpressed (“NOV”), Osteoactivin, Programmed cell death protein 1 (“PD-1”), N-acetylmuramoyl-L-alanine amidase (“PGRP-5”), Serpin A4, Secreted frizzled related protein 3 (“sFRP-3”), Thrombomodulin, Tolllike receptor 2 (“TLR2”), Tumor necrosis factor receptor superfamily member 10A (“TRAIL R1”), Transferrin (“TRF”), WIF-1ACE-2, Albumin, AMICA, Angiopoietin 4, B-cell activating factor (“BAFF”), Carbohydrate antigen 19-9 (“CA19-9”), CD 163, Clusterin, CRT AM, Chemokine (C-X-C motif) ligand 14 (“CXCL14”), Cystatin C, Decorin (“DCN”), Dickkopf-related protein 3 (“Dkk-3”), Delta-like protein 1 (“DLL1”), Fetuin A, Heparin-binding growth factor 1 (“aFGF”), Folate receptor alpha (“FOLR1”), Furin, GPCR-associated sorting protein 1 (“GASP-1”), GPCR-associated sorting protein 2 (“GASP-2”), Granulocyte colony-stimulating factor receptor (“GCSF R”), Serine protease hepsin (“HAI-2”), Interleukin-17B Receptor (“IL-17B R”), Interleukin 27 (“IL-27”), Lymphocyte-activation gene 3 (“LAG-3”), Apolipoprotein A-V (“LDL R”), Pepsinogen I, Retinol binding protein 4 (“RBP4”), SOST, Heparan sulfate proteoglycan (“Syndecan-1”), Tumor necrosis factor receptor superfamily member 13B (“TACI”), Tissue factor pathway inhibitor (“TFPI”), TSP-1, Tumor necrosis factor receptor superfamily, member 10b (“TRAIL R2”), TRANCE, Troponin I, Urokinase Plasminogen Activator (“uPA”), Cadherin 5, type 2 or VE-cadherin (vascular endothelial) also known as CD144 (“VE-Cadherin”), WNT1-inducible-signaling pathway protein 1 (“WISP-1”), and Receptor Activator of Nuclear Factor κ B (“RANK”).


In some embodiments, the cancer therapeutic is an anti-cancer compound. Exemplary anti-cancer compounds include, but are not limited to, Alemtuzumab (Campath®), Alitretinoin (Panretin®), Anastrozole (Arimidex®), Bevacizumab (Avastin®), Bexarotene (Targretin®), Bortezomib (Velcade®), Bosutinib (Bosulif®), Brentuximab vedotin (Adcetris®), Cabozantinib (Cometriq™), Carfilzomib (Kyprolis™) Cetuximab (Erbitux®), Crizotinib (Xalkori®), Dasatinib (Sprycel®), Denileukin diftitox (Ontak®), Erlotinib hydrochloride (Tarceva®), Everolimus (Afinitor®), Exemestane (Aromasin®), Fulvestrant (Faslodex®), Gefitinib (Iressa®), Ibritumomab tiuxetan (Zevalin®), Imatinib mesylate (Gleevec®), Ipilimumab (Yervoy™), Lapatinib ditosylate (Tykerb®), Letrozole (Femara®), Nilotinib (Tasigna®), Ofatumumab (Arzerra®), Panitumumab (Vectibix®), Pazopanib hydrochloride (Votrient®), Pertuzumab (Perjeta™), Pralatrexate (Folotyn®), Regorafenib (Stivarga®), Rituximab (Rituxan®), Romidepsin (Istodax®), Sorafenib tosylate (Nexavar®), Sunitinib malate (Sutent®), Tamoxifen, Temsirolimus (Torisel®), Toremifene (Fareston®), Tositumomab and 131I-tositumomab (Bexxar®), Trastuzumab (Herceptin®), Tretinoin (Vesanoid®), Vandetanib (Caprelsa®), Vemurafenib (Zelboraf®), Vorinostat (Zolinza®), and Ziv-aflibercept (Zaltrap®).


Exemplary anti-cancer compounds that modify the function of proteins that regulate gene expression and other cellular functions (e.g., HDAC inhibitors, retinoid receptor ligants) are Vorinostat (Zolinza®), Bexarotene (Targretin®) and Romidepsin (Istodax®), Alitretinoin (Panretin®), and Tretinoin (Vesanoid®).


Exemplary anti-cancer compounds that induce apoptosis (e.g., proteasome inhibitors, antifolates) are Bortezomib (Velcade®), Carfilzomib (Kyprolis™), and Pralatrexate (Folotyn®).


Exemplary anti-cancer compounds that increase anti-tumor immune response (e.g., anti CD20, anti CD52; anti-cytotoxic T-lymphocyte-associated antigen-4) are Rituximab (Rituxan®), Alemtuzumab (Campath®), Ofatumumab (Arzerra®), and Ipilimumab (Yervoy™).


Exemplary anti-cancer compounds that deliver toxic agents to cancer cells (e.g., anti-CD20-radionuclide fusions; IL-2-diphtheria toxin fusions; anti-CD30-monomethylauristatin E (MMAE)-fusions) are Tositumomab and 131I-tositumomab (Bexxar®) and Ibritumomab tiuxetan (Zevalin®), Denileukin diftitox (Ontak®), and Brentuximab vedotin (Adcetris®).


Other exemplary anti-cancer compounds are small molecule inhibitors and conjugates thereof of, e.g., Janus kinase, ALK, Bcl-2, PARP, PI3K, VEGF receptor, Braf, MEK, CDK, and HSP90.


Exemplary platinum-based anti-cancer compounds include, for example, cisplatin, carboplatin, oxaliplatin, satraplatin, picoplatin, Nedaplatin, Triplatin, and Lipoplatin. Other metal-based drugs suitable for treatment include, but are not limited to ruthenium-based compounds, ferrocene derivatives, titanium-based compounds, and gallium-based compounds.


In some embodiments, the cancer therapeutic is a radioactive moiety that comprises a radionuclide. Exemplary radionuclides include, but are not limited to Cr-51, Cs-131, Ce-134, Se-75, Ru-97, 1-125, Eu-149, Os-189m, Sb-119, 1-123, Ho-161, Sb-117, Ce-139, In-111, Rh-103m, Ga-67, T1-201, Pd-103, Au-195, Hg-197, Sr-87m, Pt-191, P-33, Er-169, Ru-103, Yb-169, Au-199, Sn-121, Tm-167, Yb-175, In-113m, Sn-113, Lu-177, Rh-105, Sn-117m, Cu-67, Sc-47, Pt-195m, Ce-141, 1-131, Tb-161, As-77, Pt-197, Sm-153, Gd-159, Tm-173, Pr-143, Au-198, Tm-170, Re-186, Ag-111, Pd-109, Ga-73, Dy-165, Pm-149, Sn-123, Sr-89, Ho-166, P-32, Re-188, Pr-142, Ir-194, In-114m/In-114, and Y-90.


In some embodiments, the cancer therapeutic is an antibiotic. For example, if the presence of a cancer-associated bacteria and/or a cancer-associated microbiome profile is detected according to the methods provided herein, antibiotics can be administered to eliminate the cancer-associated bacteria from the subject. “Antibiotics” broadly refers to compounds capable of inhibiting or preventing a bacterial infection. Antibiotics can be classified in a number of ways, including their use for specific infections, their mechanism of action, their bioavailability, or their spectrum of target microbe (e.g., Gram-negative vs. Gram-positive bacteria, aerobic vs. anaerobic bacteria, etc.) and these may be used to kill specific bacteria in specific areas of the host (“niches”) (Leekha, et al 2011. General Principles of Antimicrobial Therapy. Mayo Clin Proc. 86(2): 156-167). In certain embodiments, antibiotics can be used to selectively target bacteria of a specific niche. In some embodiments, antibiotics known to treat a particular infection that includes a cancer niche may be used to target cancer-associated microbes, including cancer-associated bacteria in that niche. In other embodiments, antibiotics are administered after the solid dosage form. In some embodiments, antibiotics are administered before the solid dosage form.


In some aspects, antibiotics can be selected based on their bactericidal or bacteriostatic properties. Bactericidal antibiotics include mechanisms of action that disrupt the cell wall (e.g., β-lactams), the cell membrane (e.g., daptomycin), or bacterial DNA (e.g., fluoroquinolones). Bacteriostatic agents inhibit bacterial replication and include sulfonamides, tetracyclines, and macrolides, and act by inhibiting protein synthesis. Furthermore, while some drugs can be bactericidal in certain organisms and bacteriostatic in others, knowing the target organism allows one skilled in the art to select an antibiotic with the appropriate properties. In certain treatment conditions, bacteriostatic antibiotics inhibit the activity of bactericidal antibiotics. Thus, in certain embodiments, bactericidal and bacteriostatic antibiotics are not combined.


Antibiotics include, but are not limited to aminoglycosides, ansamycins, carbacephems, carbapenems, cephalosporins, glycopeptides, lincosamides, lipopeptides, macrolides, monobactams, nitrofurans, oxazolidonones, penicillins, polypeptide antibiotics, quinolones, fluoroquinolone, sulfonamides, tetracyclines, and anti-mycobacterial compounds, and combinations thereof.


Aminoglycosides include, but are not limited to Amikacin, Gentamicin, Kanamycin, Neomycin, Netilmicin, Tobramycin, Paromomycin, and Spectinomycin. Aminoglycosides are effective, e.g., against Gram-negative bacteria, such as Escherichia coli, Klebsiella, Pseudomonas aeruginosa, and Francisella tularensis, and against certain aerobic bacteria but less effective against obligate/facultative anaerobes. Aminoglycosides are believed to bind to the bacterial 30S or 50S ribosomal subunit thereby inhibiting bacterial protein synthesis.


Ansamycins include, but are not limited to, Geldanamycin, Herbimycin, Rifamycin, and Streptovaricin. Geldanamycin and Herbimycin are believed to inhibit or alter the function of Heat Shock Protein 90.


Carbacephems include, but are not limited to, Loracarbef. Carbacephems are believed to inhibit bacterial cell wall synthesis.


Carbapenems include, but are not limited to, Ertapenem, Doripenem, Imipenem/Cilastatin, and Meropenem. Carbapenems are bactericidal for both Gram-positive and Gram-negative bacteria as broad-spectrum antibiotics. Carbapenems are believed to inhibit bacterial cell wall synthesis.


Cephalosporins include, but are not limited to, Cefadroxil, Cefazolin, Cefalotin, Cefalothin, Cefalexin, Cefaclor, Cefamandole, Cefoxitin, Cefprozil, Cefuroxime, Cefixime, Cefdinir, Cefditoren, Cefoperazone, Cefotaxime, Cefpodoxime, Ceftazidime, Ceftibuten, Ceftizoxime, Ceftriaxone, Cefepime, Ceftaroline fosamil, and Ceftobiprole. Selected Cephalosporins are effective, e.g., against Gram-negative bacteria and against Gram-positive bacteria, including Pseudomonas, certain Cephalosporins are effective against methicillin-resistant Staphylococcus aureus (MRSA). Cephalosporins are believed to inhibit bacterial cell wall synthesis by disrupting synthesis of the peptidoglycan layer of bacterial cell walls.


Glycopeptides include, but are not limited to, Teicoplanin, Vancomycin, and Telavancin. Glycopeptides are effective, e.g., against aerobic and anaerobic Gram-positive bacteria including MRSA and Clostridium difficile. Glycopeptides are believed to inhibit bacterial cell wall synthesis by disrupting synthesis of the peptidoglycan layer of bacterial cell walls.


Lincosamides include, but are not limited to, Clindamycin and Lincomycin. Lincosamides are effective, e.g., against anaerobic bacteria, as well as Staphylococcus, and Streptococcus. Lincosamides are believed to bind to the bacterial 50S ribosomal subunit thereby inhibiting bacterial protein synthesis.


Lipopeptides include, but are not limited to, Daptomycin. Lipopeptides are effective, e.g., against Gram-positive bacteria. Lipopeptides are believed to bind to the bacterial membrane and cause rapid depolarization.


Macrolides include, but are not limited to, Azithromycin, Clarithromycin, Dirithromycin, Erythromycin, Roxithromycin, Troleandomycin, Telithromycin, and Spiramycin. Macrolides are effective, e.g., against Streptococcus and Mycoplasma. Macrolides are believed to bind to the bacterial or 50S ribosomal subunit, thereby inhibiting bacterial protein synthesis.


Monobactams include, but are not limited to, Aztreonam. Monobactams are effective, e.g., against Gram-negative bacteria. Monobactams are believed to inhibit bacterial cell wall synthesis by disrupting synthesis of the peptidoglycan layer of bacterial cell walls.


Nitrofurans include, but are not limited to, Furazolidone and Nitrofurantoin.


Oxazolidonones include, but are not limited to, Linezolid, Posizolid, Radezolid, and Torezolid. Oxazolidonones are believed to be protein synthesis inhibitors.


Penicillins include, but are not limited to, Amoxicillin, Ampicillin, Azlocillin, Carbenicillin, Cloxacillin, Dicloxacillin, Flucloxacillin, Mezlocillin, Methicillin, Nafcillin, Oxacillin, Penicillin G, Penicillin V, Piperacillin, Temocillin and Ticarcillin. Penicillins are effective, e.g., against Gram-positive bacteria, facultative anaerobes, e.g., Streptococcus, Borrelia, and Treponema. Penicillins are believed to inhibit bacterial cell wall synthesis by disrupting synthesis of the peptidoglycan layer of bacterial cell walls.


Penicillin combinations include, but are not limited to, Amoxicillin/clavulanate, Ampicillin/sulbactam, Piperacillin/tazobactam, and Ticarcillin/clavulanate.


Polypeptide antibiotics include, but are not limited to, Bacitracin, Colistin, and Polymyxin B and E. Polypeptide Antibiotics are effective, e.g., against Gram-negative bacteria. Certain polypeptide antibiotics are believed to inhibit isoprenyl pyrophosphate involved in synthesis of the peptidoglycan layer of bacterial cell walls, while others destabilize the bacterial outer membrane by displacing bacterial counter-ions.


Quinolones and Fluoroquinolone include, but are not limited to, Ciprofloxacin, Enoxacin, Gatifloxacin, Gemifloxacin, Levofloxacin, Lomefloxacin, Moxifloxacin, Nalidixic acid, Norfloxacin, Ofloxacin, Trovafloxacin, Grepafloxacin, Sparfloxacin, and Temafloxacin. Quinolones/Fluoroquinolone are effective, e.g., against Streptococcus and Neisseria. Quinolones/Fluoroquinolone are believed to inhibit the bacterial DNA gyrase or topoisomerase IV, thereby inhibiting DNA replication and transcription.


Sulfonamides include, but are not limited to, Mafenide, Sulfacetamide, Sulfadiazine, Silver sulfadiazine, Sulfadimethoxine, Sulfamethizole, Sulfamethoxazole, Sulfanilimide, Sulfasalazine, Sulfisoxazole, Trimethoprim-Sulfamethoxazole (Co-trimoxazole), and Sulfonamidochrysoidine. Sulfonamides are believed to inhibit folate synthesis by competitive inhibition of dihydropteroate synthetase, thereby inhibiting nucleic acid synthesis.


Tetracyclines include, but are not limited to, Demeclocycline, Doxycycline, Minocycline, Oxytetracycline, and Tetracycline. Tetracyclines are effective, e.g., against Gram-negative bacteria. Tetracyclines are believed to bind to the bacterial 30S ribosomal subunit thereby inhibiting bacterial protein synthesis.


Anti-mycobacterial compounds include, but are not limited to, Clofazimine, Dapsone, Capreomycin, Cycloserine, Ethambutol, Ethionamide, Isoniazid, Pyrazinamide, Rifampicin, Rifabutin, Rifapentine, and Streptomycin.


Suitable antibiotics also include arsphenamine, chloramphenicol, fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin, quinupristin/dalfopristin, tigecycline, tinidazole, trimethoprim amoxicillin/clavulanate, ampicillin/sulbactam, amphomycin ristocetin, azithromycin, bacitracin, buforin II, carbomycin, cecropin Pl, clarithromycin, erythromycins, furazolidone, fusidic acid, Na fusidate, gramicidin, imipenem, indolicidin, josamycin, magainan II, metronidazole, nitroimidazoles, mikamycin, mutacin B-Ny266, mutacin B-JH1 140, mutacin J-T8, nisin, nisin A, novobiocin, oleandomycin, ostreogrycin, piperacillin/tazobactam, pristinamycin, ramoplanin, ranalexin, reuterin, rifaximin, rosamicin, rosaramicin, spectinomycin, spiramycin, staphylomycin, streptogramin, streptogramin A, synergistin, taurolidine, teicoplanin, telithromycin, ticarcillin/clavulanic acid, triacetyloleandomycin, tylosin, tyrocidin, tyrothricin, vancomycin, vemamycin, and virginiamycin.


In some embodiments, the additional pharmaceutical agent is an immunosuppressive agent, a DMARD, a pain-control drug, a steroid, a non-steroidal antiinflammatory drug (NSAID), or a cytokine antagonist, and combinations thereof. Representative agents include, but are not limited to, cyclosporin, retinoids, corticosteroids, propionic acid derivative, acetic acid derivative, enolic acid derivatives, fenamic acid derivatives, Cox-2 inhibitors, lumiracoxib, ibuprophen, cholin magnesium salicylate, fenoprofen, salsalate, difunisal, tolmetin, ketoprofen, flurbiprofen, oxaprozin, indomethacin, sulindac, etodolac, ketorolac, nabumetone, naproxen, valdecoxib, etoricoxib, MK0966; rofecoxib, acetominophen, Celecoxib, Diclofenac, tramadol, piroxicam, meloxicam, tenoxicam, droxicam, lornoxicam, isoxicam, mefanamic acid, meclofenamic acid, flufenamic acid, tolfenamic, valdecoxib, parecoxib, etodolac, indomethacin, aspirin, ibuprophen, firocoxib, methotrexate (MTX), antimalarial drugs (e.g., hydroxychloroquine and chloroquine), sulfasalazine, Leflunomide, azathioprine, cyclosporin, gold salts, minocycline, cyclophosphamide, D-penicillamine, minocycline, auranofin, tacrolimus, myocrisin, chlorambucil, TNF alpha antagonists (e.g., TNF alpha antagonists or TNF alpha receptor antagonists), e.g., ADALIMUMAB (Humira®), ETANERCEPT (Enbrel®), INFLIXIMAB (Remicade®; TA-650), CERTOLIZUMAB PEGOL (Cimzia®; CDP870), GOLIMUMAB (Simpom®; CNTO 148), ANAKINRA (Kineret®), RITUXIMAB (Rituxan®; MabThera®), ABATACEPT (Orencia®), TOCILIZUMAB (RoActemra/Actemra®), integrin antagonists (TYSABRI® (natalizumab)), IL-1 antagonists (ACZ885 (Ilaris)), Anakinra (Kineret®)), CD4 antagonists, IL-23 antagonists, IL-20 antagonists, IL-6 antagonists, BLyS antagonists (e.g., Atacicept, Benlysta®/LymphoStat-B® (belimumab)), p38 Inhibitors, CD20 antagonists (Ocrelizumab, Ofatumumab (Arzerra®)), interferon gamma antagonists (Fontolizumab), prednisolone, Prednisone, dexamethasone, Cortisol, cortisone, hydrocortisone, methylprednisolone, betamethasone, triamcinolone, beclometasome, fludrocortisone, deoxycorticosterone, aldosterone, Doxycycline, vancomycin, pioglitazone, SBI-087, SCIO-469, Cura-100, Oncoxin+Viusid, TwHF, Methoxsalen, Vitamin D—ergocalciferol, Milnacipran, Paclitaxel, rosig tazone, Tacrolimus (Prograf®), RADOO1, rapamune, rapamycin, fostamatinib, Fentanyl, XOMA 052, Fostamatinib disodium, rosightazone, Curcumin (Longvida™), Rosuvastatin, Maraviroc, ramipnl, Milnacipran, Cobiprostone, somatropin, tgAAC94 gene therapy vector, MK0359, GW856553, esomeprazole, everolimus, trastuzumab, JAK1 and JAK2 inhibitors, pan JAK inhibitors, e.g., tetracyclic pyridone 6 (P6), 325, PF-956980, denosumab, IL-6 antagonists, CD20 antagonistis, CTLA4 antagonists, IL-8 antagonists, IL-21 antagonists, IL-22 antagonist, integrin antagonists (Tysarbri® (natalizumab)), VGEF antagnosits, CXCL antagonists, MMP antagonists, defensin antagonists, IL-1 antagonists (including IL-1 beta antagonsits), and IL-23 antagonists (e.g., receptor decoys, antagonistic antibodies, etc.).


In some embodiments, the additional pharmaceutical agent is an immunosuppressive agent. Examples of immunosuppressive agents include, but are not limited to, corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, immunosuppressive drugs, cyclosporin A, mercaptopurine, azathiopurine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anti-cholinergic drugs for rhinitis, TLR antagonists, inflammasome inhibitors, anti-cholinergic decongestants, mast-cell stabilizers, monoclonal anti-IgE antibodies, vaccines (e.g., vaccines used for vaccination where the amount of an allergen is gradually increased), cytokine inhibitors, such as anti-IL-6 antibodies, TNF inhibitors such as infliximab, adalimumab, certolizumab pegol, golimumab, or etanercept, iand combinations thereof


Administration

In certain aspects, provided herein is a method of delivering a solid dosage form described herein to a subject. In some embodiments of the methods provided herein, the solid dosage form is administered in conjunction with the administration of an additional pharmaceutical agent. In some embodiments, the solid dosage form comprises a pharmaceutical agent that comprises bacteria and/or mEVs co-formulated with the additional pharmaceutical agent. In some embodiments, the solid dosage form is co-administered with the additional pharmaceutical agent. In some embodiments, the additional pharmaceutical agent is administered to the subject before administration of the solid dosage form (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or 55 minutes before, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or 23 hours before, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 days before). In some embodiments, the additional pharmaceutical agent is administered to the subject after administration of the solid dosage form (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or 55 minutes after, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or 23 hours after, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 days after). In some embodiments, the same mode of delivery is used to deliver both the solid dosage form and the additional pharmaceutical agent. In some embodiments, different modes of delivery are used to administer the solid dosage form and the additional pharmaceutical agent. For example, in some embodiments the solid dosage form is administered orally while the additional pharmaceutical agent is administered via injection (e.g., an intravenous, intramuscular and/or intratumoral injection).


In certain embodiments, the solid dosage form described herein can be administered in conjunction with any other conventional anti-cancer treatment, such as, for example, radiation therapy and surgical resection of the tumor. These treatments may be applied as necessary and/or as indicated and may occur before, concurrent with or after administration of the solid dosage form described herein.


The dosage regimen can be any of a variety of methods and amounts, and can be determined by one skilled in the art according to known clinical factors. As is known in the medical arts, dosages for any one patient can depend on many factors, including the subject's species, size, body surface area, age, sex, immunocompetence, and general health, the particular microorganism to be administered, duration and route of administration, the kind and stage of the disease, for example, tumor size, and other compounds such as drugs being administered concurrently or near-concurrently. In addition to the above factors, such levels can be affected by the infectivity of the microorganism, and the nature of the microorganism, as can be determined by one skilled in the art. In the present methods, appropriate minimum dosage levels of microorganisms can be levels sufficient for the microorganism to survive, grow and replicate. The dose of a pharmaceutical agent (e.g., in a solid dosage form) described herein may be appropriately set or adjusted in accordance with the dosage form, the route of administration, the degree or stage of a target disease, and the like. For example, the general effective dose of the agents may range between 0.01 mg/kg body weight/day and 1000 mg/kg body weight/day, between 0.1 mg/kg body weight/day and 1000 mg/kg body weight/day, 0.5 mg/kg body weight/day and 500 mg/kg body weight/day, 1 mg/kg body weight/day and 100 mg/kg body weight/day, or between 5 mg/kg body weight/day and 50 mg/kg body weight/day. The effective dose may be 0.01, 0.05, 0.1, 0.5, 1, 2, 3, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 500, or 1000 mg/kg body weight/day or more, but the dose is not limited thereto.


In some embodiments, the dose administered to a subject is sufficient to prevent disease (e.g., autoimmune disease, inflammatory disease, metabolic disease, dysbiosis, or cancer), delay its onset, or slow or stop its progression, or relieve one or more symptoms of the disease. One skilled in the art will recognize that dosage will depend upon a variety of factors including the strength of the particular agent (e.g., pharmaceutical agent) employed, as well as the age, species, condition, and body weight of the subject. The size of the dose will also be determined by the route, timing, and frequency of administration as well as the existence, nature, and extent of any adverse side-effects that might accompany the administration of a particular pharmaceutical agent and the desired physiological effect.


Suitable doses and dosage regimens can be determined by conventional range-finding techniques known to those of ordinary skill in the art. Generally, treatment is initiated with smaller dosages, which are less than the optimum dose of the compound. Thereafter, the dosage is increased by small increments until the optimum effect under the circumstances is reached. An effective dosage and treatment protocol can be determined by routine and conventional means, starting e.g., with a low dose in laboratory animals and then increasing the dosage while monitoring the effects, and systematically varying the dosage regimen as well. Animal studies are commonly used to determine the maximal tolerable dose (“MTD”) of bioactive agent per kilogram weight. Those skilled in the art regularly extrapolate doses for efficacy, while avoiding toxicity, in other species, including humans.


In accordance with the above, in therapeutic applications, the dosages of the pharmaceutical agents used in accordance with the invention vary depending on the active agent, the age, weight, and clinical condition of the recipient patient, and the experience and judgment of the clinician or practitioner administering the therapy, among other factors affecting the selected dosage. For example, for cancer treatment, the dose should be sufficient to result in slowing, and preferably regressing, the growth of a tumor and most preferably causing complete regression of the cancer, or reduction in the size or number of metastases. As another example, the dose should be sufficient to result in slowing of progression of the disease for which the subject is being treated, and preferably amelioration of one or more symptoms of the disease for which the subject is being treated.


Separate administrations can include any number of two or more administrations, including two, three, four, five or six administrations. One skilled in the art can readily determine the number of administrations to perform or the desirability of performing one or more additional administrations according to methods known in the art for monitoring therapeutic methods and other monitoring methods provided herein. Accordingly, the methods provided herein include methods of providing to the subject one or more administrations of a solid dosage form, where the number of administrations can be determined by monitoring the subject, and, based on the results of the monitoring, determining whether or not to provide one or more additional administrations. Deciding on whether or not to provide one or more additional administrations can be based on a variety of monitoring results.


The time period between administrations can be any of a variety of time periods. The time period between administrations can be a function of any of a variety of factors, including monitoring steps, as described in relation to the number of administrations, the time period for a subject to mount an immune response. In one example, the time period can be a function of the time period for a subject to mount an immune response; for example, the time period can be more than the time period for a subject to mount an immune response, such as more than about one week, more than about ten days, more than about two weeks, or more than about a month; in another example, the time period can be less than the time period for a subject to mount an immune response, such as less than about one week, less than about ten days, less than about two weeks, or less than about a month.


In some embodiments, the delivery of an additional pharmaceutical agent in combination with the solid dosage form described herein reduces the adverse effects and/or improves the efficacy of the additional pharmaceutical agent.


The effective dose of an additional pharmaceutical agent described herein is the amount of the additional pharmaceutical agent that is effective to achieve the desired therapeutic response for a particular subject, composition, and mode of administration, with the least toxicity to the subject. The effective dosage level can be identified using the methods described herein and will depend upon a variety of pharmacokinetic factors including the activity of the particular compositions or agents administered, the route of administration, the time of administration, the rate of excretion of the particular compound being employed, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compositions employed, the age, sex, weight, condition, general health and prior medical history of the subject being treated, and like factors well known in the medical arts. In general, an effective dose of an additional pharmaceutical agent will be the amount of the additional pharmaceutical agent which is the lowest dose effective to produce a therapeutic effect. Such an effective dose will generally depend upon the factors described above.


The toxicity of an additional pharmaceutical agent is the level of adverse effects experienced by the subject during and following treatment. Adverse events associated with additional therapy toxicity can include, but are not limited to, abdominal pain, acid indigestion, acid reflux, allergic reactions, alopecia, anaphylasix, anemia, anxiety, lack of appetite, arthralgias, asthenia, ataxia, azotemia, loss of balance, bone pain, bleeding, blood clots, low blood pressure, elevated blood pressure, difficulty breathing, bronchitis, bruising, low white blood cell count, low red blood cell count, low platelet count, cardiotoxicity, cystitis, hemorrhagic cystitis, arrhythmias, heart valve disease, cardiomyopathy, coronary artery disease, cataracts, central neurotoxicity, cognitive impairment, confusion, conjunctivitis, constipation, coughing, cramping, cystitis, deep vein thrombosis, dehydration, depression, diarrhea, dizziness, dry mouth, dry skin, dyspepsia, dyspnea, edema, electrolyte imbalance, esophagitis, fatigue, loss of fertility, fever, flatulence, flushing, gastric reflux, gastroesophageal reflux disease, genital pain, granulocytopenia, gynecomastia, glaucoma, hair loss, hand-foot syndrome, headache, hearing loss, heart failure, heart palpitations, heartburn, hematoma, hemorrhagic cystitis, hepatotoxicity, hyperamylasemia, hypercalcemia, hyperchloremia, hyperglycemia, hyperkalemia, hyperlipasemia, hypermagnesemia, hypernatremia, hyperphosphatemia, hyperpigmentation, hypertriglyceridemia, hyperuricemia, hypoalbuminemia, hypocalcemia, hypochloremia, hypoglycemia, hypokalemia, hypomagnesemia, hyponatremia, hypophosphatemia, impotence, infection, injection site reactions, insomnia, iron deficiency, itching, joint pain, kidney failure, leukopenia, liver dysfunction, memory loss, menopause, mouth sores, mucositis, muscle pain, myalgias, myelosuppression, myocarditis, neutropenic fever, nausea, nephrotoxicity, neutropenia, nosebleeds, numbness, ototoxicity, pain, palmar-plantar erythrodysesthesia, pancytopenia, pericarditis, peripheral neuropathy, pharyngitis, photophobia, photosensitivity, pneumonia, pneumonitis, proteinuria, pulmonary embolus, pulmonary fibrosis, pulmonary toxicity, rash, rapid heart beat, rectal bleeding, restlessness, rhinitis, seizures, shortness of breath, sinusitis, thrombocytopenia, tinnitus, urinary tract infection, vaginal bleeding, vaginal dryness, vertigo, water retention, weakness, weight loss, weight gain, and xerostomia. In general, toxicity is acceptable if the benefits to the subject achieved through the therapy outweigh the adverse events experienced by the subject due to the therapy.


Immune Disorders

In some embodiments, the methods and solid dosage forms described herein relate to the treatment or prevention of a disease or disorder associated a pathological immune response, such as an autoimmune disease, an allergic reaction and/or an inflammatory disease. In some embodiments, the disease or disorder is an inflammatory bowel disease (e.g., Crohn's disease or ulcerative colitis). In some embodiments, the disease or disorder is psoriasis. In some embodiments, the disease or disorder is atopic dermatitis.


The methods and solid dosage forms described herein can be used to treat any subject in need thereof. As used herein, a “subject in need thereof” includes any subject that has a disease or disorder associated with a pathological immune response (e.g., an inflammatory bowel disease), as well as any subject with an increased likelihood of acquiring a such a disease or disorder.


The solid dosage forms described herein can be used, for example, as a pharmaceutical composition for preventing or treating (reducing, partially or completely, the adverse effects of) an autoimmune disease, such as chronic inflammatory bowel disease, systemic lupus erythematosus, psoriasis, muckle-wells syndrome, rheumatoid arthritis, multiple sclerosis, or Hashimoto's disease; an allergic disease, such as a food allergy, pollenosis, or asthma; an infectious disease, such as an infection with Clostridium difficile; an inflammatory disease such as a TNF-mediated inflammatory disease (e.g., an inflammatory disease of the gastrointestinal tract, such as pouchitis, a cardiovascular inflammatory condition, such as atherosclerosis, or an inflammatory lung disease, such as chronic obstructive pulmonary disease); a pharmaceutical composition for suppressing rejection in organ transplantation or other situations in which tissue rejection might occur; a supplement, food, or beverage for improving immune functions; or a reagent for suppressing the proliferation or function of immune cells.


In some embodiments, the methods and solid dosage forms provided herein are useful for the treatment of inflammation. In certain embodiments, the inflammation of any tissue and organs of the body, including musculoskeletal inflammation, vascular inflammation, neural inflammation, digestive system inflammation, ocular inflammation, inflammation of the reproductive system, and other inflammation, as discussed below.


Immune disorders of the musculoskeletal system include, but are not limited, to those conditions affecting skeletal joints, including joints of the hand, wrist, elbow, shoulder, jaw, spine, neck, hip, knew, ankle, and foot, and conditions affecting tissues connecting muscles to bones such as tendons. Examples of such immune disorders, which may be treated with the methods and compositions described herein include, but are not limited to, arthritis (including, for example, osteoarthritis, rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, acute and chronic infectious arthritis, arthritis associated with gout and pseudogout, and juvenile idiopathic arthritis), tendonitis, synovitis, tenosynovitis, bursitis, fibrositis (fibromyalgia), epicondylitis, myositis, and osteitis (including, for example, Paget's disease, osteitis pubis, and osteitis fibrosa cystic).


Ocular immune disorders refers to a immune disorder that affects any structure of the eye, including the eye lids. Examples of ocular immune disorders which may be treated with the methods and compositions described herein include, but are not limited to, blepharitis, blepharochalasis, conjunctivitis, dacryoadenitis, keratitis, keratoconjunctivitis sicca (dry eye), scleritis, trichiasis, and uveitis.


Examples of nervous system immune disorders which may be treated with the methods and solid dosage forms described herein include, but are not limited to, encephalitis, Guillain-Barre syndrome, meningitis, neuromyotonia, narcolepsy, multiple sclerosis, myelitis and schizophrenia. Examples of inflammation of the vasculature or lymphatic system which may be treated with the methods and compositions described herein include, but are not limited to, arthrosclerosis, arthritis, phlebitis, vasculitis, and lymphangitis.


Examples of digestive system immune disorders which may be treated with the methods and solid dosage forms described herein include, but are not limited to, cholangitis, cholecystitis, enteritis, enterocolitis, gastritis, gastroenteritis, inflammatory bowel disease, ileitis, and proctitis. Inflammatory bowel diseases include, for example, certain art-recognized forms of a group of related conditions. Several major forms of inflammatory bowel diseases are known, with Crohn's disease (regional bowel disease, e.g., inactive and active forms) and ulcerative colitis (e.g., inactive and active forms) the most common of these disorders. In addition, the inflammatory bowel disease encompasses irritable bowel syndrome, microscopic colitis, lymphocytic-plasmocytic enteritis, coeliac disease, collagenous colitis, lymphocytic colitis and eosinophilic enterocolitis. Other less common forms of IBD include indeterminate colitis, pseudomembranous colitis (necrotizing colitis), ischemic inflammatory bowel disease, Behcet's disease, sarcoidosis, scleroderma, IBD-associated dysplasia, dysplasia associated masses or lesions, and primary sclerosing cholangitis.


Examples of reproductive system immune disorders which may be treated with the methods and solid dosage forms described herein include, but are not limited to, cervicitis, chorioamnionitis, endometritis, epididymitis, omphalitis, oophoritis, orchitis, salpingitis, tubo-ovarian abscess, urethritis, vaginitis, vulvitis, and vulvodynia.


The methods and solid dosage forms described herein may be used to treat autoimmune conditions having an inflammatory component. Such conditions include, but are not limited to, acute disseminated alopecia universalise, Behcet's disease, Chagas' disease, chronic fatigue syndrome, dysautonomia, encephalomyelitis, ankylosing spondylitis, aplastic anemia, hidradenitis suppurativa, autoimmune hepatitis, autoimmune oophoritis, celiac disease, Crohn's disease, diabetes mellitus type 1, giant cell arteritis, goodpasture's syndrome, Grave's disease, Guillain-Barre syndrome, Hashimoto's disease, Henoch-Schonlein purpura, Kawasaki's disease, lupus erythematosus, microscopic colitis, microscopic polyarteritis, mixed connective tissue disease, Muckle-Wells syndrome, multiple sclerosis, myasthenia gravis, opsoclonus myoclonus syndrome, optic neuritis, ord's thyroiditis, pemphigus, polyarteritis nodosa, polymyalgia, rheumatoid arthritis, Reiter's syndrome, Sjogren's syndrome, temporal arteritis, Wegener's granulomatosis, warm autoimmune haemolytic anemia, interstitial cystitis, Lyme disease, morphea, psoriasis, sarcoidosis, scleroderma, ulcerative colitis, and vitiligo.


The methods and solid dosage forms described herein may be used to treat T-cell mediated hypersensitivity diseases having an inflammatory component. Such conditions include, but are not limited to, contact hypersensitivity, contact dermatitis (including that due to poison ivy), uticaria, skin allergies, respiratory allergies (hay fever, allergic rhinitis, house dustmite allergy) and gluten-sensitive enteropathy (Celiac disease).


Other immune disorders which may be treated with the methods and solid dosage forms include, for example, appendicitis, dermatitis, dermatomyositis, endocarditis, fibrositis, gingivitis, glossitis, hepatitis, hidradenitis suppurativa, iritis, laryngitis, mastitis, myocarditis, nephritis, otitis, pancreatitis, parotitis, percarditis, peritonoitis, pharyngitis, pleuritis, pneumonitis, prostatistis, pyelonephritis, and stomatisi, transplant rejection (involving organs such as kidney, liver, heart, lung, pancreas (e.g., islet cells), bone marrow, cornea, small bowel, skin allografts, skin homografts, and heart valve xengrafts, sewrum sickness, and graft vs host disease), acute pancreatitis, chronic pancreatitis, acute respiratory distress syndrome, Sexary's syndrome, congenital adrenal hyperplasis, nonsuppurative thyroiditis, hypercalcemia associated with cancer, pemphigus, bullous dermatitis herpetiformis, severe erythema multiforme, exfoliative dermatitis, seborrheic dermatitis, seasonal or perennial allergic rhinitis, bronchial asthma, contact dermatitis, atopic dermatitis, drug hypersensistivity reactions, allergic conjunctivitis, keratitis, herpes zoster ophthalmicus, iritis and oiridocyclitis, chorioretinitis, optic neuritis, symptomatic sarcoidosis, fulminating or disseminated pulmonary tuberculosis chemotherapy, idiopathic thrombocytopenic purpura in adults, secondary thrombocytopenia in adults, acquired (autoimmune) haemolytic anemia, leukaemia and lymphomas in adults, acute leukaemia of childhood, regional enteritis, autoimmune vasculitis, multiple sclerosis, chronic obstructive pulmonary disease, solid organ transplant rejection, sepsis. Preferred treatments include treatment of transplant rejection, rheumatoid arthritis, psoriatic arthritis, multiple sclerosis, Type 1 diabetes, asthma, inflammatory bowel disease, systemic lupus erythematosus, psoriasis, chronic obstructive pulmonary disease, and inflammation accompanying infectious conditions (e.g., sepsis).


Metabolic Disorders

In some embodiments, the methods and solid dosage forms described herein relate to the treatment or prevention of a metabolic disease or disorder a, such as type II diabetes, impaired glucose tolerance, insulin resistance, obesity, hyperglycemia, hyperinsulinemia, fatty liver, non-alcoholic steatohepatitis, hypercholesterolemia, hypertension, hyperlipoproteinemia, hyperlipidemia, hypertriglylceridemia, ketoacidosis, hypoglycemia, thrombotic disorders, dyslipidemia, non-alcoholic fatty liver disease (NAFLD), Nonalcoholic Steatohepatitis (NASH) or a related disease. In some embodiments, the related disease is cardiovascular disease, atherosclerosis, kidney disease, nephropathy, diabetic neuropathy, diabetic retinopathy, sexual dysfunction, dermatopathy, dyspepsia, or edema. In some embodiments, the methods and pharmaceutical compositions described herein relate to the treatment of Nonalcoholic Fatty Liver Disease (NAFLD) and Nonalcoholic Steatohepatitis (NASH).


The methods and solid dosage forms described herein can be used to treat any subject in need thereof. As used herein, a “subject in need thereof” includes any subject that has a metabolic disease or disorder, as well as any subject with an increased likelihood of acquiring a such a disease or disorder.


The solid dosage forms described herein can be used, for example, for preventing or treating (reducing, partially or completely, the adverse effects of) a metabolic disease, such as type II diabetes, impaired glucose tolerance, insulin resistance, obesity, hyperglycemia, hyperinsulinemia, fatty liver, non-alcoholic steatohepatitis, hypercholesterolemia, hypertension, hyperlipoproteinemia, hyperlipidemia, hypertriglylceridemia, ketoacidosis, hypoglycemia, thrombotic disorders, dyslipidemia, non-alcoholic fatty liver disease (NAFLD), Nonalcoholic Steatohepatitis (NASH), or a related disease. In some embodiments, the related disease is cardiovascular disease, atherosclerosis, kidney disease, nephropathy, diabetic neuropathy, diabetic retinopathy, sexual dysfunction, dermatopathy, dyspepsia, or edema.


Cancer


In some embodiments, the methods and solid dosage forms described herein relate to the treatment of cancer. In some embodiments, any cancer can be treated using the methods described herein. Examples of cancers that may treated by methods and solid dosage forms described herein include, but are not limited to, cancer cells from the bladder, blood, bone, bone marrow, brain, breast, colon, esophagus, gastrointestine, gum, head, kidney, liver, lung, nasopharynx, neck, ovary, prostate, skin, stomach, testis, tongue, or uterus. In addition, the cancer may specifically be of the following histological type, though it is not limited to these: neoplasm, malignant; carcinoma; carcinoma, undifferentiated; giant and spindle cell carcinoma; small cell carcinoma; papillary carcinoma; squamous cell carcinoma; lymphoepithelial carcinoma; basal cell carcinoma; pilomatrix carcinoma; transitional cell carcinoma; papillary transitional cell carcinoma; adenocarcinoma; gastrinoma, malignant; cholangiocarcinoma; hepatocellular carcinoma; combined hepatocellular carcinoma and cholangiocarcinoma; trabecular adenocarcinoma; adenoid cystic carcinoma; adenocarcinoma in adenomatous polyp; adenocarcinoma, familial polyposis coli; solid carcinoma; carcinoid tumor, malignant; branchiolo-alveolar adenocarcinoma; papillary adenocarcinoma; chromophobe carcinoma; acidophil carcinoma; oxyphilic adenocarcinoma; basophil carcinoma; clear cell adenocarcinoma; granular cell carcinoma; follicular adenocarcinoma; papillary and follicular adenocarcinoma; nonencapsulating sclerosing carcinoma; adrenal cortical carcinoma; endometroid carcinoma; skin appendage carcinoma; apocrine adenocarcinoma; sebaceous adenocarcinoma; ceruminous adenocarcinoma; mucoepidermoid carcinoma; cystadenocarcinoma; papillary cystadenocarcinoma; papillary serous cystadenocarcinoma; mucinous cystadenocarcinoma; mucinous adenocarcinoma; signet ring cell carcinoma; infiltrating duct carcinoma; medullary carcinoma; lobular carcinoma; inflammatory carcinoma; paget's disease, mammary; acinar cell carcinoma; adenosquamous carcinoma; adenocarcinoma w/squamous metaplasia; thymoma, malignant; ovarian stromal tumor, malignant; thecoma, malignant; granulosa cell tumor, malignant; and roblastoma, malignant; sertoli cell carcinoma; leydig cell tumor, malignant; lipid cell tumor, malignant; paraganglioma, malignant; extra-mammary paraganglioma, malignant; pheochromocytoma; glomangiosarcoma; malignant melanoma; amelanotic melanoma; superficial spreading melanoma; malig melanoma in giant pigmented nevus; epithelioid cell melanoma; blue nevus, malignant; sarcoma; fibrosarcoma; fibrous histiocytoma, malignant; myxosarcoma; liposarcoma; leiomyosarcoma; rhabdomyosarcoma; embryonal rhabdomyosarcoma; alveolar rhabdomyosarcoma; stromal sarcoma; mixed tumor, malignant; mullerian mixed tumor; nephroblastoma; hepatoblastoma; carcinosarcoma; mesenchymoma, malignant; brenner tumor, malignant; phyllodes tumor, malignant; synovial sarcoma; mesothelioma, malignant; dysgerminoma; embryonal carcinoma; teratoma, malignant; struma ovarii, malignant; choriocarcinoma; mesonephroma, malignant; hemangiosarcoma; hemangioendothelioma, malignant; kaposi's sarcoma; hemangiopericytoma, malignant; lymphangiosarcoma; osteosarcoma; juxtacortical osteosarcoma; chondrosarcoma; chondroblastoma, malignant; mesenchymal chondrosarcoma; giant cell tumor of bone; ewing's sarcoma; odontogenic tumor, malignant; ameloblastic odontosarcoma; ameloblastoma, malignant; ameloblastic fibrosarcoma; pinealoma, malignant; chordoma; glioma, malignant; ependymoma; astrocytoma; protoplasmic astrocytoma; fibrillary astrocytoma; astroblastoma; glioblastoma; oligodendroglioma; oligodendroblastoma; primitive neuroectodermal; cerebellar sarcoma; ganglioneuroblastoma; neuroblastoma; retinoblastoma; olfactory neurogenic tumor; meningioma, malignant; neurofibrosarcoma; neurilemmoma, malignant; granular cell tumor, malignant; malignant lymphoma; Hodgkin's disease; Hodgkin's lymphoma; paragranuloma; malignant lymphoma, small lymphocytic; malignant lymphoma, large cell, diffuse; malignant lymphoma, follicular; mycosis fungoides; other specified non-Hodgkin's lymphomas; malignant histiocytosis; multiple myeloma; mast cell sarcoma; immunoproliferative small intestinal disease; leukemia; lymphoid leukemia; plasma cell leukemia; erythroleukemia; lymphosarcoma cell leukemia; myeloid leukemia; basophilic leukemia; eosinophilic leukemia; monocytic leukemia; mast cell leukemia; megakaryoblastic leukemia; myeloid sarcoma; and hairy cell leukemia.


In some embodiments, the cancer comprises breast cancer (e.g., triple negative breast cancer).


In some embodiments, the cancer comprises colorectal cancer (e.g., microsatellite stable (MSS) colorectal cancer).


In some embodiments, the cancer comprises renal cell carcinoma.


In some embodiments, the cancer comprises lung cancer (e.g., non small cell lung cancer).


In some embodiments, the cancer comprises bladder cancer.


In some embodiments, the cancer comprises gastroesophageal cancer.


In some embodiments, the methods and solid dosage forms provided herein relate to the treatment of a leukemia. The term “leukemia” includes broadly progressive, malignant diseases of the hematopoietic organs/systems and is generally characterized by a distorted proliferation and development of leukocytes and their precursors in the blood and bone marrow. Non-limiting examples of leukemia diseases include, acute nonlymphocytic leukemia, chronic lymphocytic leukemia, acute granulocytic leukemia, chronic granulocytic leukemia, acute promyelocytic leukemia, adult T-cell leukemia, aleukemic leukemia, a leukocythemic leukemia, basophilic leukemia, blast cell leukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross' leukemia, Rieder cell leukemia, Schilling's leukemia, stem cell leukemia, subleukemic leukemia, undifferentiated cell leukemia, hairy-cell leukemia, hemoblastic leukemia, hemocytoblastic leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, leukopenic leukemia, lymphatic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphogenous leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia, megakaryocytic leukemia, micromyeloblastic leukemia, monocytic leukemia, myeloblastic leukemia, myelocytic leukemia, myeloid granulocytic leukemia, myelomonocytic leukemia, Naegeli leukemia, plasma cell leukemia, plasmacytic leukemia, and promyelocytic leukemia.


In some embodiments, the methods and solid dosage forms provided herein relate to the treatment of a carcinoma. The term “carcinoma” refers to a malignant growth made up of epithelial cells tending to infiltrate the surrounding tissues, and/or resist physiological and non-physiological cell death signals and gives rise to metastases. Non-limiting exemplary types of carcinomas include, acinar carcinoma, acinous carcinoma, adenocystic carcinoma, adenoid cystic carcinoma, carcinoma adenomatosum, carcinoma of adrenal cortex, alveolar carcinoma, alveolar cell carcinoma, basal cell carcinoma, carcinoma basocellulare, basaloid carcinoma, basosquamous cell carcinoma, bronchioalveolar carcinoma, bronchiolar carcinoma, bronchogenic carcinoma, cerebriform carcinoma, cholangiocellular carcinoma, chorionic carcinoma, colloid carcinoma, comedo carcinoma, corpus carcinoma, cribriform carcinoma, carcinoma en cuirasse, carcinoma cutaneum, cylindrical carcinoma, cylindrical cell carcinoma, duct carcinoma, carcinoma durum, embryonal carcinoma, encephaloid carcinoma, epiennoid carcinoma, carcinoma epitheliale adenoides, exophytic carcinoma, carcinoma ex ulcere, carcinoma fibrosum, gelatiniform carcinoma, gelatinous carcinoma, giant cell carcinoma, signet-ring cell carcinoma, carcinoma simplex, small-cell carcinoma, solanoid carcinoma, spheroidal cell carcinoma, spindle cell carcinoma, carcinoma spongiosum, squamous carcinoma, squamous cell carcinoma, string carcinoma, carcinoma telangiectaticum, carcinoma telangiectodes, transitional cell carcinoma, carcinoma tuberosum, tuberous carcinoma, verrucous carcinoma, carcinoma villosum, carcinoma gigantocellulare, glandular carcinoma, granulosa cell carcinoma, hair-matrix carcinoma, hematoid carcinoma, hepatocellular carcinoma, Hurthle cell carcinoma, hyaline carcinoma, hypernephroid carcinoma, infantile embryonal carcinoma, carcinoma in situ, intraepidermal carcinoma, intraepithelial carcinoma, Krompecher's carcinoma, Kulchitzky-cell carcinoma, large-cell carcinoma, lenticular carcinoma, carcinoma lenticulare, lipomatous carcinoma, lymphoepithelial carcinoma, carcinoma medullare, medullary carcinoma, melanotic carcinoma, carcinoma molle, mucinous carcinoma, carcinoma muciparum, carcinoma mucocellulare, mucoepidermoid carcinoma, carcinoma mucosum, mucous carcinoma, carcinoma myxomatodes, naspharyngeal carcinoma, oat cell carcinoma, carcinoma ossificans, osteoid carcinoma, papillary carcinoma, periportal carcinoma, preinvasive carcinoma, prickle cell carcinoma, pultaceous carcinoma, renal cell carcinoma of kidney, reserve cell carcinoma, carcinoma sarcomatodes, schneiderian carcinoma, scirrhous carcinoma, and carcinoma scroti.


In some embodiments, the methods and solid dosage forms provided herein relate to the treatment of a sarcoma. The term “sarcoma” generally refers to a tumor which is made up of a substance like the embryonic connective tissue and is generally composed of closely packed cells embedded in a fibrillar, heterogeneous, or homogeneous substance. Sarcomas include, but are not limited to, chondrosarcoma, fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, Abemethy's sarcoma, adipose sarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma, chorio carcinoma, embryonal sarcoma, Wilms' tumor sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, immunoblastic sarcoma of B cells, lymphoma, immunoblastic sarcoma of T-cells, Jensen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukosarcoma, malignant mesenchymoma sarcoma, parosteal sarcoma, reticulocytic sarcoma, Rous sarcoma, serocystic sarcoma, synovial sarcoma, and telangiectaltic sarcoma.


Additional exemplary neoplasias that can be treated using the methods and solid dosage forms described herein include Hodgkin's Disease, Non-Hodgkin's Lymphoma, multiple myeloma, neuroblastoma, breast cancer, ovarian cancer, lung cancer, rhabdomyosarcoma, primary thrombocytosis, primary macroglobulinemia, small-cell lung tumors, primary brain tumors, stomach cancer, colon cancer, malignant pancreatic insulanoma, malignant carcinoid, premalignant skin lesions, testicular cancer, lymphomas, thyroid cancer, neuroblastoma, esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, cervical cancer, endometrial cancer, plasmacytoma, colorectal cancer, rectal cancer, and adrenal cortical cancer.


In some embodiments, the cancer treated is a melanoma. The term “melanoma” is taken to mean a tumor arising from the melanocytic system of the skin and other organs. Non-limiting examples of melanomas are Harding-Passey melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, acral-lentiginous melanoma, amelanotic melanoma, benign juvenile melanoma, Cloudman's melanoma, S91 melanoma, nodular melanoma subungal melanoma, and superficial spreading melanoma.


Particular categories of tumors that can be treated using methods and solid dosage forms described herein include lymphoproliferative disorders, breast cancer, ovarian cancer, prostate cancer, cervical cancer, endometrial cancer, bone cancer, liver cancer, stomach cancer, colon cancer, pancreatic cancer, cancer of the thyroid, head and neck cancer, cancer of the central nervous system, cancer of the peripheral nervous system, skin cancer, kidney cancer, as well as metastases of all the above. Particular types of tumors include hepatocellular carcinoma, hepatoma, hepatoblastoma, rhabdomyosarcoma, esophageal carcinoma, thyroid carcinoma, ganglioblastoma, fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, Ewing's tumor, leimyosarcoma, rhabdotheliosarcoma, invasive ductal carcinoma, papillary adenocarcinoma, melanoma, pulmonary squamous cell carcinoma, basal cell carcinoma, adenocarcinoma (well differentiated, moderately differentiated, poorly differentiated or undifferentiated), bronchioloalveolar carcinoma, renal cell carcinoma, hypernephroma, hypernephroid adenocarcinoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, testicular tumor, lung carcinoma including small cell, non-small and large cell lung carcinoma, bladder carcinoma, glioma, astrocyoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, retinoblastoma, neuroblastoma, colon carcinoma, rectal carcinoma, hematopoietic malignancies including all types of leukemia and lymphoma including: acute myelogenous leukemia, acute myelocytic leukemia, acute lymphocytic leukemia, chronic myelogenous leukemia, chronic lymphocytic leukemia, mast cell leukemia, multiple myeloma, myeloid lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, plasmacytoma, colorectal cancer, and rectal cancer.


Cancers treated in certain embodiments also include precancerous lesions, e.g., actinic keratosis (solar keratosis), moles (dysplastic nevi), acitinic chelitis (farmer's lip), cutaneous horns, Barrett's esophagus, atrophic gastritis, dyskeratosis congenita, sideropenic dysphagia, lichen planus, oral submucous fibrosis, actinic (solar) elastosis and cervical dysplasia.


Cancers treated in some embodiments include non-cancerous or benign tumors, e.g., of endodermal, ectodermal or mesenchymal origin, including, but not limited to cholangioma, colonic polyp, adenoma, papilloma, cystadenoma, liver cell adenoma, hydatidiform mole, renal tubular adenoma, squamous cell papilloma, gastric polyp, hemangioma, osteoma, chondroma, lipoma, fibroma, lymphangioma, leiomyoma, rhabdomyoma, astrocytoma, nevus, meningioma, and ganglioneuroma.


Other Diseases and Disorders

In some embodiments, the methods and solid dosage forms described herein relate to the treatment of liver diseases. Such diseases include, but are not limited to, Alagille Syndrome, Alcohol-Related Liver Disease, Alpha-1 Antitrypsin Deficiency, Autoimmune Hepatitis, Benign Liver Tumors, Biliary Atresia, Cirrhosis, Galactosemia, Gilbert Syndrome, Hemochromatosis, Hepatitis A, Hepatitis B, Hepatitis C, Hepatic Encephalopathy, Intrahepatic Cholestasis of Pregnancy (ICP), Lysosomal Acid Lipase Deficiency (LAL-D), Liver Cysts, Liver Cancer, Newborn Jaundice, Primary Biliary Cholangitis (PBC), Primary Sclerosing Cholangitis (PSC), Reye Syndrome, Type I Glycogen Storage Disease, and Wilson Disease.


The methods and solid dosage forms described herein may be used to treat neurodegenerative and neurological diseases. In certain embodiments, the neurodegenerative and/or neurological disease is Parkinson's disease, Alzheimer's disease, prion disease, Huntington's disease, motor neuron diseases (MND), spinocerebellar ataxia, spinal muscular atrophy, dystonia, idiopathicintracranial hypertension, epilepsy, nervous system disease, central nervous system disease, movement disorders, multiple sclerosis, encephalopathy, peripheral neuropathy or post-operative cognitive dysfunction.


Dysbiosis

In recent years, it has become increasingly clear that the gut microbiome (also called the “gut microbiota”) can have a significant impact on an individual's health through microbial activity and influence (local and/or distal) on immune and other cells of the host (Walker, W. A., Dysbiosis. The Microbiota in Gastrointestinal Pathophysiology. Chapter 25. 2017; Weiss and Thierry, Mechanisms and consequences of intestinal dysbiosis. Cellular and Molecular Life Sciences. (2017) 74(16):2959-2977. Zurich Open Repository and Archive, doi: https://doi.org/10.1007/s00018-017-2509-x)).


A healthy host-gut microbiome homeostasis is sometimes referred to as a “eubiosis” or “normobiosis,” whereas a detrimental change in the host microbiome composition and/or its diversity can lead to an unhealthy imbalance in the microbiome, or a “dysbiosis” (Hooks and O'Malley. Dysbiosis and its discontents. American Society for Microbiology. October 2017. Vol. 8. Issue 5. mBio 8:e01492-17. https://doi.org/10.1128/mBio.01492-17). Dysbiosis, and associated local or distal host inflammatory or immune effects, may occur where microbiome homeostasis is lost or diminished, resulting in: increased susceptibility to pathogens; altered host bacterial metabolic activity; induction of host proinflammatory activity and/or reduction of host anti-inflammatory activity. Such effects are mediated in part by interactions between host immune cells (e.g., T cells, dendritic cells, mast cells, NK cells, intestinal epithelial lymphocytes (IEC), macrophages and phagocytes) and cytokines, and other substances released by such cells and other host cells.


A dysbiosis may occur within the gastrointestinal tract (a “gastrointestinal dysbiosis” or “gut dysbiosis”) or may occur outside the lumen of the gastrointestinal tract (a “distal dysbiosis”). Gastrointestinal dysbiosis is often associated with a reduction in integrity of the intestinal epithelial barrier, reduced tight junction integrity and increased intestinal permeability. Citi, S. Intestinal Barriers protect against disease, Science 359:1098-99 (2018); Srinivasan et al., TEER measurement techniques for in vitro barrier model systems. J. Lab. Autom. 20:107-126 (2015). A gastrointestinal dysbiosis can have physiological and immune effects within and outside the gastrointestinal tract.


The presence of a dysbiosis has been associated with a wide variety of diseases and conditions including: infection, cancer, autoimmune disorders (e.g., systemic lupus erythematosus (SLE)) or inflammatory disorders (e.g., functional gastrointestinal disorders such as inflammatory bowel disease (IBD), ulcerative colitis, and Crohn's disease), neuroinflammatory diseases (e.g., multiple sclerosis), transplant disorders (e.g., graft-versus-host disease), fatty liver disease, type I diabetes, rheumatoid arthritis, Sjögren's syndrome, celiac disease, cystic fibrosis, chronic obstructive pulmonary disorder (COPD), and other diseases and conditions associated with immune dysfunction. Lynch et al., The Human Microbiome in Health and Disease, N. Engl. J. Med 0.375:2369-79 (2016), Carding et al., Dysbiosis of the gut microbiota in disease. Microb. Ecol. Health Dis. (2015); 26: 10: 3402/mehd.v26.2619; Levy et al, Dysbiosis and the Immune System, Nature Reviews Immunology 17:219 (April 2017)


Exemplary solid dosage forms disclosed herein can treat a dysbiosis and its effects by modifying the immune activity present at the site of dysbiosis. As described herein, such compositions can modify a dysbiosis via effects on host immune cells, resulting in, e.g., an increase in secretion of anti-inflammatory cytokines and/or a decrease in secretion of pro-inflammatory cytokines, reducing inflammation in the subject recipient or via changes in metabolite production.


Exemplary solid dosage forms disclosed herein that are useful for treatment of disorders associated with a dysbiosis contain one or more types of immunomodulatory bacteria (e.g., anti-inflammatory bacteria) and/or mEVs (microbial extracellular vesicles) derived from such bacteria. Such compositions are capable of affecting the recipient host's immune function, in the gastrointestinal tract, and/or a systemic effect at distal sites outside the subject's gastrointestinal tract.


Exemplary solid dosage forms disclosed herein that are useful for treatment of disorders associated with a dysbiosis contain a population of immunomodulatory bacteria of a single bacterial species (e.g., a single strain) (e.g., anti-inflammatory bacteria) and/or mEVs derived from such bacteria. Such compositions are capable of affecting the recipient host's immune function, in the gastrointestinal tract, and/or a systemic effect at distal sites outside the subject's gastrointestinal tract.


In one embodiment, solid dosage forms containing an isolated population of immunomodulatory bacteria (e.g., anti-inflammatory bacterial cells) and/or mEVs derived from such bacteria are administered (e.g., orally) to a mammalian recipient in an amount effective to treat a dysbiosis and one or more of its effects in the recipient. The dysbiosis may be a gastrointestinal tract dysbiosis or a distal dysbiosis.


In another embodiment, solid dosage forms of the instant invention can treat a gastrointestinal dysbiosis and one or more of its effects on host immune cells, resulting in an increase in secretion of anti-inflammatory cytokines and/or a decrease in secretion of pro-inflammatory cytokines, reducing inflammation in the subject recipient.


In another embodiment, the solid dosage forms can treat a gastrointestinal dysbiosis and one or more of its effects by modulating the recipient immune response via cellular and cytokine modulation to reduce gut permeability by increasing the integrity of the intestinal epithelial barrier.


In another embodiment, the solid dosage forms can treat a distal dysbiosis and one or more of its effects by modulating the recipient immune response at the site of dysbiosis via modulation of host immune cells.


Other exemplary solid dosage forms are useful for treatment of disorders associated with a dysbiosis, which compositions contain one or more types of bacteria and/or mEVs capable of altering the relative proportions of host immune cell subpopulations, e.g., subpopulations of T cells, immune lymphoid cells, dendritic cells, NK cells and other immune cells, or the function thereof, in the recipient.


Other exemplary solid dosage forms are useful for treatment of disorders associated with a dysbiosis, which compositions contain a population of immunomodulatory bacteria and/or mEVs of a single bacterial species, e.g., a single strain) capable of altering the relative proportions of immune cell subpopulations, e.g., T cell subpopulations, immune lymphoid cells, NK cells and other immune cells, or the function thereof, in the recipient subject.


In one embodiment, the invention provides methods of treating a gastrointestinal dysbiosis and one or more of its effects by orally administering to a subject in need thereof a solid dosage form which alters the microbiome population existing at the site of the dysbiosis. The solid dosage forms can contain one or more types of immunomodulatory bacteria and/or mEVs or a population of immunomodulatory bacteria and/or mEVs of a single bacterial species (e.g., a single strain).


In one embodiment, the invention provides methods of treating a distal dysbiosis and one or more of its effects by orally administering to a subject in need thereof a solid dosage form which alters the subject's immune response outside the gastrointestinal tract. The solid dosage forms can contain one or more types of immunomodulatory bacteria and/or mEVs or a population of immunomodulatory bacteria and/or mEVs of a single bacterial species (e.g., a single strain).


In exemplary embodiments, solid dosage forms useful for treatment of disorders associated with a dysbiosis stimulate secretion of one or more anti-inflammatory cytokines by host immune cells. Anti-inflammatory cytokines include, but are not limited to, IL-10, IL-13, IL-9, IL-4, IL-5, TGFβ, and combinations thereof. In other exemplary embodiments, solid dosage forms useful for treatment of disorders associated with a dysbiosis that decrease (e.g., inhibit) secretion of one or more pro-inflammatory cytokines by host immune cells. Pro-inflammatory cytokines include, but are not limited to, IFNγ, IL-12p′70, IL-1α, IL-6, IL-8, MCP1, MIP1α, MIP1β, TNFα, and combinations thereof. Other exemplary cytokines are known in the art and are described herein.


In another aspect, the invention provides a method of treating or preventing a disorder associated with a dysbiosis in a subject in need thereof, comprising administering (e.g., orally administering) to the subject a solid dosage form in the form of a probiotic or medical food comprising bacteria and/or mEVs in an amount sufficient to alter the microbiome at a site of the dysbiosis, such that the disorder associated with the dysbiosis is treated.


In another embodiment, a solid dosage form of the instant invention in the form of a probiotic or medical food may be used to prevent or delay the onset of a dysbiosis in a subject at risk for developing a dysbiosis.


Methods of Making Enhanced Bacteria

In certain aspects, provided herein are methods of making engineered bacteria for the production of the bacteria and/or mEVs (such as smEVs and/or pmEVs) described herein. In some embodiments, the engineered bacteria are modified to enhance certain desirable properties. For example, in some embodiments, the engineered bacteria are modified to enhance the immunomodulatory and/or therapeutic effect of the bacteria and/or mEVs (such as smEVs and/or pmEVs) (e.g., either alone or in combination with another pharmaceutical agent), to reduce toxicity and/or to improve bacterial and/or mEV (such as smEV and/or pmEV) manufacturing (e.g., higher oxygen tolerance, improved freeze-thaw tolerance, shorter generation times). The engineered bacteria may be produced using any technique known in the art, including but not limited to site-directed mutagenesis, transposon mutagenesis, knock-outs, knock-ins, polymerase chain reaction mutagenesis, chemical mutagenesis, ultraviolet light mutagenesis, transformation (chemically or by electroporation), phage transduction, directed evolution, CRISPR/Cas9, or any combination thereof.


In some embodiments of the methods provided herein, the bacterium is modified by directed evolution. In some embodiments, the directed evolution comprises exposure of the bacterium to an environmental condition and selection of bacterium with improved survival and/or growth under the environmental condition. In some embodiments, the method comprises a screen of mutagenized bacteria using an assay that identifies enhanced bacterium. In some embodiments, the method further comprises mutagenizing the bacteria (e.g., by exposure to chemical mutagens and/or UV radiation) or exposing them to a pharmaceutical agent (e.g., antibiotic) followed by an assay to detect bacteria having the desired phenotype (e.g., an in vivo assay, an ex vivo assay, or an in vitro assay).


Gamma-Irradiation: Sample Protocol:

Powders are gamma-irradiated at 17.5 kGy radiation unit at ambient temperature. Frozen biomasses are gamma-irradiated at 25 kGy radiation unit in the presence of dry ice.


Frozen Biomass Preparation: Sample Protocol


After a desired level of bacterial culture growth is achieved, centrifuge cultures, discard the supernatant, leaving the pellet as dry as possible. Vortex the pellet to loosen the biomass. Resuspend pellet in desired cryoprotectant solution, transfer to cryogenic tube and snap freeze in liquid nitrogen. Store in −80 degree C. freezer.


Powder Preparation: Sample Protocol

After desired level of bacterial culture growth is achieved, centrifuge cultures, discard the supernatant, leaving the pellet as dry as possible. Resuspend pellet in desired cryoprotectant solution to create a formulated cell paste. The cryoprotectant may contain, e.g., maltodextrin, sodium ascorbate, sodium glutamate, and/or calcium chloride. Load the formulated cell paste onto stainless steel trays and load into a freeze drier, e.g., operating in automated mode with defined cycle parameters. The freeze dried product is fed into a milling machine and the resulting powder is collected.


Powders are stored (e.g., in vacuum sealed bags) at 2-8 degrees C. (e.g., at 4 degrees C.), e.g., in a desiccator.


EXAMPLES
Example 1: Preparation of Lactococcus lactis spp. Cremoris Powder

The fermentation broth was harvested by continuous centrifugation with a flow rate of 2500 L/h and expulsion time of 150 seconds. The concentrated cells were collected and the supernatant is discarded.


The cryoprotectant solution components were maltodextrin (16% w/w), sodium ascorbate (8% w/w), sodium glutamate (8% w/w), and calcium chloride (8% w/w). They were first dissolved in a mixing tank and pasteurized; the solution was cooled to 4-10 degrees C.


The cooled cryoprotectant solution was added to the concentrated cells at a ratio of 25% (w/w) and mixed to give a formulated cell paste.


The formulated cell paste was loaded onto multiple stainless-steel trays. The freeze-drier was operated in an automated mode with defined cycle parameters. At the end of cycle, the freeze-dried product was removed from the tray and stored in multiple polyethylene bags prior to milling.


The freeze-dried product was fed into a milling machine and collected into a double polyethylene bags. The bags were checked with a metal detector (given the milling machine is a metal blender) and then stored at 2-8m degrees C. prior to final packaging.


Freeze-dried powder (1 kg aliquots) was placed into a polyethylene bag which was then packed into a PET-AL-PE foil pouch and heat sealed. Long term storage conditions for the finished pouches were 2-8 degrees C.


Example 2: Enteric Coated Minitablets Significantly Enhance L. lactis Spp. Cremoris Pharmacological Activity at Low Doses

Method: Mice were immunized intra-dermally with a KLH-DTH emulsion on Day 0. Mice were dosed with either dexamethasone intraperitoneally (17 ug per mouse in 100 ul of PBS) as a positive control, or orally with sucrose vehicle alone as a negative control, or with Lactococcus lactis spp. Cremoris powder resuspended in a sucrose delivery buffer or with enteric coated 2 mm minitablets containing different doses of Lactococcus lactis spp. Cremoris powder (0.1 mg, 0.35 mg, 1 mg, or 3.5 mg) (see FIG. 1) on days 1-8. The coating is provided in Table 5. On day 8, mice were challenged intra-dermally in the left ear with bug of KLH and 24 hours later the change in ear thickness from baseline was assessed.


Results: When delivered in enteric coated minitablets, 3.5 mg and 1 mg doses of L. lactis spp. Cremoris powder led to a significant reduction in ear swelling compared to vehicle control.









TABLE 5







Enteric coating (on dry basis) on L. lactis


spp. Cremoris minitablets (2 mm)










Enteric coating
Enteric coating (mg/cm2


Component
(mg)
surface)












EUDRAGIT ® L 30 D-55
0.97
6.6


Triethylcitrate
0.19
1.32


Talc
0.48
3.3









Example 3: Methacrylic Acrylate Copolymer Coating

Table 6 presents a coating suspension including Kollicoat MAE 100P as the enteric polymer, plasticizers (1,2-propylene glycol, triethyl citrate or polyethylene glycols) ranges from 10-25% based on the polymer weight, and anti-tacking agent ranges from 15-25% based on the polymer weight.









TABLE 6







Kollicoat ® Coating Suspension Composition











Excipient
Function
(% w/w)















Kollicoat ® MAE 100P
Enteric Polymer
15.00



Triethyl Citrate (TEC)
Plasticizer
2.25



Talc
Anti-tacking
3.00




agent/Pigment



Water

79.75



Total

100.00










Coating Suspension Preparation Procedure





    • a. Divided the water into three portions

    • b. Dissolved TEC into portion 1 water (solution 1)

    • c. Re-dispersed polymer into portion 2 water slowly, stirred with a magnetic stirring bar for 2 hrs, ensured polymer was fully hydrated/dispersed with no lumps (suspension 2)

    • d. Dispensed talc into portion 3 water slowly to hydrate, homogenized the talc suspension with a Silverson high shear homogenizer for 3 minutes at 6000 RPM to ensure no lump (suspension 3)

    • e. Added solution 1 into suspension 2, followed by the addition of suspension 3

    • f. Mixed for 15 minutes and pass the suspension through USP #60 mesh

    • g. The final suspension was subject for coating





Coating Equipment and Processing Parameters









TABLE 7







Process 1 (Mini tablets)










Coating Equipment
VFC-Lab Micro Fluid Bed















Batch size
20
g



Nozzle diameter
0.8
mm



Spray rate
0.5-0.8
g/min



Nozzle air
21-25
PSI



Inlet air Tm
50-55°
C.



Exhaust Tm
34-37°
C.



Pump rate
10-12
RPM

















TABLE 8







Process 2 (Single Tablet)










Coating Equipment
O'hara LC M10 Pan Coater















Batch size
650
g



Nozzle diameter
0.8
mm



Spray rate
5
g/min



Atomization Air Pressure
25.4
PSI



Pattern Air Pressure
20.5
PSI



Supply Air Volume
90
cfm



Inlet air Tm
47-50°
C.



Exhaust Tm
35-38°
C.



Drum Size
12
in



Drum Speed
12
RPM










Example 4: Coating Tablets

Tablets of Prevotella Strain B 50329 (NRRL accession number B 50329) and tablets of Veillonella bacteria (deposited as ATCC designation number PTA-125691) were prepared. Placebo tablets were also coated.


The tablets of Prevotella Strain B 50329 were 650 mg. Placebo tablets were also prepared.


The tablets of the Veillonella strain were 400 mg. Tablets were prepared in two strengths (high and low doses). Placebo tablets were also prepared.


Table 9 provides the formulation compositions of the coating suspensions.









TABLE 9







Formulation compositions of coating suspensions










Sub-coat
Top-coat (Enteric)



Composition %
Composition %


Material
(w/w)
(w/w)












Kollidon MAE 100P

15.00


TEC

2.25


Talc

3.00


Additional Water

79.75


Opadry II White
15.0



Product code: 85F18422


WFI
85.0



Total
100.0
100.0









The tablets were coated as follows.


Coating Suspension Manufacturing Procedure:





    • 1. Divided the water into two portions and dispensed part one of the water for injection into a tared stainless-steel vessel.

    • 2. Weighed and dispensed the Triethyl Citrate into a suitable tared container.

    • 3. Added the dispensed Triethyl Citrate to the water while mixing with the overhead stirrer.

    • 4. Weighed and dispensed the Talc into a suitable tared container.

    • 5. Added the dispensed Talc slowly to the water/Triethyl Citrate solution, while mixing with the overhead stirrer.

    • 6. Once the Talc was fully hydrated, transferred the vessel to the Silverson. Homogenized for a minimum of 10 minutes, ensuring that all Talc had been fully dispersed/homogenized, without any lumps and with no material stuck to the mixer head.

    • 7. Dispensed Part Two of the Water for injection into a tared stainless-steel vessel.

    • 8. Weighed and dispensed the Kollicoat into a suitable tared container.

    • 9. Added the dispensed Kollicoat slowly to the water from step 7 while mixing with the overhead stirrer.

    • 10. Continued mixing until all the Kollicoat had been added and is fully hydrated and dispersed without any lumps and with no material stuck to the paddle.

    • 11. Transferred the Water/Triethyl Citrate/Talc suspension to the overhead stirrer and started mixing.

    • 12. Whilst continuing to mix, transferred the Kollicoat suspension into the vessel. Mixed for a minimum of 45 minutes at an appropriate speed to form a vortex without any aeration.

    • 13. Passed the coating suspension through a 500 μm sieve into a stainless-steel vessel. Ensured all solids passed through the mesh.





Table 10 provides the process parameters for enteric coating.









TABLE 10







Process Parameters of Enteric coating










Active
Placebo













Bed Temperature (° C.)
30-35
30-35


Drum Speed (rpm)
17
17


Inlet Airflow (m3/hr)
170
170-180


Cabinet Pressure (Pa)
−60
−60


Inlet Air Temperature (° C.)
46-49
46-52


Atomising Air Pressure
1.6
1.6


(bar)


Spray Rate
6 g/min/kg-5.9 g/min
6 g/min/kg-5.8 g/min



consistent - 1450 capsules
consistent - 1456 tablets


Distance to bed
15 cm
15 cm


Angle to capsule bed
90-15° to the bed
90-15° to the bed


Baffles
No (batch too big)
No (batch too big)


Nozzle size
0.8 mm
0.8 mm


Drum size
15″ drum
15″ drum


Coating efficiency overall
93.5%
96.0%









Table 11 provides the disintegration results for the Prevotella Strain B 50329 (active) and placebo tablets.









TABLE 11








Prevotella Strain B Disintegration Results










Results



(hh:mm:ss)











Batch
Storage
Time Point
0.1M
6.8 pH


Reference
Condition
(Months)
HCl
Buffer





Active
2-8° C.
Initial
DND*
First: 00:12:56






Last: 00:14:36


Placebo


DND
First: 00:10:21






Last: 00:14:10


Active

T = 1 month
DND
First: 00:13:09






Last: 00:15:11


Placebo


DND
First: 00:06:21






Last: 00:07:41


Active
25° C., 60%
T = 1 month
DND
First: 00:12:18






Last: 00:15:18


Placebo
RH

DND
First: 00:06:26






Last: 00:08:23


Active
30° C., 65%
T = 1 month
DND
First: 00:14:06






Last: 00:15:50


Placebo
RH

DND
First: 00:07:05






Last: 00:09:04


Active
40° C., 75%
T = 1 month
DND
First: 00:11:47






Last: 00:13:07


Placebo
RH

DND
First: 00:08:05






Last: 00:09:16





DND*: Did not disintegrate;


RH: relative humidity






Table 12 provides the disintegration results for the high and low dose tablets of the Veillonella strain.









TABLE 12








Veillonella Tablets Disintegration Results











Results (hh:mm:ss)












Batch
Storage
Time Point
0.1M
6.8 pH


Reference
Condition
(Months)
HCl
Buffer





High Dose
2-8° C.
Initial
DND*
00:19:08


Low Dose
2-8° C.
Initial
DND*
00:09:05





*DND—Did not disintegrate






Example 5: Coating Capsules

Capsules were prepared for:

    • Prevotella Strain B 50329 (NRRL accession number B 50329)
    • Veillonella bacteria (deposited as ATCC designation number PTA-125691)
    • Lactococcus lactis cremoris Strain A (deposited as ATCC designation number PTA-125368)
    • Bifidobacterium bacteria (deposited as ATCC designation number PTA-125097)


The capsules were all size 0.


Capsules of the Veillonella strain were prepared in two strengths (high and low doses).


Capsules were banded with an HPMC-based banding solution prior to enteric coating.


Table 13 provides the formulation compositions of the coating suspensions.









TABLE 13







Composition of Coating Solutions








Coating Suspension



Ingredients













Eudragit L30-D55
Enteric Coating Agent
39.72
USP/Ph. Eur.


Triethyl citrate
Plasticizer
2.31
USP/Ph. Eur.


Talc
Antiadhesive
5.78
USP/Ph. Eur.


Water for Injectiona
Solvent
52.19
USP/Ph. Eur.






aRemoved during processing







The capsules were coated as follows:


Coating Suspension Preparation Procedure:





    • 1. Weighed and dispensed the Water for injection into a tared stainless-steel vessel.

    • 2. Weighed and dispensed the Triethyl Citrate into a suitable tared container.

    • 3. Weighed and dispensed the Talc into a suitable tared container.

    • 4. Added the Triethyl Citrate and Talc to the water and dispersed by stirring gently with a palette knife until there was no talc floating on the surface of the water. Ensured that the talc was fully wetted before commencing stirring.

    • 5. Homogenized using the Silverson mixer for a minimum of 10 mins.

    • 6. Weighed and dispensed the Eudragit L30-D55 into a suitable tared container.

    • 7. Stirred the Eudragit L30-D55 into the Triethyl Citrate/Talc suspension using an overhead mixer. Recorded the mixing speed. Maintained sufficient mixing to prevent further air ingress.

    • 8. Continued mixing for a minimum of 30 minutes.

    • 9. Passed the coating suspension through a 500 μm sieve into a second stainless steel vessel.





Table 14 provides the process parameters of enteric coating.









TABLE 14







Process Parameters of Enteric Coating










Parameter
Settings







Bed Temperature (° C.)
26-30



Inlet Airflow (m3/hr)
150-180



Drum Speed (RPM)
18



Cabinet Pressure (Pa)
−60



Inlet Air Temperature (° C.)
45



Atomising Air Pressure (bar)
1.4











Spray Rate
12
g/min/kg



Distance to bed
15
cm










Angle to capsule bed
90-15° to the bed











Nozzle size
0.8
mm










Drum size
15″ drum










Table 15 provides the disintegration results for Prevotella Strain B capsules.









TABLE 15







Disintegration results (Prevotella Strain B)











Time
Results (hh:mm:ss)














Batch
Storage
(Months)
0.1M
6.8 pH



Reference
Condition
Point
HCl
Buffer







Prevotella
2-8° C.
Initial
DND*
00:10:10



active







DND*: Did not disintegrate






Table 16 provides the disintegration results for the Veillonella strain capsules.









TABLE 16







Disintegration Results (Veillonella)









Results



(hh:mm:ss)












Storage
Time Point
0.1M
6.8 pH


Batch Reference
Condition
(Months)
HCl
Buffer





Low dose
2-8° C.
Initial
DND*
First: 00:05:42






Last: 00:07:05


High dose

Initial
DND
First: 00:06:04






Last: 00:13:28





*DND—Did not disintegrate






Example 6: Representative Strains as Sources for EVs

Secreted microbial extracellular vesicles (smEVs) were isolated from the strains listed in Table J. Information on the Gram staining, cell wall structure, and taxonomic classification for each strain is also provided in Table J.


Bacteria of the taxonomic groups listed in Table J (e.g., class, order, family, genus, species or strain) can be used in the solid dosage forms described herein.


mEVs of bacteria of the taxonomic groups listed in Table J (e.g., class, order, family, genus, species or strain) can be used in the solid dosage forms described herein.









TABLE J







Strains from which extracellular vesicles (EVs) were isolated















Cell








envelope






Strain
Gram-stain
structure
Phylum
Class
Order
Family






Parabacteroides distasonis

Gram-stain-
diderm
Bacteroidota
Bacteroidia
Bacteroidales
Porphyromonadaceae


DRLU022118 A ILEUM-6
negative








Parabacteroides goldsteinii S4

Gram-stain-
diderm
Bacteroidota
Bacteroidia
Bacteroidales
Porphyromonadaceae



negative








Prevotella histicola

Gram-stain-
diderm
Bacteroidota
Bacteroidia
Bacteroidales
Prevotellaceae



negative








Prevotella histicola

Gram-stain-
diderm
Bacteroidota
Bacteroidia
Bacteroidales
Prevotellaceae



negative








Fournierella massiliensis S10

Gram-stain-
monoderm
Firmicutes
Clostridia
Eubacteriales
Oscillospiraceae


GIMucosa-297
negative




(formely








Ruminococcaceae)



Harryflintia acetispora S4-M5

Gram-stain-
monoderm
Firmicutes
Clostridia
Eubacteriales
Oscillospiraceae



negative








Blautia massiliensis S1046-4A5

Gram-stain-
monoderm
Firmicutes
Clostridia
Eubacteriales
Lachnospiraceae



negative








Mediterraneibacter/[Ruminococcus]

Gram-stain-
monoderm
Firmicutes
Clostridia
Eubacteriales
Lachnospiraceae



gnavus S10 GIMucosa-412

negative








Clostridioides difficile S10 GImucosa-

Gram-stain-
monoderm
Firmicutes
Clostridia
Eubacteriales
Peptostreptococcaceae


525
positive








Aminipila sp. S16-M4

Gram-stain-
monoderm
Firmicutes
Clostridia
Eubacteriales
Clostridiales Family



positive




XIII/Incertae sedis








41/[Eubacteriales, no








family]



Megasphaera sp. S29-N3

Gram-stain-
diderm
Firmicutes
Negativicutes
Veillonellales
Veillonellaceae



negative








Megasphaera sp. S1007

Gram-stain-
diderm
Firmicutes
Negativicutes
Veillonellales
Veillonellaceae



negative








Selenomonas felix S34N-300R

Gram-stain-
diderm
Firmicutes
Negativicutes
Selenomonadales
Selenomonadaceae



negative








Veillonella parvula S14Ileum-201

Gram-stain-
diderm
Firmicutes
Negativicutes
Veillonellales
Veillonellaceae



negative








Propionispora sp. DSM100705-1A

Gram-stain-
diderm
Firmicutes
Negativicutes
Selenomonadales
Sporomusaceae



negative








Rarimicrobium hominis S24RS2-T2-5

Gram-stain-
diderm
Synergistota
Synergistia
Synergistales
Synergistaceae



negative








Cloacibacillus evryensis S29-M8

Gram-stain-
diderm
Synergistota
Synergistia
Synergistales
Synergistaceae



negative








Veillonella parvula S14-205

Gram-stain-
diderm
Firmicutes
Negativicutes
Veillonellales
Veillonellaceae



negative








Veillonella sp/dispar ECD01-DP-201

Gram-stain-
diderm
Firmicutes
Negativicutes
Veillonellales
Veillonellaceae



negative








Veillonella parvulal dispar ECD01-

Gram-stain-
diderm
Firmicutes
Negativicutes
Veillonellales
Veillonellaceae


DP-223
negative








Veillonella parvula S16 GIMucosa-95

Gram-stain-
diderm
Firmicutes
Negativicutes
Veillonellales
Veillonellaceae



negative









Example 7: Delayed-Type Hypersensitivity (DTH) is an Animal Model

Delayed-type hypersensitivity (DTH) is an animal model of atopic dermatitis (or allergic contact dermatitis), as reviewed by Petersen et al. (In vivo pharmacological disease models for psoriasis and atopic dermatitis in drug discovery. Basic & Clinical Pharm & Toxicology. 2006. 99(2): 104-115; see also Irving C. Allen (ed.) Mouse Models of Innate Immunity: Methods and Protocols, Methods in Molecular Biology, 2013. vol. 1031, DOI 10.1007/978-1-62703-481-4_13). Several variations of the DTH model have been used and are well known in the art (Irving C. Allen (ed.). Mouse Models of Innate Immunity: Methods and Protocols, Methods in Molecular Biology. Vol. 1031, DOI 10.1007/978-1-62703-481-4_13, Springer Science+Business Media, LLC 2013).


DTH can be induced in a variety of mouse and rat strains using various haptens or antigens, for example an antigen emulsified with an adjuvant. DTH is characterized by sensitization as well as an antigen-specific T cell-mediated reaction that results in erythema, edema, and cellular infiltration—especially infiltration of antigen presenting cells (APCs), eosinophils, activated CD4+ T cells, and cytokine-expressing Th2 cells.


Generally, mice are primed with an antigen administered in the context of an adjuvant (e.g., Complete Freund's Adjuvant) in order to induce a secondary (or memory) immune response measured by swelling and antigen-specific antibody titer.


Dexamethasone, a corticosteroid, is a known anti-inflammatory that ameliorates DTH reactions in mice and serves as a positive control for suppressing inflammation in this model (Taube and Carlsten, Action of dexamethasone in the suppression of delayed-type hypersensitivity in reconstituted SCID mice. Inflamm Res. 2000. 49(10): 548-52). For the positive control group, a stock solution of 17 mg/mL of Dexamethasone is prepared on Day 0 by diluting 6.8 mg Dexamethasone in 400 μL 96% ethanol. For each day of dosing, a working solution is prepared by diluting the stock solution 100× in sterile PBS to obtain a final concentration of 0.17 mg/mL in a septum vial for intraperitoneal dosing. Dexamethasone-treated mice receive 100 μL Dexamethasone i.p. (5 mL/kg of a 0.17 mg/mL solution). Frozen sucrose serves as the negative control (vehicle).


Solid dosage forms are tested for their efficacy in the mouse model of DTH, either alone or in combination, with or without the addition of other anti-inflammatory treatments. For example, 6-8 week old C57Bl/6 mice are obtained from Taconic (Germantown, NY), or other vendor. Groups of mice are administered four subcutaneous (s.c.) injections at four sites on the back (upper and lower) of antigen (e.g., Ovalbumin (OVA) or Keyhole Limpet Hemocyanin (KLH)) in an effective dose (e.g., 50 ul total volume per site). For a DTH response, animals are injected intradermally (i.d.) in the ears under ketamine/xylazine anesthesia (approximately 50 mg/kg and 5 mg/kg, respectively). Some mice serve as control animals. Some groups of mice are challenged with 10 ul per ear (vehicle control (0.01% DMSO in saline) in the left ear and antigen (21.2 ug (12 nmol) in the right ear) on day 8. To measure ear inflammation, the ear thickness of manually restrained animals is measured using a Mitutoyo micrometer. The ear thickness is measured before intradermal challenge as the baseline level for each individual animal. Subsequently, the ear thickness is measured two times after intradermal challenge, at approximately 24 hours and 48 hours (i.e., days 9 and 10).


Treatment with a solid dosage form is initiated at some point, either around the time of priming or around the time of DTH challenge. For example, a solid dosage form may be administered at the same time as the subcutaneous injections (day 0), or it may be administered prior to, or upon, intradermal injection. A solid dosage form is administered (e.g., orally) at varied doses and at defined intervals. Examples are provided in the above examples. Some mice may receive a solid dosage form every day (e.g., starting on day 0), while others may receive a solid dosage form at alternative intervals (e.g., every other day, or once every three days).


As an example, an emulsion of Keyhole Limpet Hemocyanin (KLH) and Complete Freund's Adjuvant (CFA) can be prepared freshly on the day of immunization (day 0). To this end, 8 mg of KLH powder is weighed and is thoroughly re-suspended in 16 mL saline. An emulsion is prepared by mixing the KLH/saline with an equal volume of CFA solution (e.g., 10 mL KLH/saline+10 mL CFA solution) using syringes and a luer lock connector. KLH and CFA are mixed vigorously for several minutes to form a white-colored emulsion to obtain maximum stability. A drop test is performed to check if a homogenous emulsion is obtained.


On day 0, C57Bl/6J female mice, approximately 7 weeks old, are primed with KLH antigen in CFA by subcutaneous immunization (4 sites, 50 μL per site). A solid dosage form is administered as described herein.


On day 8, mice are challenged intradermally (i.d.) with 10 μg KLH in saline (in a volume of 10 μL) in the left ear. Ear pinna thickness is measured at 24 hours following antigen challenge. The effectiveness of a solid dosage form at suppressing inflammation is determined by ear thickness.


For future inflammation studies, some groups of mice may be treated with anti-inflammatory agent(s) (e.g., anti-CD154, blockade of members of the TNF family, or other treatment), and/or an appropriate control (e.g., vehicle or control antibody) at various timepoints and at effective doses.


At various timepoints, serum samples may be taken. Other groups of mice may be sacrificed and lymph nodes, spleen, mesenteric lymph nodes (MLN), the small intestine, colon, and other tissues may be removed for histology studies, ex vivo histological, cytokine and/or flow cytometric analysis using methods known in the art. Some mice are exsanguinated from the orbital plexus under O2/CO2 anesthesia and ELISA assays performed.


Tissues may be dissociated using dissociation enzymes according to the manufacturer's instructions. Cells are stained for analysis by flow cytometry using techniques known in the art. Staining antibodies can include anti-CD11c (dendritic cells), anti-CD80, anti-CD86, anti-CD40, anti-MHCII, anti-CD8a, anti-CD4, and anti-CD103. Other markers that may be analyzed include pan-immune cell marker CD45, T cell markers (CD3, CD4, CD8, CD25, Foxp3, T-bet, Gata3, Rory-gamma-t, Granzyme B, CD69, PD-1, CTLA-4), and macrophage/myeloid markers (CD11b, MHCII, CD206, CD40, CSF1R, PD-L1, Gr-1, F4/80). In addition to immunophenotyping, serum cytokines can be analyzed including, but not limited to, TNFa, IL-17, IL-13, IL-12p70, IL12p40, IL-10, IL-6, IL-5, IL-4, IL-2, IL-1b, IFNy, GM-CSF, G-CSF, M-CSF, MIG, IP10, MIP1b, RANTES, and MCP-1. Cytokine analysis may be carried out on immune cells obtained from lymph nodes or other tissue, and/or on purified CD45+ infiltrated immune cells obtained ex vivo. Finally, immunohistochemistry is carried out on various tissue sections to measure T cells, macrophages, dendritic cells, and checkpoint molecule protein expression.


Ears may be removed from the sacrificed animals and placed in cold EDTA-free protease inhibitor cocktail (Roche). Ears are homogenized using bead disruption and supernatants analyzed for various cytokines by Luminex kit (EMD Millipore) as per manufacturer's instructions. In addition, cervical lymph nodes are dissociated through a cell strainer, washed, and stained for FoxP3 (PE-FJK-16s) and CD25 (FITC-PC61.5) using methods known in the art.


In order to examine the impact and longevity of DTH protection, rather than being sacrificed, some mice may be rechallenged with the challenging antigen at a later time and mice analyzed for susceptibility to DTH and severity of response.


Example 7: Oral Administration

A subject can self-administer a solid dosage form orally in the morning with water, refraining from consuming acidic drinks 1 hour either side of dosing and from eating 2 hours before dosing and 1 hour after dosing.


INCORPORATION BY REFERENCE

All publications patent applications mentioned herein are hereby incorporated by reference in their entirety as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.


EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

Claims
  • 1. A solid dosage form comprising a pharmaceutical agent, wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), and wherein the solid dosage form is enterically coated.
  • 2. The solid dose form of claim 1, wherein the solid dose form is for oral administration and/or for therapeutic use.
  • 3. The solid dose form of claim 1 or claim 2 comprising a therapeutically effective amount of the pharmaceutical agent.
  • 4. The solid dosage form of any one of claims 1 to 3, wherein the solid dosage form comprises a capsule.
  • 5. The solid dosage form of claim 4, wherein the enterically coated capsule is a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule.
  • 6. The solid dosage form of claim 1, wherein the solid dosage form comprises an enterically coated tablet.
  • 7. The solid dosage form of claim 6, wherein the enterically coated tablet is a 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm, 11 mm, 12 mm, 13 mm, 14 mm, 15 mm, 16 mm, 17 mm, or 18 mm tablet.
  • 8. The solid dosage form of claim 1, wherein the solid dosage form comprises a minitablet.
  • 9. The solid dosage form of claim 8, wherein the minitablet is a 1 mm minitablet, 1.5 mm minitablet, 2 mm minitablet, 3 mm minitablet, or 4 mm minitablet.
  • 10. The solid dosage form of claim 8 or 9, wherein a plurality of minitablets are contained in a capsule.
  • 11. The solid dosage form of claim 10, wherein the capsule is a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule.
  • 12. The solid dosage form of claim 11, wherein the capsule is a size 0 capsule.
  • 13. The solid dosage form of claim 12, wherein the size 0 capsule comprises 31-35 minitablets.
  • 14. The solid dosage form of claim 13, wherein the capsule comprises about 33 minitablets.
  • 15. The solid dosage form of any one of claims 8 to 14, wherein the minitablets are 3 mm minitablets.
  • 16. The solid dosage form of any one of claims 8 to 15, wherein the capsule comprises HPMC (hydroxyl propyl methyl cellulose) or gelatin.
  • 17. The solid dosage form of any one of claims 1 to 6, wherein the enteric coating comprises one enteric coating.
  • 18. The solid dosage form of any one of claims 1 to 17, wherein the enteric coating comprises an inner enteric coating and an outer enteric coating, and wherein the inner and outer enteric coatings do not contain identical components in identical amounts.
  • 19. The solid dosage form of claim any one of claims 1 to 18, wherein the enteric coating comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1).
  • 20. The solid dosage form of claim any one of claims 1 to 19, wherein the enteric coating comprises one enteric coating which comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1).
  • 21. The solid dosage form of any one of claims 1 to 20, wherein the enteric coating comprises cellulose acetate phthalate (CAP), cellulose acetate trimellitate (CAT), poly(vinyl acetate phthalate) (PVAP), hydroxypropyl methylcellulose phthalate (HPMCP), a fatty acid, a wax, shellac (esters of aleurtic acid), a plastic, a plant fiber, zein, Aqua-Zein (an aqueous zein formulation containing no alcohol), amylose starch, a starch derivative, a dextrin, a methyl acrylate-methacrylic acid copolymer, cellulose acetate succinate, hydroxypropyl methyl cellulose acetate succinate (hypromellose acetate succinate), a methyl methacrylate-methacrylic acid copolymer, or sodium alginate.
  • 22. The solid dosage form of any one of claims 1 to 21, wherein the enteric coating comprises an anionic polymeric material.
  • 23. The solid dosage form of any one of claims 1 to 22, wherein the pharmaceutical agent comprises bacteria.
  • 24. The solid dosage form of any one of claims 1 to 23, wherein the pharmaceutical agent comprises microbial extracellular vesicles (mEV).
  • 25. The solid dosage form of any one of claims 1 to 24, wherein the pharmaceutical agent comprises isolated bacteria.
  • 26. The solid dosage form of any one of claims 23 to 25, wherein at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is the bacteria.
  • 27. The solid dosage form of any one of claims 23 to 26, wherein the bacteria comprise bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.
  • 28. The solid dosage form of any one of claims 23 to 27, wherein the bacteria comprise live bacteria.
  • 29. The solid dosage form of any one of claims 23 to 28, wherein the bacteria comprise dead bacteria.
  • 30. The solid dosage form of any one of claims 23 to 29, wherein the bacteria comprise non-replicating bacteria.
  • 31. The solid dosage form of any one of claims 23 to 30, wherein the bacteria are from one strain of bacteria.
  • 32. The solid dosage form of any one of claims 23 to 31, wherein the bacteria are lyophilized.
  • 33. The solid dosage form of claim 32, wherein the lyophilized bacteria are in admixture with a pharmaceutically acceptable excipient.
  • 34. The solid dosage form of any one of claims 23 to 33, wherein the bacteria are gamma irradiated.
  • 35. The solid dosage form of any one of claims 23 to 34, wherein the bacteria are UV irradiated.
  • 36. The solid dosage form of any one of claims 23 to 35, wherein the bacteria are heat inactivated.
  • 37. The solid dosage form of claim 36, wherein the bacteria are heat inactivated at about 50° C. for at least two hours or at about 90° C. for at least two hours.
  • 38. The solid dosage form of any one of claims 23 to 37, wherein the bacteria are acid treated.
  • 39. The solid dosage form of any one of claims 23 to 38, wherein the bacteria are oxygen sparged.
  • 40. The solid dosage form of claim 39, wherein the bacteria are oxygen sparged at 0.1 vvm for two hours.
  • 41. The solid dosage form of any one of claims 23 to 40, wherein the bacteria are Gram positive bacteria.
  • 42. The solid dosage form of any one of claims 23 to 40, wherein the bacteria are Gram negative bacteria.
  • 43. The solid dosage form of any one of claims 23 to 42, wherein the bacteria are aerobic bacteria.
  • 44. The solid dosage form of any one of claims 23 to 42, wherein the bacteria are anaerobic bacteria.
  • 45. The solid dosage form of any one of claims 23 to 44, wherein the bacteria are acidophile bacteria.
  • 46. The solid dosage form of any one of claims 23 to 44, wherein the bacteria are alkaliphile bacteria.
  • 47. The solid dosage form of any one of claims 23 to 44, wherein the bacteria are neutralophile bacteria.
  • 48. The solid dosage form of any one of claims 23 to 47, wherein the bacteria are fastidious bacteria.
  • 49. The solid dosage form of any one of claims 23 to 47, wherein the bacteria are nonfastidious bacteria.
  • 50. The solid dosage form of any one of claims 23 to 49, wherein the bacteria are from a class, order, family, genus, species and/or strain listed in Table 1, Table 2, or Table 3.
  • 51. The solid dosage form of claim 50, wherein the bacteria are from a bacterial strain listed in Table 1, Table 2, or Table 3.
  • 52. The solid dosage form of any one of claims 23 to 51, wherein the bacteria are from bacteria from a class, order, family, genus, species and/or strain listed in Table J.
  • 53. The solid dosage form of claim 52, wherein the bacteria are from a bacterial strain listed in Table J.
  • 54. The solid dosage form of any one of claims 1 to 22, wherein the pharmaceutical agent comprises isolated mEVs.
  • 55. The solid dosage form of claim 54 comprising a therapeutically effective amount of the isolated mEVs.
  • 56. The solid dosage form of claim 54 or 55, wherein at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is the isolated mEVs.
  • 57. The solid dosage form of any one of claims 54 to 56, wherein the mEVs comprise secreted mEVs (smEVs).
  • 58. The solid dosage form of any one of claims 54 to 57, wherein the mEVs comprise processed mEVs (pmEVs).
  • 59. The solid dosage form of claim 58, wherein the pmEVs are produced from bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.
  • 60. The solid dosage form of claim 58 or 59, wherein the pmEVs are produced from live bacteria.
  • 61. The solid dosage form of claim 58 or 59, wherein the pmEVs are produced from dead bacteria.
  • 62. The solid dosage form of claim 58 or 59, wherein the pmEVs are produced from non-replicating bacteria.
  • 63. The solid dosage form of any one of claims 54 to 62, wherein the mEVs are from one strain of bacteria.
  • 64. The solid dosage form of any one of claims 54 to 63, wherein the mEVs are lyophilized.
  • 65. The solid dosage form of claim 64, wherein the lyophilized mEVs are in admixture with a pharmaceutically acceptable excipient).
  • 66. The solid dosage form of any one of claims 54 to 65, wherein the mEVs are gamma irradiated.
  • 67. The solid dosage form of any one of claims 54 to 66, wherein the mEVs are UV irradiated.
  • 68. The solid dosage form of any one of claims 54 to 67, wherein the mEVs are heat inactivated.
  • 69. The solid dosage form of claim 68, wherein the mEVs are heat inactivated at about 50° C. for at least two hours or at about 90° C. for at least two hours.
  • 70. The solid dosage form of any one of claims 54 to 69, wherein the mEVs are acid treated.
  • 71. The solid dosage form of any one of claims 54 to 70, wherein the mEVs are oxygen sparged.
  • 72. The solid dosage form of claim 71, wherein the mEVs are oxygen sparged at 0.1 vvm for two hours.
  • 73. The solid dosage form of any one of claims 54 to 72, wherein the mEVs are from Gram positive bacteria.
  • 74. The solid dosage form of any one of claims 54 to 72, wherein the mEVs are from Gram negative bacteria.
  • 75. The solid dosage form of any one of claims 45 to 74, wherein the mEVs are from aerobic bacteria.
  • 76. The solid dosage form of any one of claims 54 to 74, wherein the mEVs are from anaerobic bacteria.
  • 77. The solid dosage form of any one of claims 54 to 76, wherein the mEVs are from acidophile bacteria.
  • 78. The solid dosage form of any one of claims 54 to 76, wherein the mEVs are from alkaliphile bacteria.
  • 79. The solid dosage form of any one of claims 54 to 76, wherein the mEVs are from neutralophile bacteria.
  • 80. The solid dosage form of any one of claims 54 to 79, wherein the mEVs are from fastidious bacteria.
  • 81. The solid dosage form of any one of claims 54 to 79, wherein the mEVs are from nonfastidious bacteria.
  • 82. The solid dosage form of any one of claims 54 to 81, wherein the mEVs are from bacteria of a class, order, family, genus, species and/or strain listed in Table 1, Table 2, or Table 3.
  • 83. The solid dosage form claim 82, wherein the mEVs are from a bacterial strain listed in Table 1, Table 2, or Table 3.
  • 84. The solid dosage form of any one of claims 54 to 83, wherein the mEVs are from bacteria of a class, order, family, genus, species and/or strain listed in Table J.
  • 85. The solid dosage form of claim 84, wherein the mEVs are from a bacterial strain listed in Table J.
  • 86. The solid dosage form of any one of claims 23 to 53, wherein the dose of bacteria is about 1×107 to about 2×1012 cells, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.
  • 87. The solid dosage form of claim 86, wherein the dose of bacteria is about 3×1010 or about 1.5×1011 or about 1.5×1012.
  • 88. The solid dosage form of claim 86, wherein the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×109, about 3×109, about 5×109, about 1.5×1010, about 3×1010, about 5×1010, about 1.5×1011, about 1.5×1012, or about 2×1012 cells, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.
  • 89. The solid dosage form of any one of claims 1 to 88, wherein the dose of the pharmaceutical agent is about 10 mg to about 1500 mg, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.
  • 90. The solid dosage form of any one of claims 1 to 88, wherein the dose of the pharmaceutical agent is about 30 mg to about 1300 mg by weight, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.
  • 91. The solid dosage form of claim 90, wherein the dose is about 25, about 30, about 35, about 50, about 75, about 100, about 120, about 150, about 250, about 300, about 350, about 400, about 500, about 600, about 700, about 750, about 800, about 900, about 1000, about 1100, about 1200, about 1250, about 1300, about 2000, about 2500, about 3000, or about 3500 mg, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule
  • 92. The solid dosage form of any one of claims 1 to 88, wherein the dose of the pharmaceutical agent is about 2×106 to about 2×1016 particles, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.
  • 93. The solid dosage form of claim 92, wherein particle count is determined by nanoparticle tracking analysis (NTA).
  • 94. The solid dosage form of any one of claims 1 to 88, wherein the dose of the pharmaceutical agent is about 5 mg to about 900 mg total protein, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.
  • 95. The solid dosage form of claim 94, wherein total protein is determined by Bradford assay or by BCA.
  • 96. The solid dosage form of any one of claims 1 to 95, wherein the solid dosage form further comprises one or more additional pharmaceutical agents.
  • 97. The solid dosage form of any one of claims 1 to 96, wherein the solid dosage form further comprises an excipient.
  • 98. The solid dosage form of claim 97, wherein the excipient is a diluent, a binder and/or an adhesive, a disintegrant, a lubricant and/or a glidant, a coloring agent, a flavoring agent, and/or a sweetening agent.
  • 99. A method of treating a subject, the method comprising administering to the subject a solid dosage form of any one of claims 1 to 98.
  • 100. The solid dosage form of any one of claims 1 to 98 for use in treating a subject.
  • 101. Use of a solid dosage form of any one of claims 1 to 98 for the preparation of a medicament for treating a subject.
  • 102. The method, solid dosage form, or use of any one of claims 99 to 101, wherein the solid dosage form is orally administered.
  • 103. The method, solid dosage form, or use of any one of claims 99 to 102, wherein the solid dosage form is administered on an empty stomach.
  • 104. The method, solid dosage form, or use of any one of claims 99 to 103, wherein the solid dosage form is administered 1, 2, 3, or 4 times a day.
  • 105. The method, solid dosage form, or use of any one of claims 99 to 104, wherein the solid dosage form comprises a tablet or a plurality of minitablets within a capsule, and 1, 2, 3, or 4 solid dosage forms are administered 1, 2, 3, or 4 times a day.
  • 106. The method, solid dosage form, or use of any one of claims 99 to 105, wherein the subject is in need of treatment and/or prevention of a cancer.
  • 107. The method, solid dosage form, or use of any one of claims 99 to 105, wherein the subject is in need of treatment and/or prevention of an autoimmune disease.
  • 108. The method, solid dosage form, or use of any one of claims 99 to 105, wherein the subject is in need of treatment and/or prevention of an inflammatory disease.
  • 109. The method, solid dosage form, or use of any one of claims 99 to 105, wherein the subject is in need of treatment and/or prevention of a metabolic disease.
  • 110. The method, solid dosage form, or use of any one of claims 99 to 105, wherein the subject is in need of treatment and/or prevention of dysbiosis.
  • 111. The method, solid dosage form, or use of any one of claims 99 to 110, wherein the solid dosage form is administered in combination with an additional pharmaceutical agent.
  • 112. A method for preparing an enterically coated capsule comprising a pharmaceutical agent, wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising: a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;b) loading the pharmaceutical agent and pharmaceutically acceptable excipient into a capsule; andc) enterically coating the capsule, thereby preparing the enterically coated capsule.
  • 113. The method of claim 112, wherein the method comprises combining the pharmaceutical agent with a pharmaceutically acceptable excipient prior to loading into the capsule.
  • 114. The method of claim 112, wherein the method comprises banding the capsule after loading the capsule and prior to enterically coating the capsule.
  • 115. A method for preparing an enterically coated tablet comprising a pharmaceutical agent, wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising: a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;b) compressing the pharmaceutical agent and pharmaceutically acceptable excipient, thereby forming a tablet; andc) enterically coating the tablet, thereby preparing an enterically coated tablet.
  • 116. A method for preparing an enterically coated minitablet comprising a pharmaceutical agent, wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising: a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;b) compressing the pharmaceutical agent and pharmaceutically acceptable excipient, thereby forming a minitablet; andc) enterically coating the minitablet, thereby preparing the enterically coated minitablet.
  • 117. The method of claim 116, wherein the minitablet is loaded into a capsule.
  • 118. A method for preparing a capsule comprising enterically coated minitablets comprising a pharmaceutical agent, wherein the pharmaceutical agent comprises bacteria and/or microbial extracellular vesicles (mEVs), the method comprising: a) combining the pharmaceutical agent with a pharmaceutically acceptable excipient;b) compressing the pharmaceutical agent and pharmaceutically acceptable excipient, thereby forming a minitablet;c) enterically coating the minitablet, thereby preparing an enterically coated minitablet, andd) loading the capsule with one or more enterically coated minitablets, thereby preparing the capsule.
  • 119. The method of any one of claims 112 to 118, wherein the pharmaceutical agent comprises a therapeutically effective amount of bacteria and/or mEVs.
CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No. 62/954,153, filed on Dec. 27, 2019; the entire contents of said application are incorporated herein in their entirety by this reference.

PCT Information
Filing Document Filing Date Country Kind
PCT/US20/66828 12/23/2020 WO
Provisional Applications (1)
Number Date Country
62954153 Dec 2019 US