MICROBIAL CONSORTIA FOR THE TREATMENT OF DISEASE

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Mar. 10, 2021, is named FBI-002WO_SL.txt and is 878,406 bytes in size.

FIELD OF THE INVENTION

The invention generally relates to microbial consortia for administration to an animal for degradation of a disease-associated metabolic substrate.

BACKGROUND

The gastrointestinal tract comprises various biological niches along its longitudinal length having different physical, chemical, and nutrient compositions. As a consequence of these diverse conditions, specific microbial communities are established within a particular biological niche. The microbial species comprising a specific microbial community are highly responsive to their local environment and produce an array of bioactive molecules that facilitate host engraftment, inter-microbial communication, nutrient metabolism, and inclusion or exclusion of competing microbial species. Adding further complexity, there is substantial diversity of microbial species and strains in the human GI tract between individuals, which is attributed to a number of factors including genetics, diet, antibiotic and antifungal use, surgical intervention (e.g., gastric by-pass/bowel resection), presence of inflammatory bowel disease and/or irritable bowel syndrome, and other environmental influences. However, despite this interindividual diversity, the functional attributes of the varying human gut microbiota are relatively consistent among healthy adults and comprise core metabolic pathways involved in carbohydrate metabolism, amino acid metabolism, fermentation, and oxidative phosphorylation.

Modulation of microbial species in the GI tract through the use of antibiotics, antifungals, and more recently, fecal microbial transplantation (“FMT”), have been approaches clinically investigated for the treatment and/or prevention of certain diseases and disorders. For example, Dodd et al. (Nature, 2007, 551: 648-652) have proposed FMT as a therapeutic to modulate the levels of aromatic amino acid metabolites in the serum of gnotobiotic mice, which affect intestinal permeability and systemic immunity. In further examples, administration of bacterial compositions has also been proposed as a method for treating Clostridium difficile infection, ulcerative colitis, cholestatic disease, and hyperoxaluria (see e.g., US 2018/0353554, WO 2019/036510, U.S. RE39,585).

As a modality for treating various diseases and/or conditions, there is a need for microbial compositions comprising a plurality of microbial species having improved therapeutic efficacy and an ability to efficiently engraft in a host, grow, and metabolize pathogenic substrates to non-pathogenic metabolic products within the various biological niches of the GI tract and within the diverse GI environments of different individuals.

SUMMARY OF THE INVENTION

Disclosed here is a microbial consortium for administration to an animal comprising a plurality of active microbes and an effective amount of a supportive community of microbes. In some embodiments, the plurality of active microbes metabolize a first metabolic substrate to produce one or more than one metabolite, wherein the first metabolic substrate causes or contributes to disease in an animal.

In some embodiments, the supportive community of microbes comprises between 1 and 300 microbial strains and meets one, two, three, or four of the following conditions:

- 1) the supportive community of microbes metabolizes one or more than one metabolite produced by the plurality of active microbes, wherein the one or more than one metabolite inhibits metabolism of the first metabolic substrate by one or more of the plurality of active microbes,
- 2) the supportive community of microbes increases the flux of a precursor of the first metabolic substrate into a biochemical pathway that converts said precursor into a metabolite that is not the first metabolic substrate,
- 3) the supportive community of microbes enhances one or more than one characteristic of the plurality of active microbes when administered to an animal selected from the group consisting of: a) gastrointestinal engraftment, b) biomass, c) first metabolic substrate metabolism, and d) longitudinal stability as compared to administration of the plurality of active microbes in the absence of the supportive community of microbes, and
- 4) the supportive community of microbes catalyzes one or more than one reaction selected from the group consisting of: fermentation of polysaccharides to one or more than one of the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H₂, and CO₂, fermentation of amino acids to one or more than one of the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, phloretate, 3-(1H-indol-3-yl)propanoate, 5-aminopentanoate, H₂, H₂S, and CO₂, synthesis of one or more than one of the group consisting of methane from H₂and CO₂, methane from formate and H₂, acetate from H₂and CO₂, acetate from formate and H₂, acetate and sulfide from H₂, CO₂, and sulfate, propionate and CO₂from succinate, succinate from H₂and fumarate; synthesis of succinate from formate and fumarate, and butyrate, acetate, H₂, and CO₂from lactate, deconjugation of conjugated bile acids to produce primary bile acids, conversion of cholic acid (CA) to 7-oxocholic acid, conversion of 7-oxocholic acid to 7-beta-cholic acid (7betaCA), conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA).

In some embodiments, the first metabolic substrate metabolizing activity of at least one of the plurality of active microbes is significantly different when measured in a standardized substrate metabolization assay at two pH values within a range of 4 to 8, and wherein the difference between the two pH values is at least one pH unit.

In some embodiments, the first metabolic substrate metabolizing activity of at least one of the plurality of active microbes is significantly different when measured in a standardized substrate metabolization assay at two first metabolic substrate concentrations within a 100 fold range, and wherein the difference between the two first metabolic substrate concentrations is at least 1.2-fold.

In some embodiments, the supportive community of microbes comprises at least three, at least four, at least five, or six phyla selected from Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, and Euryarchaeota.

In some embodiments, the supportive community of microbes comprises one or more of the subclades Bacteroidales, Clostridiales, Erysipelotrichales. Negativicutes, Coriobacteriia, Bifidobacteriales, or Methanobacteriales.

In some embodiments, the first metabolic substrate is oxalate. In some embodiments, the supportive community of microbes catalyzes synthesis of methane from formate and H₂.

In some embodiments, the plurality of active microbes comprises Oxalobacter formigenes. In some embodiments the supportive community of microbes comprises a Bacteroidetes and a Euryarchaeota. In some embodiments, the supportive community of microbes comprises a Bateroides and Methanobrevibacter. In further embodiments, the supportive community of microbes comprises Bacteroides thetaiotaomicron and/or Bacteroides vulgatus, and Methanobrevibacter smithii.

In some embodiments, the supportive community of microbes metabolizes one or more than one metabolite produced by the plurality of active microbes, wherein the one or more than one metabolite inhibits metabolism of the plurality of active microbes.

In some embodiments, the supportive community of microbes enhances one or more than one characteristic of the plurality of active microbes when administered to an animal selected from the group consisting of gastrointestinal engraftment, biomass, first metabolic substrate metabolism, and longitudinal stability as compared to administration of the plurality of active microbes in the absence of the supportive community of microbes.

In some embodiments, the supportive community catalyzes one or more than one reaction selected from the group consisting of:

- fermentation of polysaccharides to one or more than one of the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H₂, and CO₂,
- fermentation of amino acids to one or more than one of the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, phloretate, 3-(1H-indol-3-yl)propanoate, 5-aminopentanoate, H₂, H₂S, and CO₂, synthesis of one or more than one of the group consisting of methane from H₂and CO₂, methane from formate and H₂, acetate from H₂and CO₂, acetate from formate and H₂, acetate and sulfide from H₂, CO₂, and sulfate, propionate and CO₂from succinate, succinate from H₂and fumarate; synthesis of succinate from formate and fumarate, and butyrate, acetate, H₂, and CO₂from lactate, and
- deconjugation of conjugated bile acids to produce primary bile acids, conversion of cholic acid (CA) to 7-oxocholic acid, conversion of 7-oxocholic acid to 7-beta-cholic acid (7betaCA), conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA).

In some embodiments, the supportive community of microbes comprises between 20 and 200 microbial strains. In some embodiments, the supportive community comprises at least 4 phyla selected from the group consisting of Bacteroidetes, Firmicutes, Actinobacteria, and Proteobacteria. In some embodiments, the supportive community comprises a Ruminococcus, Clostridium, Bacteroides, Neglecta, Bifidobacterium, Egerthella, Clostridiaceae, Parabacteroides, Bilophila, Dorea, Collinsella, and Faecalibacterium.

In some embodiments, the supportive community comprises Ruminococcus bromii, Clostridium citroniae, Bacteroides salyersiae, Neglecta timonensis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Eggerthella lenta, Clostridiaceae sp., Bifidobacterium dentium, Parabacteroides merdae, Bilophila wadsworthia, Bacteroides caccae, Dorea longicatena, Collinsella aerofaciens, Clostridium scindens, Faecalibacterium prausnitzii, Clostridium symbiosum, and Bacteroides vulgatus.

In some embodiments, the supportive community comprises an Acidaminococcus, an Akkermansia, an Alistipes, an Anaerofustis, an Anaerostipes, an Anaerotruncus, a Bacteroides, a Barnesiella, a Bifidobacterium, a Bilophila, a Blautia, a Butyricimonas, a Catabacter hongkongensis, a Clostridiaceae, a Clostridiales, a Clostridium, a Collinsella, a Coprococcus, a Dialister, a Dielma, a Dorea, an Eggerthella, an Eisenbergiella, a Eubacterium, a Faecalibacterium, a Fusicatenibacter saccharivorans, a Gordonibacter pamelaeae, a Holdemanella, a Hungatella, a Lachnoclostridium, Lachnospiraceae, a Lactobacillus, a Longicatena, a Megasphaera, a Methanobrevibacter, a Monoglobus, a Neglecta, a Parabacteroides, a Paraprevotella, a Parasutterella, a Phascolarctobacterium, a Porphyromonas, a Roseburia hominis, a Ruminococcaceae, a Ruminococcus, a Ruthenibacterium, a Senegalimassilia, a Sutterella, and a Turicibacter.

In some embodiments, the supportive community comprises or consists of Acidaminococcus intestine, Akkermansia mucimphila, Alistipes onderdonkii, Alistipes putredinis, Alistipes senegalensis, Alistipes shahii, Alistipes sp., Alistipes timonensis, Anaerofustis stercorihominis, Anaerostipes hadrus, Anaerotruncus massiliensis, Bacteroides caccae, Bacteroides coprocola, Bacteroides faecis, Bacteroides finegoldii, Bacteroides fragilis, Bacteroides kribbi, Bacteroides massiliensis, Bacteroides nordii, Bacteroides ovatus, Bacteroides salyersiae, Bacteroides stercorirosoris, Bacteroides stercoris, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bacteroides xylanisolvens, Barnesiella intestinihominis, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium catenulatum, Bifidobacterium dentium, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bilophila wadsworthia, Blautia faecis, Blautia hydrogenotrophica, Blautia massiliensis, Blautia obeum, Blautia wexlerae, Butyricimonas faecihominis, Catabacter hongkongensis, Clostridiaceae sp., Clostridiales sp., Clostridium aldenense, Clostridium bolteae, Clostridium citroniae, Clostridium clostridioforme, Clostridium fessum, Clostridium scindens, Collinsella aerofaciens, Coprococcus comes, Coprococcus eutactus, Dialister invisus, Dialister succinatiphilus, Dielma fastidiosa, Dorea formicigenerans, Dorea longicatena, Eggerthella lenta, Eisenbergiella tayi, Eubacterium eligens, Eubacterium hallii, Eubacterium rectale, Eubacterium siraeum, Eubacterium ventriosum, Eubacterium xylanophilum, Faecalibacterium prausnitzii, Fusicatenibacter saccharivorans, Gordonibacter pamelaeae, Holdemanella biformis, Hungatella effluvia, Lachnoclostridium pacaense, Lachnospiraceae sp., Lactobacillus rogosae, Longicatena caecimuris, Megasphaera massiliensis, Methanobrevibacter smithii, Monoglobus pectinilyticus, Neglecta timonensis, Parabacteroides distasonis, Parabacteroides merdae, Paraprevotella clara, Parasutterella excrementihominis, Phascolarctobacterium faecium, Porphyromonas asaccharolytica, Roseburia hominis, Ruminococcaceae sp., Ruminococcus bromii, Ruminococcus faecis, Ruthenibacterium lactatiformans, Senegalimassilia anaerobia, Sutterella massiliensis, Sutterella wadsworthensis, and Turicibacter sanguinis.

In some embodiments, the supportive community of microbes comprises an Akkermansia, an Alistipes, an Anaerostipes, a Bacteroides, a Bifidobacterium, a Bilophila, a Blautia, a Clostridium, a Collinsella aerofaciens, a Coprococcus, Dialister, a Dorea, an Eggerthella, an Eisenbergiella, a Eubacterium, a Faecalibacterium, a Fusicatenibacter, a Gordonibacter, a Holdemanella, a Hungatella, a Lachnoclostridium, a Lachnospiraceae, a Lactobacillus, aMonoglobus, a Neglecta, a Parabacteroides, a Paraprevotella, a Parasutterella, a Phascolarctobacterium, a Porphyromonas, a Roseburia, a Ruminococcaceae, a Ruminococcus, a Ruthenibacterium, and a Sutterella.

In some embodiments, the supportive community of microbes comprises or consists of Akkermansia mucimphila, Alistipes onderdonkii, Alistipes putredinis, Alistipes shahii, Alistipes timonensis, Anaerostipes hadrus, Bacteroides caccae, Bacteroides fragilis, Bacteroides kribbi, Bacteroides koreensis, Bacteroides massiliensis, Bacteroides nordii, Bacteroides salyersiae, Bacteroides stercorirosoris, Bacteroides stercoris, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bacteroides xylanisolvens, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Bifidobacterium dentium, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bilophila wadsworthia, Bilophila wadsworthia, Blautia faecis, Blautia obeum, Blautia wexlerae, Clostridium aldenense, Clostridium bolteae, Clostridium citroniae, Clostridium clostridioforme, Clostridium fessum, Clostridium scindens, Collinsella aerofaciens, Coprococcus comes, Coprococcus eutactus, Dialister invisus, Dialister succinatiphilus, Dorea formicigenerans, Dorea longicatena, Eggerthella lenta, Eisenbergiella tayi, Eubacterium eligens, Eubacterium rectale, Faecalibacterium prausnitzii, Fusicatenibacter saccharivorans, Gordonibacter pamelaeae, Holdemanella biformis, Hungatella effluvia, Lachnoclostridium pacaense, Lachnospiraceae sp., Lactobacillus rogosae, Monoglobus pectinilyticus, Neglecta timonensis, Parabacteroides distasonis, Parabacteroides merdae, Paraprevotella clara, Parasutterella excrementihominis, Phascolarctobacterium faecium, Porphyromonas asaccharolytica, Roseburia hominis, Ruminococcaceae sp., Ruminococcus bromii, Ruminococcus faecis, Ruthenibacterium lactatiformans, Sutterella massiliensis, and Sutterella wadsworthensis.

In some embodiments, the microbial consortium or the supportive community of microbes comprises 20 to 200, 70 to 80, 80 to 90, 100 to 110, or 150 to 160 microbial strains.

In some embodiments, the supportive community of microbes comprises between 100 and 150 microbial strains.

In some embodiments, the plurality of active microbes and the supportive community of microbes are selected from a group of microbes each comprising a 16S sequence at least 80% identical, at least 90% identical, or at least 97% identical to any one of the microbes listed in Table 4, 22, 23, 20, 16, 17, 18 or 19.

In some embodiments, the plurality of active microbes and the supportive community of microbes consist of a group of microbes each comprising a 16S sequence at least 80% identical, at least 90% identical, or at least 97% identical to any one of the microbes listed in Table 22, 23, 20, 16, 17, 18 or 19.

In some embodiments, the first metabolic substrate metabolizing activity of one of the plurality of active microbes is significantly different compared to the first metabolic substrate activity of at least one other of the plurality of active microbes when measured in a standardized substrate metabolization assay under the same conditions.

In some embodiments, one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a lower pH compared to at least one other of the plurality of active microbes at the same lower pH. In some embodiments, one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a lower pH compared to a first metabolic substrate metabolizing activity of the same active microbe at a higher pH. In some embodiments the lower pH is at 4.5±0.5.

In some embodiments, one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a higher pH compared to at least one other of the plurality of active microbes at the same higher pH. In some embodiments, one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a higher pH compared to a first metabolic substrate activity of the same active microbe at a lower pH. In some embodiments, the higher pH is at 7.5±0.5.

In some embodiments, one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a lower pH and one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a higher pH. In some embodiments, the difference between the two pH values is at least 1.5, 2.0, 2.5, 3.0, 3.5, or 4.0 pH units.

In some embodiments, one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a lower concentration of first metabolic substrate compared to the first metabolic substrate activity of at least one other of the plurality of active microbes when measured in a standardized substrate metabolization assay under the same conditions. In some embodiments, one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a lower concentration of first metabolic substrate compared to a first metabolic substrate metabolizing activity of the same active microbe at a higher concentration of first metabolic substrate. In some embodiments, one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a higher concentration of first metabolic substrate compared to the first metabolic substrate activity of at least one other of the plurality of active microbes when measured in a standardized substrate metabolization assay under the same conditions. In some embodiments, one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a lower concentration of first metabolic substrate compared to a first metabolic substrate metabolizing activity of the same active microbe at a higher concentration of first metabolic substrate.

In some embodiments one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a lower first metabolic substrate concentration and one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at a higher first metabolic substrate concentration. In some embodiments, the difference between the two first metabolic substrate concentrations is at least 1.2 fold, 2.0 fold, 3.0 fold, 4.0 fold, 5.0 fold, 6.0 fold, 7.0 fold, 8.0 fold, 9.0 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, 100 fold, or greater than 100 fold.

In some embodiments, the microbial consortium of the present invention comprises a plurality of active microbes comprising 2 to 200 microbial strains. In certain embodiments, the plurality of active microbes comprises 2 to 20 microbial strains.

In some embodiments of the present invention, the first metabolic substrate is oxalate. In some embodiments, the one or more than one metabolite is selected from the group consisting of formate and carbon dioxide (CO₂). In some embodiments, at least one of the plurality of active microbes has a higher oxalate metabolizing activity at 0.75 mM of oxalate compared to the oxalate metabolizing activity of at least one other of the plurality of active microbes when measured in a standardized oxalate metabolization assay under the same conditions. In some embodiments, one of the plurality of active microbes has a higher oxalate metabolizing activity at 0.75 mM of oxalate compared to an oxalate metabolizing activity of the same active microbe at a higher concentration of oxalate. In some embodiments, at least one of the plurality of active microbes has a higher oxalate metabolizing activity at 40 mM of oxalate compared to the oxalate metabolizing activity of at least one other of the plurality of active microbes when measured in a standardized oxalate metabolization assay under the same conditions. In some embodiments, one of the plurality of active microbes has a higher oxalate metabolizing activity at 40 mM of oxalate compared to an oxalate metabolizing activity of the same active microbe at a lower concentration of oxalate. In some embodiments, one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at 0.75 mM of oxalate and another one of the plurality of active microbes has a higher first metabolic substrate metabolizing activity at 40 mM of oxalate.

In some embodiments, the standardized substrate metabolization assay comprises analysis of sample microbial cultures using a colorimetric enzyme assay that measures the activity of oxalate oxidase in a culture sample comprising the microbial consortium, wherein the culture sample comprises three or more microbial strains in an appropriate culture medium incubated for 1 hour to 120 hours in the presence of oxalate at a concentration of 0.5 mM to 50 mM, at a pH of 3.5 to 8.0, and at a temperature of 35° C. to 40° C.

In some embodiments, the standardized substrate metabolization assay comprises liquid chromatography-mass spectrometry, wherein the culture sample comprises three or more microbial strains in an appropriate culture medium incubated for 1 hour to 120 hours in the presence of oxalate at a concentration of 0.5 mM to 50 mM, at a pH of 3.5 to 8.0, and at a temperature of 35° C. to 40° C.

In some embodiments, the microbial consortium of the present invention further comprises: a fermenting microbe that metabolizes a fermentation substrate to one or more than one fermentation product; and a synthesizing microbe that catalyzes a synthesis reaction that combines the one or more than one metabolite and the one or more than one fermentation product to generate one or more than one synthesis product.

In some embodiments the one or more than one fermentation product is a second metabolic substrate for the plurality of active microbes or a third metabolic substrate for the synthesizing microbe. In some embodiments the one or more than one synthesis product is a second metabolic substrate for the plurality of active microbes or a fourth metabolic substrate for the fermenting microbe. In some embodiments the fermentation substrate is a polysaccharide and the one or more than one fermentation product is selected from the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H₂, and CO₂. In some embodiments, the fermentation substrate is an amino acid and the one or more than one fermentation product is selected from the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, phloretate, 3-(1H-indol-3-yl)propanoate, 5-aminopentanoate, H₂, H₂S, and CO₂.

In some embodiments the reaction catalyzed by the synthesizing microbe is selected from the group consisting of: synthesis of methane from H₂and CO₂, methane from formate and H₂, acetate from H₂and CO₂, acetate from formate and H₂, acetate and sulfide from H₂, CO₂, and sulfate, propionate and CO₂from succinate, succinate from H₂and fumarate; synthesis of succinate from formate and fumarate, and butyrate, acetate, H₂, and CO₂from lactate.

In some embodiments, the microbial consortium, when administered to an animal on a high oxalate diet, significantly reduces oxalate concentration in a sample selected from the group consisting of blood, serum, stool, or urine, as compared to a sample collected from a corresponding control animal on a high oxalate diet that has not been administered with the microbial consortium.

In some embodiments, the plurality of active microbes comprises 3 microbial strains. In some embodiments, the plurality of active microbes comprises 3 Proteobacteria strains. In some embodiments, the plurality of active microbes comprises 3 Oxalobacter formigenes strains.

In some embodiments, the first metabolic substrate is a bile acid. For example, in some embodiments, the bile acid is lithocholic acid (LCA) or deoxycholic acid (DCA). In In some embodiments, the one or more than one metabolite produced by the plurality of active microbes is a secondary bile acid. For example, in some embodiments, the secondary bile acid is selected from the group consisting of iso-lithocholic acid (iso-LCA), or iso-deoxycholic acid (iso-DCA). In some embodiments, the the supportive community of microbes enhances the conversion of one or more conjugated bile acids selected from the group consisting of taurochenodeoxycholic acid (TCDCA), glycochenodeoxycholic acid (GCDCA), taurocholic acid (TCA), and glycocholic acid (GCA), to cholic acid (CA) or chenodeoxycholic acid (CDCA). In some embodiments, the supportive community of microbes enhances the conversion of CA to 7-beta-cholic acid (7betaCA). In other embodiments, the supportive community of microbes enhances the conversion of CDCA to ursodeoxycholic acid (UDCA).

In some embodiments, at least one of the plurality of active microbes has a higher bile acid metabolization activity at a bile acid concentration of 0.1 mM compared to the bile acid metabolization activity of at least one other of the plurality of active microbes when measured in a standardized bile acid metabolization assay under the same conditions. In some embodiments, at least one of the plurality of active microbes has a higher bile acid metabolizing activity at a bile acid concentration of 0.1 mM compared to a bile acid metabolizing activity of the same active microbe at a higher bile acid concentration. In some embodiments, at least one of the plurality of active microbes has a higher bile acid metabolization activity at a bile acid concentration of 10 mM compared to the bile acid metabolization activity of at least one other of the plurality of active microbes when measured in a standardized bile acid metabolization assay under the same conditions. In some embodiments, at least one of the plurality of active microbes has a higher bile acid metabolizing activity at a bile acid concentration of 10 mM compared to a bile acid metabolizing activity of the same active microbe at a lower bile acid concentration. In some embodiments, one of the plurality of active microbes has a higher bile acid metabolization activity at 0.1 mM of bile acid and another one of the plurality of active microbes has a higher bile acid metabolization activity at 10 mM of bile acid.

In some embodiments, the standardized substrate metabolization assay comprises using liquid chromatography-mass spectrometry to determine the bile acid profile in a culture sample comprising the microbial consortium, wherein the culture sample comprises three or more microbial strains in an appropriate culture media incubated for 1 hour to 96 hours in the presence of bile acids at a concentration of 0.1 mM to 10 mM, at a pH of 3.5 to 8.0, and at a temperature of 35° C. to 40° C.

In some embodiments, the plurality of active microbes comprises one or more microbial phyla selected from Firmicutes and Actinobacteria. In some embodiments, the plurality of active microbes comprises one or more microbial strain selected from Eggerthella lenta and Clostridium scindens.

In some embodiments, the microbial consortium of the present invention is administered as a pre-determined dose ranging from 1×10⁶to 1×10¹³total colony forming units (CFU)/kg.

In some embodiments, the microbial consortium, when administered to the animal, decreases a concentration of the first metabolic substrate in the animal.

In some embodiments the animal provides an experimental model of the disease.

The present disclosure also provides a pharmaceutical composition comprising a microbial consortium and a pharmaceutically acceptable carrier or excipient.

Also provided in the present disclosure is a method of treating a subject diagnosed with or at risk for a metabolic disease or condition selected from the group consisting of primary hyperoxaluria, secondary hyperoxaluria, cholestatic diseases (e.g. primary sclerosing cholangitis, primary biliary cholangitis, progressive familial intrahepatic cholestasis, or nonalcoholic steatohepatitis), and multiple sclerosis with a microbial consortium of the present invention.

In some embodiments, administration of the pharmaceutical composition disclosed herein reduces levels of the first metabolic substrate in a subject by at least 20%, at least 40%, at least 60%, or at least 80% as compared to an untreated control subject or as compared to pre-administration levels of the first metabolic substrate in the subject. In some embodiments, the first metabolic substrate is oxalate. In other embodiments, the first metabolic substrate is DCA or LCA. In some embodiments the level of first metabolic substrate is determined from a blood, serum, stool, or urine sample.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a bar graph of % in vitro growth inhibition of supportive community strains in the presence of 0.5% oxalate (closed bars) or 0.125% oxalate (open bars) in culture media,

FIG. 2A shows a bar graph of in vitro oxalate-metabolizing activities of active microbial strains cultured for 72 hours in Mega Media, pH 7.5, containing 7.5 mM oxalate (closed bars) or 750 μM oxalate (open bars). FIG. 2B shows a bar graph of in vitro oxalate-metabolizing activities of active microbial strains cultured for 72 hours in Chopped Meat Media, pH 7.5, containing 7.5 mM oxalate (closed bars) or 750 μM oxalate (open bars).

FIG. 3A shows a bar graph of in vitro oxalate-metabolizing activities of active microbial strains cultured for 72 hours in Mega Media, at pH 4.5 (closed bars) or 7.2 (open bars), containing 7.5 mM oxalate. FIG. 3B shows a bar graph of in vitro oxalate-metabolizing activities of active microbial strains cultured for 72 hours in Chopped Meat Media, at pH 4.5 (closed bars) or 7.2 (open bars), containing 7.5 mM oxalate.

FIG. 4A shows a bar graph of in vitro oxalate levels (as measured by Absorbance₅₉₅) in microbial cultures comprising Oxalobacter formigenes only, active strains only, supportive strains only, or both active and supportive strains in Mega Medium. FIG. 4B shows a bar graph of in vitro oxalate levels (as measured by Absorbance₅₉₅) in microbial cultures comprising Oxalobacter formigenes only, active strains only, supportive strains only, or both active and supportive strains in Chopped Meat Medium at pH 7.2. Absorbance₅₉₅was measured at the start of microbial culture incubation with 7.5 mM oxalate (t=0 hours, closed bars) and after 72 hours incubation with 7.5 mM oxalate (t=72 hours, open bars).

FIG. 5 shows the percent body weight gain (FIG. 5A), and food consumption (FIG. 5B) of gnotobiotic Balb/c mice on a normal or high oxalate diet, uncolonized or treated by gavage with Oxalobacter formigenes only, active strains only (actives), supportive strains only (supportives), or both active and supportive strains (full community).

FIG. 6 shows urinary oxalate concentrations of gnotobiotic Balb/c mice on a normal (no-oxalate) (FIG. 6A) or high oxalate (oxalate-supplemented) (FIG. 6B) diet, uncolonized (control) or treated by gavage with Oxalobacter formigenes only (formigenes), active strains only (Active), supportive strains only (Support), or both active and supportive strains (Active+Support).

FIG. 7 shows serum liver enzyme/function levels in gnotobiotic Balb/c mice on a normal (non-bold) or high oxalate diet (bold), treated by gavage with Oxalobacter formigenes only (O. formigenes), active strains only (Active), supportive strains only (Supportive), both active and supportive strains (Active+Supportive), or saline vehicle control (Saline). ALT=Alanine transaminase (FIG. 7A), AST=Aspartate transaminase (FIG. 7B), ALB=Albumin (FIG. 7C), ALP=Alanine phosphatase (FIG. 7D), A/G Ratio=Albumin/Globulin Ratio (FIG. 7E), TBIL=Total Bilirubin (FIG. 7F), GGT=Gamma-glutamyl transferase (FIG. 7G), TP=Prothrombin Time (FIG. 7H).

FIG. 8 shows serum kidney enzyme/function levels in gnotobiotic Balb/c mice on a normal (non-bold) or high oxalate diet (bold), treated by gavage with Oxalobacter formigenes only (O. formigenes), active strains only (Active), supportive strains only (Supportive), both active and supportive strains (Active+Supportive), or saline vehicle control (Saline). UREA=Urea (FIG. 8A), CREA=Creatinine (FIG. 8B), PHOS=Phosphorus (FIG. 8C), CA=Calcium (FIG. 8D), CL=Chloride FIG. 8E), NA=Sodium (FIG. 8F), K=Potassium (FIG. 8G), GLOB=Globulin (FIG. 8H).

FIG. 9 shows serum triglyceride (TRIG, FIG. 9A), cholesterol (CHOL, FIG. 9B), glucose (GLUC, FIG. 9C), and creatine kinase (CK, FIG. 9D) levels in gnotobiotic Balb/c mice on a normal (non-bold) or high oxalate diet (bold), treated by gavage with Oxalobacter formigenes only (O. formigenes), active strains only (Active), supportive strains only (Supportive), both active and supportive strains (Active+Supportive), or saline vehicle control.

FIG. 10 shows microbial species in fecal samples collected at the time of gavage or 2 weeks post-gavage from gnotobiotic Balb/c mice on a normal (Control; FIG. 10A, FIG. 10B, and FIG. 10C) or high oxalate (High-Ox; FIG. 10D, FIG. 10E, and FIG. 10F) diet, treated with active strains only (Actives; FIG. 10A and FIG. 10D), supportive strains only (Supportives; FIG. 10B and FIG. 10E), or active and supportive strains (Actives+Supportives; FIG. 10C and FIG. 10F).

FIG. 11 shows a bar graph of in vitro oxalate levels (as measured by LC-MS) in microbial cultures comprising a donor-derived strain grown in YCFAC base medium for 120 h at either pH 7.0 (white bars), pH 6.0 (grey bars), or pH 5.0 (black bars). % oxalate remaining is calculated relative to the amount of oxalate present at the start of the assay (2 mM). Oxalate levels in the pH 6.0 and pH 7.0 O. formigenes cultures (FBI00067) were below the limit of detection at the conclusion of the assay (<1.9% and <1.7% oxalate remaining, respectively).

FIG. 12 shows growth of cultures of donor-derived O. formigenes strains grown in YCFAC base medium supplemented with the indicated concentration of oxalate (0 mM, 2 mM, 40 mM, 80 mM, 120 mM, 160 mM) and grown for 144 hours (x-axis). Cultures are monitored by turbidity (OD600; y-axis). FIG. 12A-C show culture growth at pH 7.0 for the indicated strains, FIG. 12D-F show culture growth at pH 6.0 for the indicated strains, and FIG. 12G-I show culture growth at pH 5.0 for the indicated strains.

FIG. 13 shows urinary oxalate levels in germ-free C57Bl/6NTac mice (n=4 per condition) fed a low-complexity high-oxalate diet, uncolonized (−) or treated by gavage with one of 5 candidate microbial consortia (I to V) or a proof-of-concept consortium (+).

FIG. 14 shows urinary oxalate levels in germ-free C57Bl/6NTac mice (n=4 per condition) fed a high-complexity diet and given oxalate-supplemented drinking water, uncolonized (−) or treated by gavage with one of 5 candidate microbial consortia (I to V) or a positive-control consortium (+).

FIG. 15 shows urinary oxalate levels in germ-free C57Bl/6NTac mice (n=4 per condition) which were colonized with a non-oxalate-controlling human microbiome prior to the study. Mice were fed a high-complexity diet and given oxalate-supplemented drinking water, cleared of the human microbiome by antibiotic treatment, and were either left uncolonized (−) or were recolonized by gavage with one of 5 candidate microbial consortia (I to V), a positive-control consortium containing commercial strains (+), or a collection of donor-derived strains (“Putative Oxalate Degraders Only”) comprising 3 O. formigenes strains and a set of additional strains which had been preliminarily classified as oxalate-degrading.

FIG. 16 shows the diversity of microbial strains in fecal samples from the mice of FIG. 15 (measured by metagenomic sequencing).

FIG. 17 shows the relative abundance (FIG. 17A) and absolute abundance (FIG. 17B) of O. formigenes in feces of germ-free mice treated with a candidate microbial consortium (I to V) or a supportive community alone that lacks O. formigenes.

FIG. 18 shows the concentration of various bile acid compounds (including TCA, CA, and DCA) in cultures of commercial strains that were spiked with 100 μM TCA and incubated for 24 h at 37° C.

DETAILED DESCRIPTION

Disclosed herein are microbial consortia for administration to an animal comprising a plurality of active microbes which metabolize a first metabolic substrate which causes or contributes to disease in the animal. The microbial consortia disclosed herein further comprise an effective amount of a supportive community of microbes that metabolize one or more than one metabolite produced by the plurality of active microbes, and wherein the one or more than one metabolite inhibits metabolism of the plurality of active microbes. These microbial consortia are advantageous in having enhanced characteristics when administered to an animal as compared to administration of the plurality of active microbes alone Enhanced characteristics of the microbial consortia include one or more of improved gastrointestinal engraftment, increased biomass, increased metabolism of the first metabolic substrate, and improved longitudinal stability.

To facilitate an understanding of the present invention, a number of terms and phrases are defined below.

The term “a” and “an” as used herein mean “one or more” and include the plural unless the context is appropriate

As used herein, the term “active microbes” refers to microbes that express sufficient amounts of one or more than one metabolic enzyme to metabolize a substrate that causes or contributes to disease in an animal.

As used herein, the term “biomass,” refers to the total mass of one or more than one microbe, or consortium in a given area or volume.

As used herein, the term “microbial consortium,” refers to a mixture of two or more microbial strains wherein one microbial strain in the mixture has a beneficial or desired effect on another microbial strain in the mixture.

As used herein, the term “gastrointestinal engraftment” refers to the establishment of one or more than one microbe, or microbial consortium, in one or more than one niche of the gastrointestinal tract that, prior to administration of the one or more than one microbe, or microbial consortium, is absent in the one or more than one microbe, or microbial consortium. Gastrointestinal engraftment may be transient, or may be persistent.

As used herein, the term “effective amount” refers to an amount sufficient to achieve a beneficial or desired result. In some embodiments, an effective amount can be improved gastrointestinal engraftment of one or more than one of the plurality of active microbes, increased biomass of one or more than one of the plurality of active microbes, increased metabolism of the first metabolic substrate, or improved longitudinal stability).

As used herein, the term “fermenting microbe” refers to a microbe that expresses sufficient amounts of one or more than one enzyme to catalyze a fermentation reaction in a gastrointestinal niche.

As used herein, the term “longitudinal stability” refers to the ability of one or more than one microbe, or microbial consortium to remain engrafted and metabolically active in one of more than one niche of the gastrointestinal tract despite transient or long-term environmental changes to the gastrointestinal niche.

As used herein, the term “metabolism,” “metabolize,” “metabolization,” or variants thereof refers to the biochemical conversion of a metabolic substrate to a metabolic product. In some embodiments, metabolization includes isomerization.

As used herein, the term “microbe” refers to a microbial organism including, but not limited to, bacteria, archaea, protozoa, and unicellular fungi.

As used herein, the term “microbial consortium” refers to a preparation of two or more microbes wherein the metabolic product of one of the two or more microbes is the metabolic substrate for one other microbe comprising the consortium.

As used herein, the term “pharmaceutical composition” refers to the combination of an active agent with a carrier, inert or active, making the composition especially suitable for therapeutic use in vivo or ex vivo.

As used herein, the term “pharmaceutically acceptable carrier” refers to any of the standard pharmaceutical carriers, such as phosphate buffered saline solution, water, emulsions (e.g., such as oil/water or water/oil emulsions), and various types of wetting agents. The compositions also can include stabilizers and preservatives. For examples of carriers, stabilizers, and adjuvants, see e.g., Martin, Remington's Pharmaceutical Sciences, 15^thEd. Mack Publ. Co., Easton, Pa. [1975].

As used herein, “significantly” or “significant” refers to a change or alteration in a measurable parameter to a statistically significant degree as determined in accordance with an appropriate statistically relevant test. For example, in some embodiments, a change or alteration is significant if it is statistically significant in accordance with, e.g., a Student's t-test, chi-square, or Mann Whitney test.

As used herein, the term “standardized substrate metabolization assay” refers to an experimental assay known to persons of ordinary skill in the art used to quantify the amount of substrate converted to a metabolic product.

As used herein, the term “subject” refers to an organism to be treated by the microbial consortium and compositions described herein. Such organisms preferably include, but are not limited to, mammals (e.g., murines, simians, equines, bovines, porcines, canines, felines, and the like), and more preferably include humans.

As used herein, the term “supportive community” refers to one or more than one microbial strain that, when administered with an active microbe, enhances one or more than one characteristic of the active microbe selected from the group consisting of gastrointestinal engraftment, biomass, metabolic substrate metabolism, and longitudinal stability.

As used herein, the term “synthesizing microbe” refers to a microbe that expresses sufficient amounts of one or more than one enzyme to catalyze the combination of one or more than one metabolite produced by an active microbe, and one or more than one fermentation product produced by a fermenting microbe in a gastrointestinal niche.

The term percent “identity” or “sequence identity,” in the context of two or more nucleic acid or polypeptide sequences, refer to two or more sequences or subsequences that have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned for maximum correspondence, as measured using one of the sequence comparison algorithms described below (e.g., BLASTP and BLASTN or other algorithms available to persons of skill) or by visual inspection. Depending on the application, the percent “identity” can exist over a region of the sequence being compared, e.g., over a functional domain, or, alternatively, exist over the full length of the two sequences to be compared.

For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.

Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see generally Ausubel et al., infra).

One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm, which is described in Altschul et al., J. Mol. Biol. 215:403-410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov/).

When used in reference to 16S rRNA sequences, a “sequence identity” of at least 97% indicates that two microbial strains are likely to belong to the same species, whereas 16S rRNA sequences having less than 97% sequence identity indicate that two microbial strains likely belong to different species, and 16S rRNA sequences having less than 95% sequence identity indicates that two microbial strains likely belong to distinct genera (Stackebrandt E., and Goebel, B. M., Int J Syst Bact, 44 (1994) 846-849.).

Throughout the description, where compositions are described as having, including, or comprising specific components, or where processes and methods are described as having, including, or comprising specific steps, it is contemplated that, additionally, there are compositions of the present invention that consist essentially of, or consist of, the recited components, and that there are processes and methods according to the present invention that consist essentially of, or consist of, the recited processing steps.

As a general matter, compositions specifying a percentage are by weight unless otherwise specified. Further, if a variable is not accompanied by a definition, then the previous definition of the variable controls.

Biological Niches

The present invention provides microbial consortia capable of engrafting into one or more than one niche of a gastrointestinal tract where it is capable of metabolizing a substrate that causes or contributes to disease in an animal. These niches comprise specific microbial communities whose composition varies according to a number of environmental factors including, but not limited to, the particular physical compartment of the gastrointestinal tract inhabited by a microbial community, the chemical and physicochemical properties of the environment inhabited, the metabolic substrate composition of the environment inhabited, and other co-inhabiting microbial species.

Physical Compartments

A gastrointestinal tract comprises a number of physical compartments. For example, the human gastrointestinal tract includes the oral cavity, pharynx, esophagus, stomach, small intestine (duodenum, jejunum, ileum), cecum, large intestine (ascending colon, transverse colon, descending colon), and rectum. The pancreas, liver, gallbladder, and associated ducts, additionally comprise compartments of the human gastrointestinal tract. Each of these compartments has, for example, variable anatomical shape and dimension, aeration, water content, levels of mucus secretion, luminal presence of antimicrobial peptides, and presence or absence of peristaltic motility. Furthermore, the different gastrointestinal compartments vary in their pH. In humans, the pH of the oral cavity, upper stomach, lower stomach, duodenum, jejunum, ileum, and colon range from 6.5-7.5, 4.0-6.5, 1.5-4.0, 7.0-8.5, 4.0-7.0, and 4.0-7.0, respectively. Compartments of the gastrointestinal tract also differ in their levels of oxygenation which are subject to large degrees of fluctuation. For example, the luminal partial pressure of oxygen in the stomach of mice has been measured to be approximately 58 mm Hg, while the luminal partial pressure of oxygen in the distal sigmoid colon has been measured to be approximately 3 mm Hg (He et al., 1999). Oxygen levels of the gastrointestinal tract are highly determinative of the biochemical pathways utilized by commensal microbes. For example, commensal bacteria utilize aerobic respiration at oxygen concentrations above 5 mbar of 02, anaerobic respiration between 1-5 mbar of 02, and fermentation at 02 concentrations below 1 mbar. The sensitivity of microbes to 02 levels and their ability to carry out metabolic reactions under aerobic and/or anaerobic conditions influences which microbial species engraft in a particular gastrointestinal compartment.

Metabolic Compartments

In addition to the various physical and chemical environments contributing to a gastrointestinal niche, different niches comprise different metabolic substrates.

Metabolic substrates that may be present in a gastrointestinal niche may include, but are not limited to, oxalate, fructan, inulin, glucuronoxylan, arabinoxylan, glucomannan, β-mannan, dextran, starch, arabinan, xyloglucan, galacturonan, β-glucan, galactomannan, rhamnogalacturonan I, rhamnogalacturonan II, arabinogalactan, mucin O-linked glycans, yeast α-mannan, yeast β-glucan, chitin, alginate, porphyrin, laminarin, carrageenan, agarose, alternan, levan, xanthan gum, galactooligosaccharides, hyaluronan, chondrointin sulfate, dermatan sulfate, heparin sulfate, keratan sulfate, phenylalanine, tyrosine, tryptophan, leucine, valine, isoleucine, glycine, proline, asparagine, glutamine, aspartate, glutamate, cysteine, lysine, arginine, serine, methionine, alanine, arginine, histidine, ornithine, citrulline, carnitine, hydroxyproline, cholic acid, chenodeoxycholic acid, taurochenodeoxycholic acid, glycochenodeoxycholic acid, cholesterol, cinnamic acid, coumaric acid, sinapinic acid, ferulic acid, caffeic acid, quinic acid, chlorogenic acid, catechin, epicatechin, gallic acid, pyrogallol, catechol, quercetin, myricetin, campherol, luteolin, apigenin, naringenin, and hesperidin.

Microbial Consortia

The present invention provides microbial consortia comprising a plurality of active microbes and an effective amount of a supportive community of microbes. In some embodiments, a microbial consortium comprises 3 to 500 microbial strains. For example, in some embodiments, a microbial consortium comprises 3 to 500, 4 to 500, 5 to 500, 6 to 500, 7 to 500, 8 to 500, 9 to 500, 10 to 500, 11 to 500, 12 to 500, 13 to 500, 14 to 500, 15 to 500, 16 to 500, 17 to 500, 18 to 500, 19 to 500, 20 to 500, 21 to 500, 22 to 500, 23 to 500, 24 to 500, 25 to 500, 30 to 500, 35 to 500, 40 to 500, 45 to 500, 50 to 500, 60 to 500, 70 to 500, 80 to 500, 90 to 500, 100 to 500, 110 to 500, 120 to 500, 130 to 500, 140 to 500, 150 to 500, 160 to 500, 170 to 500, 180 to 500, 190 to 500, 200 to 500, 210 to 500, 220 to 500, 230 to 500, 240 to 500, 250 to 500, 260 to 500, 270 to 500, 280 to 500, 290 to 500, 300 to 500, 400 to 500, 3 to 300, 4 to 300, 5 to 300, 6 to 300, 7 to 300, 8 to 300, 9 to 300, 10 to 300, 11 to 300, 12 to 300, 13 to 300, 14 to 300, 15 to 300, 16 to 300, 17 to 300, 18 to 300, 19 to 300, 20 to 300, 21 to 300, 22 to 300, 23 to 300, 24 to 300, 25 to 300, 30 to 300, 35 to 300, 40 to 300, 45 to 300, 50 to 300, 60 to 300, 70 to 300, 80 to 300, 90 to 300, 100 to 300, 110 to 300, 120 to 300, 130 to 300, 140 to 300, 150 to 300, 160 to 300, 170 to 300, 180 to 300, 190 to 300, 200 to 300, 210 to 300, 220 to 300, 230 to 300, 240 to 300, 250 to 300, 260 to 300, 270 to 300, 280 to 300, 290 to 300, 3 to 250, 4 to 250, 5 to 250, 6 to 250, 7 to 250, 8 to 250, 9 to 250, 10 to 250, 11 to 250, 12 to 250, 13 to 250, 14 to 250, 15 to 250, 16 to 250, 17 to 250, 18 to 250, 19 to 250, 20 to 250, 21 to 250, 22 to 250, 23 to 250, 24 to 250, 25 to 250, 30 to 250, 35 to 250, 40 to 250, 45 to 250, 50 to 250, 60 to 250, 70 to 250, 80 to 250, 90 to 250, 100 to 250, 110 to 250, 120 to 250, 130 to 250, 140 to 250, 150 to 250, 160 to 250, 170 to 250, 180 to 250, 190 to 250, 200 to 250, 210 to 250, 220 to 250, 230 to 250, 240 to 250, 3 to 200, 4 to 200, 5 to 200, 6 to 200, 7 to 200, 8 to 200, 9 to 200, 10 to 200, 11 to 200, 12 to 200, 13 to 200, 14 to 200, 15 to 200, 16 to 200, 17 to 200, 18 to 200, 19 to 200, 20 to 200, 21 to 200, 22 to 200, 23 to 200, 24 to 200, 25 to 200, 30 to 200, 35 to 200, 40 to 200, 45 to 200, 50 to 200, 60 to 200, 70 to 200, 80 to 200, 90 to 200, 100 to 200, 110 to 200, 120 to 200, 130 to 200, 140 to 200, 150 to 200, 160 to 200, 170 to 200, 180 to 200, 190 to 200, 3 to 150, 4 to 150, 5 to 150, 6 to 150, 7 to 150, 8 to 150, 9 to 150, 10 to 150, 11 to 150, 12 to 150, 13 to 150, 14 to 150, 15 to 150, 16 to 150, 17 to 150, 18 to 150, 19 to 150, 20 to 150, 21 to 150, 22 to 150, 23 to 150, 24 to 150, 25 to 150, 30 to 150, 35 to 150, 40 to 150, 45 to 150, 50 to 150, 60 to 150, 70 to 150, 80 to 150, 90 to 150, 100 to 150, 110 to 150, 120 to 150, 130 to 150, 140 to 150, 3 to 100, 4 to 100, 5 to 100, 6 to 100, 7 to 100, 8 to 100, 9 to 100, 10 to 100, 11 to 100, 12 to 100, 13 to 100, 14 to 100, 15 to 100, 16 to 100, 17 to 100, 18 to 100, 19 to 100, 20 to 100, 21 to 100, 22 to 100, 23 to 100, 24 to 100, 25 to 100, 30 to 100, 35 to 100, 40 to 100, 45 to 100, 50 to 100, 60 to 100, 70 to 100, 80 to 100, 90 to 100, 3 to 75, 4 to 75, 5 to 75, 6 to 75, 7 to 75, 8 to 75, 9 to 75, 10 to 75, 11 to 75, 12 to 75, 13 to 75, 14 to 75, 15 to 75, 16 to 75, 17 to 75, 18 to 75, 19 to 75, 20 to 75, 21 to 75, 22 to 75, 23 to 75, 24 to 75, 25 to 75, 30 to 75, 35 to 75, 40 to 75, 45 to 75, 50 to 75, 60 to 75, 70 to 75, 3 to 50, 4 to 50, 5 to 50, 6 to 50, 7 to 50, 8 to 50, 9 to 50, 10 to 50, 11 to 50, 12 to 50, 13 to 50, 14 to 50, 15 to 50, 16 to 50, 17 to 50, 18 to 50, 19 to 50, 20 to 50, 21 to 50, 22 to 50, 23 to 50, 24 to 50, 25 to 50, 30 to 50, 35 to 50, 40 to 50, 45 to 50, 3 to 25, 4 to 25, 5 to 25, 6 to 25, 7 to 25, 8 to 25, 9 to 25, 10 to 25, 11 to 25, 12 to 25, 13 to 25, 14 to 25, 15 to 25, 16 to 25, 17 to 25, 18 to 25, 19 to 25, 20 to 25, 21 to 25, 22 to 25, 23 to 25, or 24 to 25 microbial strains. For example, in some embodiments, a microbial consortium comprises about 20 to about 200, about 70 to about 80, about 80 to about 90, about 100 to about 110, or about 150 to about 160 microbial strains.

In some embodiments, a microbial consortium described herein comprises a microbial strain having a relative abundance of approximately 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, 5%, 1%, 0.1%, 0.01%, 0.001%, 0.0001%, 0.00001%, or 0.000001% of the total microbial consortium. In some embodiments, the relative abundance of a microbial strain is determined by metagenomic sequencing and calculated as the percentage of reads that are classified as an identified microbial strain, divided by the genome size. For example, in some embodiments, the relative abundance of a microbial strain of the invention is determined by metagenomic shotgun sequencing.

Active Microbes

The microbial consortia of the present invention comprise a plurality of active microbes capable of metabolizing a first metabolic substrate that causes or contributes to disease in an animal. In some embodiments, the current invention provides a microbial consortium capable of metabolizing the first metabolic substrate at a pH within a range of 4 to 8. For example, in some embodiments, one or more than one of the plurality of active microbes is capable of metabolizing a first metabolic substrate at a pH within a range of 4 to 8, 4.2 to 8, 4.4 to 8, 4.6 to 8, 4.8 to 8, 5 to 8, 5.2 to 8, 5.4 to 8, 5.6 to 8, 5.8 to 8, 6 to 8, 6.2 to 8, 6.4 to 8, 6.6 to 8, 6.8 to 8, 7 to 8, 7.2 to 8, 7.4 to 8, 7.6 to 8, 7.8 to 8, 4 to 7, 4.2 to 7, 4.4 to 7, 4.6 to 7, 4.8 to 7, 5 to 7, 5.2 to 7, 5.4 to 7, 5.6 to 7, 5.8 to 7, 6 to 7, 6.2 to 7, 6.4 to 7, 6.6 to 7, 6.8 to 7, 4 to 6, 4.2 to 6, 4.4 to 6, 4.6 to 6, 4.8 to 6, 5 to 6, 5.2 to 6, 5.4 to 6, 5.6 to 6, 5.8 to 6, 4 to 6, 4.2 to 6, 4.4 to 6, 4.6 to 6, 4.8 to 6, 5 to 6, 5.2 to 6, 5.4 to 6, 5.6 to 6, or 5.8 to 6.

In some embodiments, the plurality of active microbes comprises one microbial strain having a significantly different first metabolic substrate-metabolizing activity in a standard substrate-metabolizing assay conducted at two pH values differing by 1 pH unit and within a pH range of 4 to 8. In some embodiments, the difference between the two pH values is 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.2, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, or 4.0 pH units. For example, in some embodiments, one microbial strain has significantly different first metabolic substrate-metabolizing activities in a standard substrate metabolizing assay at pH 4 and pH 8, pH 5 and pH 8, pH 6 and pH 8, pH 7 and pH 8, pH 4 and pH 7, pH 5 and pH 7, pH 6 and pH 7, pH 4 and pH 6, pH 5 and pH 6, or pH 4 and pH 5.

As used herein, “lower pH” refers to a pH in a standardized substrate metabolization assay that is lower in value as compared to another pH value. For example, a standardized substrate metabolization assay performed at pH 4.5 has a lower pH as compared to a standardized substrate metabolization assay preformed at a pH of 7.5. “Higher pH,” as used herein, refers to a pH in a standardized substrate metabolization assay that is higher in value as compared to another pH value. For example a standardized substrate metabolization assay preformed at pH 7.5 has a higher pH as compared to a standardized substrate metabolization assay performed at a pH of 4.5.

As used herein, “higher first metabolic substrate-metabolizing activity” means either a first metabolic substrate-metabolizing activity of a microbial strain that is higher as compared to a first metabolic substrate-metabolizing activity of the same microbial strain under different conditions, and/or a first metabolic substrate-metabolizing activity of a microbial strain that is higher as compared to a first metabolic substrate-metabolizing activity of a different microbial strain under the same conditions.

In some embodiments, the plurality of active microbes comprises two microbial strains having significantly different first metabolic substrate-metabolizing activities. For example, in some embodiments, one of the plurality of active microbes has a significantly higher first metabolic substrate-metabolizing activity at a lower pH as compared to the first metabolic substrate-metabolizing activity of another microbial strain in the plurality of active microbes at the same lower pH. In some embodiments, one of the plurality of active microbes has a significantly higher first metabolic substrate-metabolizing activity at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 as compared to the first metabolic substrate-metabolizing activity of another microbial strain in the plurality of active microbes at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5, respectively. In some embodiments, one of the plurality of active microbes has a significantly higher first metabolic substrate-metabolizing activity at a higher pH as compared to the first metabolic substrate-metabolizing activity of another microbial strain in the plurality of active microbes at the same higher pH. In some embodiments, one of the plurality of active microbes has a significantly higher first metabolic substrate-metabolizing activity at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 as compared to the first metabolic substrate-metabolizing activity of another microbial strain in the plurality of active microbes at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0, respectively.

In some embodiments, one of the plurality of active microbes has a significantly higher first metabolic substrate-metabolizing activity at a lower pH as compared to its first metabolic substrate-metabolizing activity at a higher pH. For example, in some embodiments one of the plurality of active microbes has a significantly higher first metabolic substrate-metabolizing activity at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 than it does at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0. In some embodiments, one of the plurality of active microbes has a significantly higher first metabolic substrate-metabolizing activity at a higher pH as compared to its first metabolic substrate-metabolizing activity at a lower pH. For example, in some embodiments one of the plurality of active microbes has a significantly higher first metabolic substrate-metabolizing activity at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 than it does at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5.

In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at a lower pH and another microbe having a higher first metabolic substrate-metabolizing activity at a higher pH. For example, in some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 8.0. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 4.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 8.0. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 8.0. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 5.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 8.0. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.0 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 8.0. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at pH 6.5 and another microbe having a higher first metabolic substrate-metabolizing activity at pH 8.0.

In some embodiments, the plurality of active microbes comprises one microbial strain having a significantly different first metabolic substrate-metabolizing activity in a standard substrate-metabolizing assay conducted at a first metabolic substrate concentration as compared to its first metabolic substrate-metabolizing activity in a standard substrate-metabolizing assay conducted at a different first metabolic substrate concentration, wherein the difference between the two first metabolic substrate concentrations is within a 100 fold range. In some embodiments, the difference between the two first metabolic concentrations is 1.2 fold. For example, in some embodiments, the difference between the two first metabolic substrate concentrations is at least 1.2 fold, 1.4 fold, 1.6 fold, 1.8 fold, 2.0 fold, 4 fold, 6 fold, 8 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold or greater.

As used herein, “lower concentration of first metabolic substrate” refers to a substrate concentration in a standardized substrate metabolization assay that is lower in value as compared to another substrate concentration. “Higher concentration of first metabolic substrate,” as used herein, refers to a substrate concentration in a standardized substrate metabolization assay that is higher in value as compared to another substrate concentration.

In some embodiments, one of the plurality of active microbes has a significantly higher first metabolic substrate-metabolizing activity at a lower concentration of first metabolic substrate as compared to its first metabolic substrate-metabolizing activity at a higher concentration of first metabolic substrate. In some embodiments, one of the plurality of active microbes has a significantly higher first metabolic substrate-metabolizing activity at a higher concentration of first metabolic substrate as compared to its first metabolic substrate-metabolizing activity at a lower concentration of first metabolic substrate.

In some embodiments, the plurality of active microbes comprises an active microbe having a higher first metabolic substrate-metabolizing activity at a lower concentration of first metabolic substrate and another microbe having a higher first metabolic substrate-metabolizing activity at a higher concentration of first metabolic substrate. For example, in some embodiments, the difference between the lower concentration of first metabolic substrate and the higher concentration of first metabolic substrate is at least 1.2 fold, 1.4 fold, 1.6 fold, 1.8 fold, 2.0 fold, 4 fold, 6 fold, 8 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold or greater.

In some embodiments, the plurality of active microbes comprises two microbial strains having significantly different growth rates. For example, in some embodiments, one of the plurality of active microbes has a significantly higher growth rate at a lower pH as compared to the growth rate of another microbial strain in the plurality of active microbes at the same lower pH. In some embodiments, one of the plurality of active microbes has a significantly higher growth rate at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 as compared to the growth rate of another microbial strain in the plurality of active microbes at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5, respectively. In some embodiments, one of the plurality of active microbes has a significantly higher growth rate at a higher pH as compared to the growth rate of another microbial strain in the plurality of active microbes at the same higher pH. In some embodiments, one of the plurality of active microbes has a significantly higher growth rate at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 as compared to the growth rate of another microbial strain in the plurality of active microbes at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0, respectively.

In some embodiments, one of the plurality of active microbes has a significantly higher growth rate at a lower pH as compared to its growth rate at a higher pH. For example, in some embodiments one of the plurality of active microbes has a significantly higher growth rate at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 than it does at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0. In some embodiments, one of the plurality of active microbes has a significantly higher growth rate at a higher pH as compared to its growth rate at a lower pH. For example, in some embodiments one of the plurality of active microbes has a significantly higher growth rate at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 than it does at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5.

In some embodiments, the plurality of active microbes comprises one microbial strain having a significantly higher growth rate when cultured in media containing a certain concentration of first metabolic substrate concentration as compared to the growth rate of another microbial strain in the plurality of active microbes cultured in the same media containing the same concentration of the first metabolic substrate. In some embodiments, the difference between the two growth rates is at least 0.2 fold, at least 0.4 fold, at least 0.6 fold, at least 0.8 fold, at least 1.0 fold, at least 1.2 fold, at least 1.4 fold, at least 1.6 fold, at least 1.8 fold, or at least 2.0 fold.

In some embodiments, the first metabolic substrate may be selected from, but not limited to, oxalate and a bile acid (e.g., lithocholic acid (LCA), deoxycholic acid (DCA)).

In some embodiments, the current disclosure provides a microbial consortium comprising a plurality of active microbes capable of metabolizing a first metabolic substrate to one or more than one metabolite. For example, in some embodiments, the one or more than one metabolite may be selected from, but not limited to, formate, CO₂, and a secondary bile acid (e.g., 3-oxo-deoxycholic acid (3 oxoDCA), 3-oxo-lithocholic acid (3oxoLCA), iso-lithocholic acid (iso-LCA), or iso-deoxycholic acid (iso-DCA)). In some embodiments, the plurality of active microbes can comprise 2 to 200 microbial strains. For example, in some embodiments, a microbial consortium comprises 2 to 10, 2 to 15, 2 to 20, 2 to 25, 2 to 30, 2 to 35, 2 to 40, 2 to 45, 2 to 50, 2 to 75, 2 to 100, 2 to 125, 2 to 150, 2 to 175, or 2 to 200 active microbial strains. In certain embodiments, the plurality of active microbes can comprise 2 to 20 microbial strains.

Oxalate Metabolizing Active Microbes

In one aspect, the current disclosure provides a microbial consortium comprising a plurality of active microbes that metabolize oxalate. In some embodiments, each of the plurality of active microbes that metabolize oxalate express sufficient amounts of one or more than one enzyme involved in oxalate metabolism. For example, in some embodiments, one or more than one active microbe expresses formyl-CoA transferase (Frc), an oxalate-formate antiporter (e.g., OxIT), and oxalyl-CoA decarboxylase (e.g., OxC), and/or oxalate decarboxylase (e.g., OxD).

In some embodiments, the plurality of active microbes that metabolize oxalate comprise 2 to 20 oxalate-metabolizing microbial strains. For example, in some embodiments, a microbial consortium comprises 2 to 20, 3 to 20, 4 to 20, 5 to 20, 6 to 20, 7 to 20, 8 to 20, 9 to 20, 10 to 20, 11 to 20, 12 to 20, 13 to 20, 14 to 20, 15 to 20, 16 to 20, 17 to 20, 18 to 20, 19 to 20, 2 to 18, 3 to 18, 4 to 18, 5 to 18, 6 to 18, 7 to 18, 8 to 18, 9 to 18, 10 to 18, 11 to 18, 12 to 18, 13 to 18, 14 to 18, 15 to 18, 16 to 18, 17 to 18, 2 to 16, 3 to 16, 4 to 16, 5 to 16, 6 to 16, 7 to 16, 8 to 16, 9 to 16, 10 to 16, 11 to 16, 12 to 16, 13 to 16, 14 to 16, 15 to 16, 2 to 14, 3 to 14, 4 to 14, 5 to 14, 6 to 14, 7 to 14, 8 to 14, 9 to 14, 10 to 14, 11 to 14, 12 to 14, 13 to 14, 2 to 13, 3 to 13, 4 to 13, 5 to 13, 6 to 13, 7 to 13, 8 to 13, 9 to 13, 10 to 13, 11 to 13, 12 to 13, 2 to 12, 3 to 12, 4 to 12, 5 to 12, 6 to 12, 7 to 12, 8 to 12, 9 to 12, 10 to 12, 11 to 12, 2 to 12, 3 to 12, 4 to 12, 5 to 12, 6 to 12, 7 to 12, 8 to 12, 9 to 12, 10 to 12, 11 to 12, 2 to 10, 3 to 10, 4 to 10, 5 to 10, 6 to 10, 7 to 10, 8 to 10, 9 to 10, 2 to 10, 3 to 10, 4 to 10, 5 to 10, 6 to 10, 7 to 10, 8 to 10, 9 to 10, 2 to 8, 3 to 8, 4 to 8, 5 to 8, 6 to 8, 7 to 8, 2 to 6, 3 to 6, 4 to 6, 5 to 6, 2 to 4, or 3 to 4 oxalate-metabolizing strains of microbes. In some embodiments, the plurality of active microbes comprises 3 strains of oxalate-metabolizing microbes. In some embodiments the plurality of active microbes consists of 3 strains of oxalate-metabolizing microbes.

In some embodiments, the plurality of active microbes that metabolize oxalate may comprise one or more microbial species selected from, but not limited to Oxalobacter formigenes, Bifidobacterium sp., Bifidobacterium dentium, Dialister invisus, Lactobacillus acidophilus, Lactobacillus gasseri, Lactobacillus helveticus, Lactobacillus reuteri, Eggerthella lenta, Lactobacillus rhamnosus, Enterococcus faecalis, Enterococcus gallinarum, Enterococcus faecium, Providencia rettgeri, Streptococcus thermophilus, Lactobacillus plantarum, Lactobacillus casei, Lactobacillus salivarius, Lactobacillus johnsii, Bifidobacterium infantis, Bifidobacterium animalis, Clostridium sporogenes, Leuconostoc lactis, Leuconostoc mesenteroides.

In some embodiments the plurality of active microbes that metabolize oxalate may comprise two or more microbial species selected from, but not limited to, Bifidobacterium dentium ATCC 27678, Enterococcus faecalis HM-432, Lactobacillus helveticus DSM 20075, Bifidobacterium dentium ATCC 27680, Lactobacillus acidophilus ATCC 4357, Lactobacillus reuteri HM-102, Bifidobacterium dentium DSM 20221, Lactobacillus acidophilus DSM 20079, Lactobacillus rhamnosus ATCC 53103, Bifidobacterium dentium DSM 20436, Lactobacillus acidophilus DSM 20242, Lactobacillus rhamnosus DSM 20245, Bifidobacterium sp. HM-868, Lactobacillus gasseri ATCC 33323, Lactobacillus rhamnosus DSM 8746, Dialister invisus DSM 15470, Lactobacillus gasseri DSMZ 107525, Lactobacillus rhamnosus HM-106, Eggerthella lenta ATCC 43055, Lactobacillus gasseri DSMZ 20077, Oxalobacter formigenes ATCC 35274, Eggerthella lenta DSM 2243, Lactobacillus gasseri HM-104, Oxalobacter formigenes DSM 4420, Enterococcus faecalis HM-202, Lactobacillus gasseri HM-644, and Oxalobacter formigenes HM-1.

In some embodiments, the plurality of active microbes comprises an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 67, SEQ ID NO: 133, or SEQ ID NO:289. In some embodiments, the plurality of active microbes comprises an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 67, SEQ ID NO: 133, or SEQ ID NO:289.

In some embodiments the plurality of active microbes comprises an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 67 and an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 133. In some embodiments, the plurality of active microbes comprises an Oxalobacter formigenes strain having a 16S sequence 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%, identical to SEQ ID NO: 67 and an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 133.

In some embodiments the plurality of active microbes comprises an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 133 and an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 289. In some embodiments, the plurality of active microbes comprises an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 133 and an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 289.

In some embodiments the plurality of active microbes comprises an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 67 and an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 289. In some embodiments, the plurality of active microbes comprises an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 67 and an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 289.

In some embodiments the plurality of active microbes comprises an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 67, an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 133, and an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 289. In some embodiments the plurality of active microbes comprises an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 67, an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 133, and an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 289.

In some embodiments the plurality of active microbes consists of an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 67, an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 133, and an Oxalobacter formigenes strain having a 16S sequence at least 80% identical to SEQ ID NO: 289. In some embodiments the plurality of active microbes consists of an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 67, an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 133, and an Oxalobacter formigenes strain having a 16S sequence 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% identical to SEQ ID NO: 289.

As used herein, “substantially metabolizing oxalate,” “substantial metabolization of oxalate,” and variants thereof, refer to a statistically significant reduction in the amount of oxalate in an in vitro assay (for example, as described in Example 3). In some embodiments, one or more than one of the plurality of active microbes is capable of substantially metabolizing oxalate at a pH within a range of 4 to 8. For example, in some embodiments, one or more than one of the plurality of active microbes is capable of metabolizing oxalate at a pH within a range of 4 to 8, 4.2 to 8, 4.4 to 8, 4.6 to 8, 4.8 to 8, 5 to 8, 5.2 to 8, 5.4 to 8, 5.6 to 8, 5.8 to 8, 6 to 8, 6.2 to 8, 6.4 to 8, 6.6 to 8, 6.8 to 8, 7 to 8, 7.2 to 8, 7.4 to 8, 7.6 to 8, 7.8 to 8, 4 to 7, 4.2 to 7, 4.4 to 7, 4.6 to 7, 4.8 to 7, 5 to 7, 5.2 to 7, 5.4 to 7, 5.6 to 7, 5.8 to 7, 6 to 7, 6.2 to 7, 6.4 to 7, 6.6 to 7, 6.8 to 7, 4 to 6, 4.2 to 6, 4.4 to 6, 4.6 to 6, 4.8 to 6, 5 to 6, 5.2 to 6, 5.4 to 6, 5.6 to 6, 5.8 to 6, 4 to 6, 4.2 to 6, 4.4 to 6, 4.6 to 6, 4.8 to 6, 5 to 6, 5.2 to 6, 5.4 to 6, 5.6 to 6, or 5.8 to 6.

In some embodiments, the plurality of active microbes comprises one microbial strain having a significantly different oxalate-metabolizing activity in a standard oxalate metabolizing assay conducted at two pH values differing by at least 1 pH unit and within a pH range of 4 to 8. For example, in some embodiments, one microbial strain has significantly different oxalate-metabolizing activities in a standard oxalate metabolizing assay at pH 4 and pH 8, pH 5 and pH 8, pH 6 and pH 8, pH 7 and pH 8, pH 4 and pH 7, pH 5 and pH 7, pH 6 and pH 7, pH 4 and pH 6, pH 5 and pH 6, or pH 4 and pH 5.

In some embodiments, oxalate-metabolizing activity is detected using a standard oxalate metabolization assay. For example, in some embodiments, oxalate-metabolizing activity is detected using a colorimetric enzyme assay that measures the activity of oxalate oxidase. In certain embodiments, relative changes in oxalate abundance in culture media inoculated with microbial strains are measured using a commercial oxalate assay kit (e.g., Sigma-Aldrich, Catalog #MAK315). In some embodiments, oxalate-metabolizing activity is detected using liquid chromatography-mass spectrometry (LC-MS/MS). In some embodiments, relative changes in oxalate abundance is compared between the abundance of oxalate at the beginning of incubation (i.e. t=0), and after 2 hours, 4 hours, 6 hours, 8, hours, 10 hours, 12 hours, 14 hours, 16 hours, 18 hours, 24 hours, 30 hours, 36 hours, 48 hours, 60, hours, 72 hours, 84 hours, 96 hours, 120 hours, or 144 hours incubation.

As used herein, “higher oxalate metabolizing activity” means either an oxalate metabolizing activity of a microbial strain that is higher as compared to an oxalate metabolizing activity of the same microbial strain under different conditions, and/or an oxalate metabolizing activity of a microbial strain that is higher as compared to an oxalate metabolizing activity of a different microbial strain under the same conditions.

In some embodiments, the plurality of active microbes comprises two microbial strains having significantly different oxalate metabolizing activities. For example, in some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at a lower pH as compared to the oxalate metabolizing activity of another microbial strain in the plurality of active microbes at the same lower pH. In some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 as compared to the oxalate metabolizing activity of another microbial strain in the plurality of active microbes at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5, respectively. In some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at a higher pH as compared to the oxalate metabolizing activity of another microbial strain in the plurality of active microbes at the same higher pH. In some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 as compared to the oxalate metabolizing activity of another microbial strain in the plurality of active microbes at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0, respectively.

In some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at a lower pH as compared to its oxalate metabolizing activity at a higher pH. For example, in some embodiments one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 than it does at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0. In some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at a higher pH as compared to its oxalate metabolizing activity at a lower pH. For example, in some embodiments one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 than it does at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5.

In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at a lower pH and another microbe having a higher oxalate metabolizing activity at a higher pH. For example, in some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.0 and another microbe having a higher oxalate metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.0 and another microbe having a higher oxalate metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.0 and another microbe having a higher oxalate metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.0 and another microbe having a higher oxalate metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.0 and another microbe having a higher oxalate metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.0 and another microbe having a higher oxalate metabolizing activity at pH 8.0. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.5 and another microbe having a higher oxalate metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.5 and another microbe having a higher oxalate metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.5 and another microbe having a higher oxalate metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.5 and another microbe having a higher oxalate metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.5 and another microbe having a higher oxalate metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 4.5 and another microbe having a higher oxalate metabolizing activity at pH 8.0. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.0 and another microbe having a higher oxalate metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.0 and another microbe having a higher oxalate metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.0 and another microbe having a higher oxalate metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.0 and another microbe having a higher oxalate metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.0 and another microbe having a higher oxalate metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.0 and another microbe having a higher oxalate metabolizing activity at pH 8.0. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.5 and another microbe having a higher oxalate metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.5 and another microbe having a higher oxalate metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.5 and another microbe having a higher oxalate metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.5 and another microbe having a higher oxalate metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.5 and another microbe having a higher oxalate metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 5.5 and another microbe having a higher oxalate metabolizing activity at pH 8.0. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.0 and another microbe having a higher oxalate metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.0 and another microbe having a higher oxalate metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.0 and another microbe having a higher oxalate metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.0 and another microbe having a higher oxalate metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.0 and another microbe having a higher oxalate metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.0 and another microbe having a higher oxalate metabolizing activity at pH 8.0. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.5 and another microbe having a higher oxalate metabolizing activity at pH 7.5. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.5 and another microbe having a higher oxalate metabolizing activity at pH 7.6. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.5 and another microbe having a higher oxalate metabolizing activity at pH 7.7. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.5 and another microbe having a higher oxalate metabolizing activity at pH 7.8. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.5 and another microbe having a higher oxalate metabolizing activity at pH 7.9. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at pH 6.5 and another microbe having a higher oxalate metabolizing activity at pH 8.0.

In some embodiments, one or more than one of the plurality of active microbes is capable of substantially metabolizing oxalate at an oxalate concentration of about 0.75 mM to about 40 mM of oxalate. For example, in some embodiments, one or more than one of the plurality of active microbes is capable of substantially metabolizing oxalate at an oxalate concentration within a range of about 0.75 mM to about 40 mM, of about 1 mM to about 40 mM, of about 2.5 mM to about 40 mM, of about 5 mM to about 40 mM, of about 7.5 mM to about 40 mM, of about 10 mM to about 40 mM, of about 15 mM to about 40 mM, of about 20 mM to about 40 mM, of about 25 mM to about 40 mM, of about 30 mM to about 40 mM, of about 0.75 mM to about 30 mM, of about 1 mM to about 30 mM, of about 2.5 mM to about 30 mM, of about 5 mM to about 30 mM, of about 7.5 mM to about 30 mM, of about 10 mM to about 30 mM, of about 15 mM to about 30 mM, of about 20 mM to about 30 mM, of about 25 mM to about 30 mM, of about 0.75 mM to about 25 mM, of about 1 mM to about 25 mM, of about 2.5 mM to about 25 mM, of about 5 mM to about 25 mM, of about 7.5 mM to about 25 mM, of about 10 mM to about 25 mM, of about 15 mM to about 25 mM, of about 20 mM to about 25 mM, of about 0.75 mM to about 20 mM, of about 1 mM to about 20 mM, of about 2.5 mM to about 20 mM, of about 5 mM to about 20 mM, of about 7.5 mM to about 20 mM, of about 10 mM to about 20 mM, of about 15 mM to about 20 mM, of about 0.75 mM to about 15 mM, of about 1 mM to about 15 mM, of about 2.5 mM to about 15 mM, of about 5 mM to about 15 mM, of about 7.5 mM to about 15 mM, of about 10 mM to about 15 mM, of about 0.75 mM to about 10 mM, of about 1 mM to about 10 mM, of about 2.5 mM to about 10 mM, of about 5 mM to about 10 mM, of about 7.5 mM to about 10 mM, of about 0.75 mM to about 5 mM, of about 1 mM to about 5 mM, of about 2.5 mM to about 5 mM, or of about 0.75 mM to about 1 mM.

In some embodiments, the plurality of active microbes comprises one microbial strain having a significantly different oxalate-metabolizing activity in a standard in vitro oxalate metabolizing assay (for example, as described in Example 3) at an oxalate concentration as compared to its oxalate-metabolizing activity in a standard in vitro oxalate metabolizing assay conducted at a different oxalate concentration, wherein the difference between the two oxalate concentrations is within 100 fold. For example, in some embodiments, one microbial strain has significantly different oxalate-metabolizing activities in a standard oxalate metabolizing assay conducted at about 0.75 mM oxalate and about 40 mM oxalate, about 1 mM and about 40 mM, about 2.5 mM and about 40 mM, about 5 mM and about 40 mM, about 7.5 mM and about 40 mM, about 10 mM and about 40 mM, about 15 mM and about 40 mM, about 20 mM and about 40 mM, about 25 mM and about 40 mM, about 30 mM and about 40 mM, about 0.75 mM and about 30 mM, about 1 mM and about 30 mM, about 2.5 mM and about 30 mM, about 5 mM and about 30 mM, about 7.5 mM and about 30 mM, about 10 mM and about 30 mM, about 15 mM and about 30 mM, about 20 mM and about 30 mM, about 25 mM and about 30 mM, about 0.75 mM and about 25 mM, about 1 mM and about 25 mM, about 2.5 mM and about 25 mM, about 5 mM and about 25 mM, about 7.5 mM and about 25 mM, about 10 mM and about 25 mM, about 15 mM and about 25 mM, about 20 mM and about 25 mM, about 0.75 mM and about 20 mM, about 1 mM and about 20 mM, about 2.5 mM and about 20 mM, about 5 mM and about 20 mM, about 7.5 mM and about 20 mM, about 10 mM and about 20 mM, about 15 mM and about 20 mM, about 0.75 mM and about 15 mM, about 1 mM and about 15 mM, about 2.5 mM and about 15 mM, about 5 mM and about 15 mM, about 7.5 mM and about 15 mM, about 10 mM and about 15 mM, about 0.75 mM and about 10 mM, about 1 mM and about 10 mM, about 2.5 mM and about 10 mM, about 5 mM and about 10 mM, about 7.5 mM and about 10 mM, about 0.75 mM and about 5 mM, about 1 mM and about 5 mM, about 2.5 mM and about 5 mM, or about 0.75 mM and about 1 mM.

In some embodiments, the plurality of active microbes comprises two microbial strains having significantly different oxalate metabolizing activities. For example, in some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at a lower concentration of oxalate as compared to the oxalate metabolizing activity of another microbial strain in the plurality of active microbes at the same lower concentration of oxalate. In some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at an oxalate concentration of 0.75 mM, 1 mM, 2.5 mM, 5 mM, or 7.5 mM, as compared to the oxalate metabolizing activity of another microbial strain in the plurality of active microbes at an oxalate concentration of 0.75 mM, 1 mM, 2.5 mM, 5 mM, or 7.5 mM, respectively. In some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at a higher concentration of oxalate as compared to the oxalate metabolizing activity of another microbial strain in the plurality of active microbes at the same higher concentration of oxalate. In some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at an oxalate concentration of 15 mM, 20 mM, 25 mM 30 mM, or 40 mM as compared to the oxalate metabolizing activity of another microbial strain in the plurality of active microbes at an oxalate concentration of 15 mM, 20 mM, 25 mM 30 mM, or 40 mM, respectively.

In some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at a lower oxalate concentration as compared to its oxalate metabolizing activity at a higher oxalate concentration. For example, in some embodiments one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at 0.75 mM, 1 mM, 2.5 mM, 5 mM, or 7.5 mM of oxalate than it does at 15 mM, 20 mM, 25 mM 30 mM, or 40 mM of oxalate. In some embodiments, one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at a higher oxalate concentration as compared to its oxalate metabolizing activity at a lower oxalate concentration. For example, in some embodiments one of the plurality of active microbes has a significantly higher oxalate metabolizing activity at 15 mM, 20 mM, 25 mM 30 mM, or 40 mM of oxalate than it does at 0.75 mM, 1 mM, 2.5 mM, 5 mM, or 7.5 mM of oxalate.

In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at a lower concentration of oxalate and another microbe having a higher oxalate metabolizing activity at a higher concentration of oxalate. For example, in some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at about 0.75 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 40 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 1 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 40 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 2.5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 40 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 40 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 7.5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 40 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 0.75 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 30 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 1 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 30 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 2.5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 30 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 30 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 7.5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 30 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 0.75 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 25 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 1 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 25 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 2.5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 25 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 25 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 7.5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 25 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 0.75 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 20 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 1 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 20 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 2.5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 20 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 20 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 7.5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 20 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 0.75 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 15 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 1 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 15 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 2.5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 15 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 15 mM oxalate. In some embodiments, the plurality of active microbes comprises an active microbe having a higher oxalate metabolizing activity at 7.5 mM oxalate and another active microbe having a higher oxalate metabolizing activity at about 15 mM oxalate.

In some embodiments, when tested in an in vitro oxalate metabolization assay (e.g., as described in Example 3 below), a plurality of active microbes of the present invention significantly reduces the concentration of oxalate present in a sample by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, or by at least 80%.

In some embodiments, a plurality of active microbes of the present invention significantly reduces the concentration of oxalate present in a sample of blood, serum, bile, stool, or urine when administered to a subject by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, or by at least 80% as compared to an untreated control subject or pre-administration levels. Concentrations of oxalate in a blood, serum, bile, stool or urine sample can be measured using a liquid chromatography-mass spectrometry (LC-MS), method as described in Example 4, below.

Bile Salt Modifying Active Microbes

Unconjugated primary bile acids, cholic acid (CA) and chenodeoxycholic acid (CDCA), are substrates for 7α-dehydroxylation by select members of the gut microbiota. As shown below, 7α-dehydroxylation converts CA and CDCA to lithocholic acid (LCA) and deoxycholic acid (DCA), respectively. LCA and DCA are secondary bile acids that have been implicated in adverse health outcomes.

text missing or illegible when filed

In some embodiments, a microbial consortium disclosed herein comprises microbial strains having robust 3α-hydroxysteroid dehydrogenase (3α-HSDH) and 3β-hydroxysteroid dehydrogenase (3β-HSDH) activity. As shown below, 3α-HSDH and 3β-HSDH convert DCA and LCA into alternative secondary bile acids isoDCA and isoLCA, respectively.

text missing or illegible when filed

In some embodiments, microbial consortia provided herein comprise a plurality of active microbes expressing 3α-HSDH selected from one or more of Eggerthella lenta, Ruminococcus gnavus, Clostridium perfringens, Peptostreptococcus productus, and Clostridium scindens. In some embodiments, microbial consortia provided herein comprise a plurality of active microbes expressing 3β-HSDH selected from one or more of Peptostreptococcus productus, Clostridium innocuum, and Clostridium scindens.

In some embodiments, the plurality of active microbes comprises one or more than one microbial strain selected from: an Eggethella lenta strain having a 16S sequence at least 80% identical to SEQ ID NO: 30, an Eggethella lenta strain having a 16S sequence at least 80% identical to SEQ ID NO: 96, an Eggethella lenta strain having a 16S sequence at least 80% identical to SEQ ID NO: 170, an Eggethella lenta strain having a 16S sequence at least 80% identical to SEQ ID NO: 201, or a Clostridum scindens strain having a 16S sequence at least 80% identical to SEQ ID NO: 87.

In some embodiments, the plurality of active microbes comprises one or more than one microbial strain selected from: an Eggethella lenta strain having a 16S sequence 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% identical to SEQ ID NO: 30, an Eggethella lenta strain having a 16S sequence 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% identical to SEQ ID NO: 96, an Eggethella lenta strain having a 16S sequence 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% identical to SEQ ID NO: 170, an Eggethella lenta strain having a 16S sequence 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% identical to SEQ ID NO: 201, or a Clostridum scindens strain having a 16S sequence 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% identical to SEQ ID NO: 87.

In some embodiments, the plurality of active microbes comprises two microbial strains having significantly different bile acid-metabolizing activities. For example, in some embodiments, one of the plurality of active microbes has a significantly higher bile acid-metabolizing activity at a lower concentration of bile acid as compared to the bile acid-metabolizing activity of another microbial strain in the plurality of active microbes at the same lower concentration of bile acid. In some embodiments, one of the plurality of active microbes has a significantly higher bile acid-metabolizing activity at a bile acid concentration of 0.1 mM, 0.2 mM, 0.3 mM, 0.4 mM, 0.5 mM, 0.6 mM, 0.7 mM, 0.8 mM, 0.9 mM, 1.0 mM, as compared to the bile acid-metabolizing activity of another microbial strain in the plurality of active microbes at an oxalate concentration of 0.1 mM, 0.2 mM, 0.3 mM, 0.4 mM, 0.5 mM, 0.6 mM, 0.7 mM, 0.8 mM, 0.9 mM, or 1.0 mM, respectively. In some embodiments, one of the plurality of active microbes has a significantly higher bile acid-metabolizing activity at a higher concentration of bile acid as compared to the bile acid-metabolizing activity of another microbial strain in the plurality of active microbes at the same higher concentration of bile acid. In some embodiments, one of the plurality of active microbes has a significantly higher bile acid metabolizing activity at a bile acid concentration of 5.0 mM, 5.5 mM, 6.0 mM, 6.5 mM, 7.0 mM, 7.5 mM, 8.0 mM, 8.5 mM, 9.0 mM, 9.5 mM, or 10.0 mM as compared to the oxalate metabolizing activity of another microbial strain in the plurality of active microbes at an oxalate concentration of 5.0 mM, 5.5 mM, 6.0 mM, 6.5 mM, 7.0 mM, 7.5 mM, 8.0 mM, 8.5 mM, 9.0 mM, 9.5 mM, or 10.0 mM, respectively.

In some embodiments, one of the plurality of active microbes has a significantly higher bile acid-metabolizing activity at a lower bile acid concentration as compared to its bile acid-metabolizing activity at a higher bile acid concentration. For example, in some embodiments one of the plurality of active microbes has a significantly higher bile acid-metabolizing activity at 0.1 mM, 0.2 mM, 0.3 mM, 0.4 mM, 0.5 mM, 0.6 mM, 0.7 mM, 0.8 mM, 0.9 mM, or 1.0 mM of bile acid than it does at. 5.0 mM, 5.5 mM, 6.0 mM, 6.5 mM, 7.0 mM, 7.5 mM, 8.0 mM, 8.5 mM, 9.0 mM, 9.5 mM, or 10.0 mM of bile acid. In some embodiments, one of the plurality of active microbes has a significantly higher bile acid-metabolizing activity at a higher bile acid concentration as compared to its bile acid metabolizing activity at a lower bile acid concentration. For example, in some embodiments one of the plurality of active microbes has a significantly higher bile acid-metabolizing activity at 5.0 mM, 5.5 mM, 6.0 mM, 6.5 mM, 7.0 mM, 7.5 mM, 8.0 mM, 8.5 mM, 9.0 mM, 9.5 mM, or 10.0 mM of bile acid than it does at 0.1 mM, 0.2 mM, 0.3 mM, 0.4 mM, 0.5 mM, 0.6 mM, 0.7 mM, 0.8 mM, 0.9 mM, or 1.0 mM of bile acid.

In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid-metabolizing activity at a lower concentration of bile acid and another microbe having a higher bile acid-metabolizing activity at a higher concentration of bile acid. For example, in some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.1 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 10 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.2 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 10 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.3 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 10 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.4 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 10 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.5 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 10 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.1 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 7.5 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.2 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 7.5 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.3 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 5.0 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.4 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 7.5 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.5 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 7.5 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.1 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 5.0 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.2 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 5.0 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.3 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 5.0 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.4 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 5.0 mM bile acid. In some embodiments, the plurality of active microbes comprises an active microbe having a higher bile acid metabolizing activity at about 0.5 mM bile acid and another active microbe having a higher bile acid-metabolizing activity at about 5.0 mM bile acid.

In some embodiments, when tested in a standard in vitro bile acid metabolization assay, a plurality of active microbes of the present invention significantly reduces the concentration of lithoholic acid (LCA) and or deoxycholic acid (DCA) present in a sample by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, or by at least 80%.

In some embodiments, a plurality of active microbes of the present invention significantly reduces the concentration of LCA and/or DCA present in a sample of blood, serum, bile, stool, or urine when administered to a subject by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, or by at least 80% as comparted to an untreated control subject or pre-administration levels.

Supportive Community of Microbes

The microbial consortia of the present invention further comprise a supportive community of microbes that enhances one or more than one characteristic of the plurality of active microbes. For example, in some embodiments, the supportive community of microbes enhances gastrointestinal engraftment of the plurality of active microbes. In other embodiments, the supportive community of microbes enhances biomass of the plurality of active microbes. In other embodiments, the supportive community of microbes enhances metabolism of the first metabolic substrate by the plurality of active microbes. In other embodiments, the supportive community of microbes enhances longitudinal stability of the plurality of active microbes.

The supportive community of microbes disclosed herein metabolize one or more than one metabolite produced by the plurality of active microbes, wherein the one or more than one metabolite inhibits metabolism of the plurality of active microbes. For example, in some embodiments, the supportive community of microbes metabolizes formate produced by the plurality of active microbes, wherein the presence of formate inhibits the metabolism of oxalate by the plurality of active microbes. In some embodiments, the supportive community of microbes of the current invention catalyzes the fermentation of polysaccharides to one or more than one of the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H₂, and CO₂. In some embodiments, the supportive community of microbes catalyzes the fermentation of amino acids to one or more than one of the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, phloretate, 3-(1H-indol-3-yl)propanoate, 5-aminopentanoate, H₂, H₂S, and CO₂, In some embodiments, the supportive community catalyzes the synthesis of one or more than one of the group consisting of methane from H₂and CO₂, methane from formate and H₂, acetate from H₂and CO₂, acetate from formate and H₂, acetate and sulfide from H₂, CO₂, and sulfate, propionate and CO₂from succinate, succinate from H₂and fumarate; synthesis of succinate from formate and fumarate, and butyrate, acetate, H₂, and CO₂from lactate. In some embodiments, the supportive community of microbes of the current invention catalyzes the deconjugation of conjugated bile acids to produce primary bile acids, the conversion of cholic acid (CA) to 7-oxocholic acid, the conversion of 7-oxocholic acid to 7-beta-cholic acid (7betaCA), the conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and/or the conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA).

The supportive community of microbes of the current invention comprises between one and 300 microbial strains. For example, in some embodiments, the supportive community of microbes comprises between 1 and 300, 5 and 300, 10 and 300, 15 and 300, 20 and 300, 30 and 300, 40 and 300, 50 and 300, 60 and 300, 70 and 300, 80 and 300, 90 and 300, 100 and 300, 110 and 300, 120 and 300, 130 and 300, 140 and 300, 150 and 300, 160 and 300, 170 and 300, 180 and 300, 190 and 300, 200 and 300, 210 and 300, 220 and 300, 230 and 300, 240 and 300, 250 and 300, 260 and 300, 270 and 300, 280 and 300, 290 and 300, 1 and 250, 5 and 250, 10 and 250, 15 and 250, 20 and 250, 30 and 250, 40 and 250, 50 and 250, 60 and 250, 70 and 250, 80 and 250, 90 and 250, 100 and 250, 110 and 250, 120 and 250, 130 and 250, 140 and 250, 150 and 250, 160 and 250, 170 and 250, 180 and 250, 190 and 250, 200 and 250, 210 and 250, 220 and 250, 230 and 250, 240 and 250, 1 and 200, 5 and 200, 10 and 200, 15 and 200, 20 and 200, 30 and 200, 40 and 200, 50 and 200, 60 and 200, 70 and 200, 80 and 200, 90 and 200, 100 and 200, 110 and 200, 120 and 200, 130 and 200, 140 and 200, 150 and 200, 160 and 200, 170 and 200, 180 and 200, 190 and 200, 1 and 150, 5 and 150, 10 and 150, 15 and 150, 20 and 150, 30 and 150, 40 and 150, 50 and 150, 60 and 150, 70 and 150, 80 and 150, 90 and 150, 100 and 150, 110 and 150, 120 and 150, 130 and 150, 140 and 150, 1 and 100, 5 and 100, 10 and 100, 15 and 100, 20 and 100, 30 and 100, 40 and 100, 50 and 100, 60 and 100, 70 and 100, 80 and 100, 90 and 100, 1 and 50, 5 and 50, 10 and 50, 15 and 50, 20 and 50, 30 and 50, or 40 and 50 microbial strains. For example, in some embodiments, the supportive community of microbes comprises about 20 to about 200, about 70 to about 80, about 80 to about 90, about 100 to about 110, or about 150 to about 160 microbial strains.

In some embodiments, the supportive community of microbes comprises species of at least one, at least two, at least three, at least four, or at least five of the following phyla: Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, and Euryarchaeota. In some embodiments, the supportive community of microbes comprises species of at least one, at least two, at least three, at least four, or at least five of the following subclades: Bacteroidales, Clostridiales, Erysipelotrichales, Negativicutes, Coriobacteriia, Bifidobacteriales, and Methanobacteriales.

In some embodiments, the supportive community of microbes of the current invention consumes one or more metabolites derived from an animal diet. For example, in some embodiments, the supportive community of microbes of the current invention consumes one or more than one of the following metabolites: a-mannan, acetate, agarose, alanine, arabinan, arabinogalactan, arabinoxylan, arginine, asparagine, aspartate, b-glucans, benzoic acids, carrageenan, catechol, chlorogenic acids, chondroitin sulfate, cysteine, dextran, enterodiol, flavan-3-ols, flavanones, flavones, flavonols, folate, formate, galactomannan, galacturonan, galacturonate, glucomannan, glutamine, glycine, hyaluronan, hydrogen, hydroxyproline, inulin, isoflavones, lactate, laminarin, leucine, levan, methionine, mucin O-linked glycans, phenylalanine, proline, rhamnogalacturonan I, rhamnogalacturonan II, secoisolariciresinol diglucoside, serine, starch, tyrosine, valine, xyloglucan, and xylooligosaccharides. In some embodiments, the supportive community of microbes is designed to maximize the number of metabolites derived from the host diet that the supportive community can consume.

In some embodiments, the supportive community of microbes of the current invention consumes one or more of the following dietary, host-derived, or microbial metabolites: thiamine, methanol, indole-3-acetate, L-glutamate, L-ornithine, niacin, 2-oxobutyrate, betaine, D-fructuronate, D-gluconate, D-tagaturonate, D-turanose, inosine, glycine, histidine, L-idonate, isoleucine, serine, N-acetyl-D-mannosamine, nitrate, thymidine, uridine, butyrate, propanoate, indole, glutamine, inositol, arginine, aspartate, malate, oxalate, phenol, succinate, ethanol, hydrogen, formate, lactate, aminobenzoate, lyxose, isomaltose, phenylalanine, tyrosine, pyruvate, mannitol, sorbitol, D-tagatose, glycerol, leucine, N-acetylgalactosamine, isovalerate, biotin, isobutyrate, 2-methylbutyrate, D-galactosamine, glycolithocholate, valine, melibiose, taurolithocholate, menaquinone, chenodeoxycholic acid, cholic acid, glycochenodeoxycholate, glycocholate, glycodeoxycholate, thiosulfate, pyridoxal, bicarbonate, N-acetyl-D-glucosamine, sulfate, riboflavin, methionine, N-acetylneuraminic acid, ribose, D-galacturonate, taurochenodeoxycholate, taurocholate, arabinose, rhamnose, pantothenic acid, xylooligosaccharide, acetate, D-glucuronic acid, cysteine, adenosylcobalamin, sucrose, trehalose, urea, xylose, cellobiose, mannose, L-fucose, D-galactose, D-glucosamine, D-psicose, fructooligosaccharide, carbon dioxide, maltose, ammonia, raffinose, dextrin, lactose, glucose, and fructose.

In some embodiments, the supportive community of microbes of the current invention produces one or more of the following metabolites: dimethylamine, folic acid, butylamine, phenylethylamine, 1,2-propanediol, acetone, trimethylamine, putrescine, tyramine, 4-aminobutyrate, valerate, 1,2-ethanediol, methylamine, phenylacetate, spermidine, hydrogen sulfide, linoleic acid, formaldehyde, trimethylamine N-oxide, cadaverine, alanine, threonine, methane, and pentanol.

In some embodiments of the invention, an original dosage form of the disclosed microbial consortium comprises active microbes and supportive microbes in a colony forming unit (CFU) ratio of about 5:1, 4:1, 3:1, 2:1, 1:1, 1:2, 1:3, 1:4, 1:5. In some embodiments, an original dosage form of the disclosed microbial consortium comprises active microbes and supportive microbes in total CFU amounts within about one order of magnitude, about two orders of magnitude, about three orders of magnitude, about four orders of magnitude, about 5 orders of magnitude, about 6 orders of magnitude, about 7 orders of magnitude, about 8 orders of magnitude, about 9 orders of magnitude, or about 10 orders of magnitude of each other.

In some embodiments, the supportive community of microbes may comprise one or more than one microbial strains selected from, but not limited to, Absiella dolichum, Bacteroides uniformis, Eubacterium siraeum, Acidaminococcus fermentans, Bacteroides vulgatus, Eubacterium ventriosum, Acidaminococcus sp., Bacteroides xylanisolvens, Faecalibacterium prausnitzii, Adlercreutzia equolifaciens, Bifidobacterium breve, Granulicatella adiacens, Akkermansia mucimphila, Bifidobacterium catenulatum, Holdemanella biformis, Alistipes finegoldii, Bifidobacterium pseudocatenulatum, Holdemania filiformis, Alistipes indistinctus, Bilophila wadsworthia, Hungatella hathewayi, Alistipes onderdonkii, Blautia hansenii, Intestinibacter bartlettii, Alistipes putredinis, Blautia hydrogenotrophica, Intestinimonas butyriciproducens, Alistipes senegalensis, Blautia obeum, Lactobacillus ruminis, Alistipes shahii, Blautia sp., Marvinbryantia formatexigens, Anaerobutyricum hallii, Blautia wexlerae, Megasphaera, Anaerofustis stercorihominis, Butyricimonas virosa, Methanobrevibacter smithii, Anaerostipes caccae, Butyrivibrio crossotus, Anaerotruncus colihominis, Catenibacterium mitsuokai, Bacteroides caccae, Clostridium asparagiforme, Bacteroides cellulosilyticus, Clostridium bolteae, Mitsuokella multacida, Bacteroides coprocola, Clostridium hiranonis, Odoribacter splanchnicus, Bacteroides coprophilus, Clostridium hylemonae, Olsenella uli, Bacteroides dorei, Clostridium leptum, Oscillibacter sp., Bacteroides dorei, Clostridium methylpentosum, Parabacteroides distasonis, Bacteroides eggerthii, Clostridium orbiscindens, Parabacteroides johnsonii, Bacteroides finegoldii, Clostridium saccharolyticum, Parabacteroides merdae, Bacteroides fragilis, Clostridium scindens, Parabacteroides sp., Bacteroides intestinalis, Clostridium sp., Prevotella buccalis, Bacteroides ovatus, Prevotella copri, Bacteroides pectinophilus, Roseburia inulinivorans, Bacteroides plebeius, Clostridium spiroforme, Ruminococcus gauvreauii, Bacteroides rodentium, Collinsella aerofaciens, Ruminococcus gnavus, Collinsella stercoris, Ruminococcus lactaris, Coprococcus comes, Ruminococcus torques, Coprococcus eutactus, Slackia exigua, Desulfovibrio piger, Slackia heliotrinireducens, Dorea formicigenerans, Solobacterium moorei, Dorea longicatena, Streptococcus salivarius subsp. Thermophilus, Bacteroides stercoris, Ethanoligenens harbinense, Subdoligranulum variabile, Bacteroides thetaiotaomicron, Eubacterium rectale, Turicibacter sanguinis, and Tyzzerella nexilis.

In some embodiments the supportive community of microbes may comprise one or more than one microbial strains selected from, but not limited to, Absiella dolichum DSM 3991, Bilophila wadsworthia ATCC 49260, Intestinibacter bartlettii DSM 16795, Acidaminococcus fermentans DSM 20731, Bilophila wadsworthia DSM 11045, Intestinimonas butyriciproducens DSM 26588, Acidaminococcus sp. HM-81, Blautia hansenii DSM 20583, Lactobacillus amylovorus DSM 20552, Adlercreutzia equolifaciens DSM 19450, Blautia hydrogenotrophica DSM 10507, Lactobacillus casei subsp. casei ATCC 393, Akkermansia muciniphila ATCC BAA-835, Blautia obeum DSMZ 25238, Lactobacillus casei subsp. casei ATCC 39539, Alistipes finegoldii DSM 17242, Blautia sp. HM-1032, Lactobacillus crispatus HM-370, Alistipes indistinctus DSM 22520, Blautia wexlerae DSM 19850, Lactobacillus johnsonii HM-643, Alistipes onderdonkii DSM 19147, Butyricimonas virosa DSM 23226, Lactobacillus parafarraginis HM-478, Alistipes putredinis DSM 17216, Butyrivibrio crossotus DSM 2876, Lactobacillus plantarum ATCC 14917, Alistipes senegalensis DSM 25460, Catenibacterium mitsuokai DSM 15897, Lactobacillus plantarum ATCC 202195, Alistipes shahii DSM 19121, Cetobacterium somerae DSM 23941, Lactobacillus ruminis ATCC 25644, Anaerobutyricum hallii DSM 3353, Clostridium asparagiforme DSM 15981, Lactobacillus ruminis DSM 20404, Anaerococcus lactolyticus DSM 7456, Clostridium bolteae DSM 15670, Lactobacillus ultunensis DSM 16048, Anaerofustis stercorihominis DSM 17244, Clostridium bolteae HM-1038, Lactococcus lactis Berridge DSM 20729, Anaerostipes caccae DSM 14662, Clostridium bolteae HM-318, Marvinbryantia formatexigens DSM 14469, Anaerotruncus colihominis DSM 17241, Clostridium cadaveris HM-1040, Megasphaera indica DSM 25562, Bacteroides caccae ATCC 43185, Clostridium citroniae HM-315, Megasphaera sp. DSM 102144, Bacteroides caccae HM-728, Clostridium hiranonis DSM 13275, Methanobrevibacter smithii DSM 11975, Bacteroides cellulosilyticus DSM 14838, Clostridium hylemonae DSM 15053, Methanobrevibacter smithii DSM 2374, Bacteroides cellulosilyticus HM-726, Clostridium innocuum HM-173, Methanobrevibacter smithii DSM 2375, Bacteroides coprocola DSM 17136, Clostridium leptum DSM 753, Methanobrevibacter smithii DSM 861, Bacteroides coprophilus DSM 18228, Clostridium methylpentosum DSM 5476, Methanomassiliicoccus luminyensis DSM 25720, Bacteroides dorei DSM 17855, Clostridium saccharolyticum DSM 2544, Methanosphaera stadtmanae DSMZ 3091, Bacteroides dorei HM-29, Clostridium scindens DSM 5676, Mitsuokella multacida DSM 20544, Bacteroides dorei HM-718, Clostridium scindens VPI 12708, Odoribacter splanchnicus DSM 20712, Bacteroides eggerthii DSM 20697, Clostridium sp. ATCC 29733, Olsenella uli DSM 7084, Bacteroides eggerthii HM-210, Clostridium sp. DSM 4029, Oscillibacter sp. HM-1030, Bacteroides finegoldii DSM 17565, Clostridium sp. HM-634, Parabacteroides distasonis ATCC 8503, Bacteroides finegoldii HM-727, Clostridium sp. HM-635, Parabacteroides goldsteinii HM-1050, Bacteroides fragilis HM-20, Clostridium spiroforme DSM 1552, Parabacteroides johnsonii DSM 18315, Bacteroides fragilis HM-709, Clostridium sporogenes ATCC 15579, Parabacteroides johnsonii HM-731, Bacteroides fragilis HM-710, Clostridium sporogenes ATCC 17889, Parabacteroides merdae DSM 19495, Bacteroides intestinalis DSM 17393, Clostridium sporogenes DSM 767, Parabacteroides merdae HM-729, Bacteroides ovatus ATCC 8483, Clostridium symbiosum HM-309, Parabacteroides merdae HM-730, Bacteroides ovatus HM-222, Clostridium symbiosum HM-319, Parabacteroides sp. HM-77, Bacteroides pectinophilus ATCC 43243, Collinsella aerofaciens ATCC 25986, Peptostreptococcus anaerobius DSM 2949, Bacteroides plebeius DSM 17135, Collinsella stercoris DSM 13279, Prevotella buccae HM-45, Bacteroides rodentium DSM 26882, Coprococcus catus ATCC 27761, Prevotella buccalis DSM 20616, Bacteroides salyersiae HM-725, Coprococcus comes ATCC 27758, Prevotella copri DSM 18205, Bacteroides sp. HM-18, Coprococcus eutactus ATCC 27759, Proteocatella sphenisci DSM 23131, Bacteroides sp. HM-19, Coprococcus eutactus ATCC 51897, Providencia rettgeri ATCC BAA-2525, Bacteroides sp. HM-23, Coprococcus sp. DSM 21649, Roseburia intestinalis DSM 14610, Bacteroides sp. HM-27, Desulfovibrio piger ATCC 29098, Roseburia inulinivorans DSM 16841, Bacteroides sp. HM-28, Dialister pneumosintes ATCC 51894, Ruminococcaceae sp. HM-79, Bacteroides sp. HM-58, Dorea formicigenerans ATCC 27755, Ruminococcus albus ATCC 27210, Bacteroides stercoris DSM 19555, Dorea longicatena DSM 13814, Ruminococcus bromii ATCC 27255, Bacteroides stercoris HM-1036, Eggerthella sp. DSM 11767, Ruminococcus bromii ATCC 51896, Bacteroides thetaiotaomicron ATCC 29148, Eggerthella sp. DSM 11863, Ruminococcus gauvreauii DSM 19829, Bacteroides uniformis ATCC 8492, Eggerthella sp. HM-1099, Ruminococcus gnavus ATCC 29149, Bacteroides vulgatus ATCC 8482, Ethanoligenens harbinense DSM 18485, Ruminococcus gnavus DSM 108212, Bacteroides vulgatus HM-720, Eubacterium eligens ATCC 27750, Ruminococcus gnavus HM-1056, Bacteroides xylanisolvens DSM 18836, Eubacterium rectale ATCC 33656, Ruminococcus lactaris ATCC 29176, Bifidobacterium adolescentis HM-633, Eubacterium siraeum DSM 15702, Ruminococcus lactaris HM-1057, Bifidobacterium angulatum HM-1189, Eubacterium ventriosum ATCC 27560, Ruminococcus torques ATCC 27756, Bifidobacterium animalis DSM 20104, Faecalibacterium prausnitzii ATCC 27766, Slackia exigua DSM 15923, Bifidobacterium animalis subsp. Lactis DSMZ 10140, Faecalibacterium prausnitzii ATCC 27768, Slackia heliotrinireducens DSM 20476, Bifidobacterium bifidum ATCC 11863, Faecalibacterium prausnitzii DSM 17677, Solobacterium moorei DSM 22971, Bifidobacterium breve DSM 20213, Faecalibacterium prausnitzii HM-473, Streptococcus salivarius subsp. thermophilus ATCC BAA-491, Bifidobacterium catenulatum DSM 16992, Flavonifractor plautii HM-1044, Streptococcus thermophilus ATCC 14485, Bifidobacterium longum infantis ATCC 55813, Flavonifractor plautii HM-303, Subdoligranulum variabile DSM 15176, Bifidobacterium longum subsp. longum HM-845, Granulicatella adiacens ATCC 49175, Turicibacter sanguinis DSM 14220, Bifidobacterium longum subsp. longum HM-846, Holdemanella biformis DSM 3989, Tyzzerella nexilis DSM 1787, Bifidobacterium longum subsp. longum HM-847, Holdemania filiformis DSM 12042, Veillonella dispar ATCC 17748, Bifidobacterium longum subsp. longum HM-848, Hungatella (prev. Clostridium) hathewayi HM-308, Veillonella sp. HM-49, Bifidobacterium pseudocatenulatum DSM 20438, Hungatella hathewayi DSM 13479, and Veillonella sp. HM-64.

Conjugated primary bile acids are synthesized in the liver from cholesterol, concentrated and stored in the gallbladder, and secreted into the duodenum to facilitate the solubilization and absorption of dietary lipids. Most bile acids are reabsorbed and recycled back to the liver through enterohepatic recirculation, but a sizable fraction (5%) escapes recycling, enters the large intestine, and is heavily metabolized into secondary bile acids by resident colonic microbes. Through microbial metabolism, four conjugated primary bile acids produced in the liver: taurochenoxycholic acid (TCDCA), glycochenodeoxycholic acid (GCDCA), taurocholic acid (TCA), and glycocholic acid (GCA), can be converted into over 100 molecules that have profound effects on host physiology. The unique profile of molecules produced is dependent on the metabolic capabilities of the resident colonic microbial community. As shown below, the first metabolic step upstream of secondary bile acid production is the deconjugation of conjugated primary bile acids by microbial bile salt hydrolases (BSH).

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In some embodiments, the supportive community of microbes may comprise one or more microbial strains having robust and/or redundant BSH activity, so that deconjugation of primary bile acids can occur despite differences in host physiology, diet, plurality of active microbes present in the microbial consortium, or the pre-existing composition of the conjugated bile acid pool.

In some embodiments, the supportive community of microbes may comprise one or more than one microbial strains selected from, Alistipes indistinctus, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bacteroides xylanisolvens, Bifidobacterium angulatum, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum infantis, Bifidobacterium pseudocatenulatum, Blautia obeum, Clostridium hylemonae, Enterococcus faecalis, Hungatella hathewayi, Lactobacillus acidophilus, Methanobrevibacter smithii, Parabacteroides distasonis, Parabacteroides goldsteini, Providencia rettgeri, Roseburia inulinivorans, Ruminococcus bromii, Ruminococcus gnavus, and Turicibacter sanguinis.

In some embodiments, the current disclosure provides a microbial consortium comprising a plurality of active microbes that convert CA and CDCA into alternative secondary bile acids, thereby shifting the bile acid pool away from 7α-dehydroxylation products, LCA and DCA. For example, in some embodiments, a microbial consortium disclosed herein comprises microbial strains having robust 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 7β-hydroxysteroid dehydrogenase (7β-HSDH) activity. As shown below, 7α-HSDH creates 7oxoCA and 7oxoCDCA intermediates, and 7β-HSDH converts CA and CDCA to 7βCA and ursodeoxycholic acid (UDCA).

text missing or illegible when filed

In some embodiments, microbial consortia provided herein comprise a plurality of active microbes expressing 7α-HSDH selected from one or more of Acinetobacter calcoaceticusi, Bacteroides thetaiotaomicron, Bacteroides intestinalis, Bacteroides fragilis, Eggerthella lenta, Ruminococcus sp. In some embodiments, microbial consortia provided herein comprises a plurality of active microbes expressing 7β-HSDH selected from one or both of Ruminococcus torques and Peptostreptococcus productus.

Fermenting and Synthesizing Microbes

In some embodiments, the microbial consortium of the current invention further comprises a fermenting microbe that metabolizes a fermentation substrate to generate one or more than one fermentation product. For example, in some embodiments, the fermentation product is a second metabolic substrate for one or more of the plurality of active microbes. In some embodiments, the fermentation product is a metabolic substrate for one or more of the supportive microbes. In some embodiments, the fermentation substrate is a polysaccharide and the generated fermentation product is one or more than one of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H₂, and CO₂. In some embodiments, the fermentation substrate is an amino acid and the generated fermentation product is one or more than one of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, phloretate, 3-(1H-indol-3-yl)propanoate, 5-aminopentanoate, H₂, H₂S, and CO₂.

In some embodiments, the microbial consortium of the current invention further comprises a synthesizing microbe that catalyzes a synthesis reaction that combines the one or more than one metabolite generated by the plurality of active microbes and the one or more than one fermentation product generated by the fermenting microbe to produce one or more than one synthesis product. In some embodiments the fermentation product generated by the fermenting microbe is a third metabolic substrate for the synthesizing microbe. In some embodiments, the one or more than one synthesis product is a second metabolic substrate for the plurality of active microbes. In some embodiments, the one or more than one synthesis product is a fourth metabolic substrate for the fermenting microbe.

In some embodiments, the synthesizing microbe catalyzes the synthesis of one or more than one of methane from H₂and CO₂, methane from formate and H₂, acetate from H₂and CO₂, acetate from formate and H₂, acetate and sulfide from H₂, CO₂, and sulfate, propionate and CO₂from succinate, succinate from H₂and fumarate; synthesis of succinate from formate and fumarate, and butyrate, acetate, H₂, and CO₂from lactate.

In some embodiments, a fermenting microbe may be for example, but not limited to, Bacteroides thetaiotaomicron or Bactorides vulgatus. In some embodiments, a synthesizing microbe may be for example, but not limited to, Methanobrevibacter smithii or Methanomassiliicoccus luminyensis.

In some embodiments, the fermenting microbe is selected from a Bacteroides thetaiotaomicron strain having a 16S sequence at least 80% identical to SEQ ID NO: 20, SEQ ID NO: 76, SEQ ID NO: 139, or SEQ ID NO: 280. In some embodiments, the fermenting microbe is selected from a Bacteroides vulgatus strain having a 16S sequence at least 80% identical to SEQ ID NO: 39, SEQ ID NO: 111, SEQ ID NO: 121, SEQ ID NO: 173, SEQ ID NO: 211, SEQ ID NO: 308, SEQ ID NO: 321, or SEQ ID NO: 326. In some embodiments, the synthesizing microbe is selected from a Methanobrevibacter smithii strain having a 16S sequence at least 80% identical to SEQ ID NO: 292.

In some embodiments, the fermenting microbe is selected from a Bacteroides thetaiotaomicron strain having a 16S sequence 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% identical to SEQ ID NO: 20, SEQ ID NO: 76, SEQ ID NO: 139, or SEQ ID NO: 280. In some embodiments, the fermenting microbe is selected from a Bacteroides vulgatus strain having a 16S sequence 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% identical to SEQ ID NO: 39, SEQ ID NO: 111, SEQ ID NO: 121, SEQ ID NO: 173, SEQ ID NO: 211, SEQ ID NO: 308, SEQ ID NO: 321, or SEQ ID NO: 326. In some embodiments, the synthesizing microbe is selected from a Methanobrevibacter smithii strain having a 16S sequence 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% identical to SEQ ID NO: 292.

In some embodiments, the microbial consortium disclosed herein comprises active microbes, fermenting microbes and synthesizing microbes in a colony forming unit (CFU) ratio selected from 1:1:1, 1:2:1, 1:1:2, 2:1:1, 2:1:2, 1:3:1, 1:1:3, 3:1:1, 3:1:3, 2:3:2, 2:2:3, 3:2:2, 3:2:3, 1:5:1, 1:1:5, 5:1:1, 5:1:5, 2:5:2, 2:2:5, 5:2:2, 5:2:5, 3:5:3, 3:3:5, 5:3:3, 5:3:5, 4:5:4, 4:4:5, 5:4:4, and 5:4:5. In some embodiments, an original dosage form of the disclosed microbial consortium comprises active microbes, fermenting microbes and synthesizing microbes in total CFU amounts within about one order of magnitude, about two orders of magnitude, about three orders of magnitude, about four orders of magnitude, about 5 orders of magnitude, about 6 orders of magnitude, about 7 orders of magnitude, about 8 orders of magnitude, about 9 orders of magnitude, or about 10 orders of magnitude of each other. In other embodiments, an original dosage form of the disclosed microbial consortium comprises active microbes, fermenting microbes and synthesizing microbes in CFU amounts within about two orders of magnitude of each other. In some embodiments, an original dosage form of the disclosed microbial consortium comprises active microbes and fermenting microbes in total CFU amounts within one order of magnitude, about two orders of magnitude, about three orders of magnitude, about four orders of magnitude, about 5 orders of magnitude, about 6 orders of magnitude, about 7 orders of magnitude, about 8 orders of magnitude, about 9 orders of magnitude, or about 10 orders of magnitude of each other. In some embodiments, an original dosage form of the disclosed microbial consortium comprises active microbes and synthesizing microbes in total CFU amounts within one order of magnitude, about two orders of magnitude, about three orders of magnitude, about four orders of magnitude, about 5 orders of magnitude, about 6 orders of magnitude, about 7 orders of magnitude, about 8 orders of magnitude, about 9 orders of magnitude, or about 10 orders of magnitude of each other. In some embodiments, an original dosage form of the disclosed microbial consortium comprises fermenting microbes and synthesizing microbes in total CFU amounts within one order of magnitude, about two orders of magnitude, about three orders of magnitude, about four orders of magnitude, about 5 orders of magnitude, about 6 orders of magnitude, about 7 orders of magnitude, about 8 orders of magnitude, about 9 orders of magnitude, or about 10 orders of magnitude of each other.

Microbial Consortia Design

In some embodiments, microbial consortia disclosed herein are designed to meet one or more than one of the following criteria:

- (i) an ability to eliminate or reduce levels of a first metabolic substrate causing or contributing to a disease in an animal;
- (ii) an ability to metabolize or convert one or more than one metabolite produced by the metabolism of the first metabolic substrate;
- (iii) an ability to metabolize one or more than one nutrient typically found in the human diet;
- (iv) an ability to fulfill unique and potentially beneficial biological functions in the gastrointestinal (GI) tract (e.g., bile salt hydrolase activity or butyrate production);
- (v) an ability to engraft in various biological niches and physical and metabolic compartments of the GI tract of an animal;
- (vi) an ability to increase biomass upon engraftment in the GI tract;
- (vii) an ability to have longitudinal stability in the GI tract of an animal;
- (viii) an ability to increase the flux of a precursor of the first metabolic substrate into a biochemical pathway that converts said precursor into a metabolite that is not the first metabolic substrate;
- (ix) diversity of component microbial species across one or more than one taxonomic phyla; and
- (x) natural prevalence of component microbial species in the GI tract of healthy adults.

In some embodiments, the microbial consortia of the present invention are designed to comprise a plurality of active microbes capable of metabolizing a first metabolic substrate that causes or contributes to disease in an animal. For example, in some embodiments, the first metabolic substrate may be selected from, but not limited to, oxalate and a bile acid (e.g., lithocholic acid (LCA), deoxycholic acid (DCA)). In some embodiments, the microbial consortium is designed to be capable of metabolizing the first metabolic substrate across a variety of pH ranges found within the GI tract (e.g., pH 4 to 8). In some embodiments, the microbial consortium is designed to be capable of metabolizing the first metabolic substrate in the presence of various concentrations of first metabolic substrate as they exist in different regions of the GI tract.

For example, in designing which active microbes to include in a microbial consortium for the treatment of primary or secondary hyperoxaluria, an in vitro colorimetric assay (e.g., as described in Example 3 below) can be used to measure the capacity of a candidate microbe to metabolize oxalate in a sample. Microbes capable of reducing the concentration of oxalate present in a sample by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, or by at least 80% can be included in a microbial consortium disclosed herein.

In other embodiments, an in vivo mouse assay can be used to measure the efficacy of a designed microbial consortium of the present invention in reducing the concentration of oxalate present in a sample of blood, serum, bile, stool, or urine when administered to a subject. Concentrations of oxalate in a blood, serum, bile, stool or urine sample can be measured using a liquid chromatography-mass spectrometry (LC-MS) method as described in Example 4, below. Microbial consortia capable of reducing blood, serum, bile, stool, or urine oxalate levels by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, or by at least 80% as compared to levels in untreated controls or pre-administration levels can be candidates for further evaluation for the treatment of primary or secondary hyperoxaluria.

In some embodiments, a microbial consortium disclosed herein is designed to metabolize one or more than one metabolite produced by the plurality of active microbes, wherein the one or more than one metabolite inhibits metabolism of the plurality of active microbes. In some embodiments, the microbial consortia are designed to maximize consumption and/or production of a defined set of metabolites using a minimal number of strains. For example, in some embodiments, a microbial consortium is designed to include a microbe that metabolizes formate produced by the plurality of active microbes, wherein the presence of formate inhibits the metabolism of oxalate by the plurality of active microbes, e.g., in a negative feedback loop. In some embodiments, a microbial consortium is designed to include microbes that catalyze the fermentation of polysaccharides to one or more than one of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H₂, and CO₂. In some embodiments, a microbial consortium is designed to catalyze the fermentation of amino acids to one or more than one of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, phloretate, 3-(1H-indol-3-yl)propanoate, 5-aminopentanoate, H₂, H₂S, and CO₂. In some embodiments, the microbial consortium is designed to catalyze the synthesis of one or more than one of the group consisting of methane from H₂and CO₂, methane from formate and H₂, acetate from H₂and CO₂, acetate from formate and H₂, acetate and sulfide from H₂, CO₂, and sulfate, propionate and CO₂from succinate, succinate from H₂and fumarate; synthesis of succinate from formate and fumarate, and butyrate, acetate, H₂, and CO₂from lactate. In some embodiments, the microbial consortium is designed to catalyze the deconjugation of conjugated bile acids to produce primary bile acids, the conversion of cholic acid (CA) to 7-oxocholic acid, the conversion of 7-oxocholic acid to 7-beta-cholic acid (7betaCA), the conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and/or the conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA).

In some embodiments, a microbial consortium disclosed herein is designed to metabolize one or more than one metabolite produced by the plurality of active microbes, wherein the one or more than one metabolite inhibits metabolism of the plurality of active microbes. In some embodiments, the microbial consortia are designed to maximize consumption and/or production of a defined set of metabolites using a minimal number of strains. For example, in some embodiments, a microbial consortium is designed to include a microbe that metabolizes formate produced by the plurality of active microbes, wherein the presence of formate inhibits the metabolism of oxalate by the plurality of active microbes, e.g., in a negative feedback loop. In some embodiments, a microbial consortium is designed to include microbes that catalyze the fermentation of polysaccharides to one or more than one of acetate, propionate, succinate, lactate, butyrate, formate, H₂, and CO₂. In some embodiments, a microbial consortium is designed to catalyze the fermentation of amino acids to one or more than one of acetate, propionate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, H₂, H₂S, and CO₂. In other embodiments, a microbial consortium is designed to include microbes that catalyze the synthesis of one or more than one of methane from formate and H₂; acetate from H₂and CO₂; acetate from formate and H₂; acetate and sulfide from H₂, CO₂, and sulfate; propionate and CO₂from succinate; succinate from H₂and fumarate; synthesis of succinate from formate and fumarate and butyrate, acetate, H₂, and CO₂from lactate.

In some embodiments, microbial consortia are designed to include microbes capable of metabolizing one or more nutrient typically found in a broad spectrum of human diets. For example, in some embodiments, microbial consortia are designed include microbes capable of metabolizing one or more than one of oxalate, fructan, inulin, glucuronoxylan, arabinoxylan, glucomannan, β-mannan, dextran, starch, arabinan, xyloglucan, galacturonan, β-glucan, galactomannan, rhamnogalacturonan I, rhamnogalacturonan II, arabinogalactan, mucin O-linked glycans, yeast α-mannan, yeast β-glucan, chitin, alginate, porphyrin, laminarin, carrageenan, agarose, alternan, levan, xanthan gum, galactooligosaccharides, hyaluronan, chondrointin sulfate, dermatan sulfate, heparin sulfate, keratan sulfate, phenylalanine, tyrosine, tryptophan, leucine, valine, isoleucine, glycine, proline, asparagine, glutamine, aspartate, glutamate, cysteine, lysine, arginine, serine, methionine, alanine, arginine, histidine, ornithine, citrulline, carnitine, hydroxyproline, cholic acid, chenodeoxycholic acid, taurochenodeoxycholic acid, glycochenodeoxycholic acid, cholesterol, cinnamic acid, coumaric acid, sinapinic acid, ferulic acid, caffeic acid, quinic acid, chlorogenic acid, catechin, epicatechin, gallic acid, pyrogallol, catechol, quercetin, myricetin, campherol, luteolin, apigenin, naringenin, and hesperidin. In some embodiments, microbial consortia are designed to enrich for consumption of dietary carbon and energy sources. In other embodiments, microbial consortia are designed to enrich for the production or consumption of host metabolites, including bile acids, sugars, amino acids, vitamins, short-chain fatty acids, and gasses.

In some embodiments, microbial consortia are designed to include microbes having potentially beneficial biological functions in the GI tract. For example, microbial consortia are designed to include microbial strains having robust and/or redundant bile salt hydrolase (BSH) activity, so that deconjugation of primary bile acids can occur despite differences in host physiology, diet, plurality of active microbes present in the microbial consortium, or the pre-existing composition of the conjugated bile acid pool. In other embodiments, microbial consortia are designed to include microbial strains capable of producing butyrate from the fermentation of dietary fiber in the GI tract, which contributes to intestinal homeostasis, energy metabolism, anti-inflammatory processes, enhancement of intestinal barrier function, and mucosal immunity.

In some embodiments, microbial consortia described herein are designed to be able to engraft in various biological niches and physical and metabolic compartments of the GI tract of an animal (e.g., a human).

As used herein, “engraftment” (and grammatical variants thereof, e.g., “engraft”) refers to the ability of a microbial strain or microbial community to establish in one or more niches of the gut of an animal. Operationally, a microbial strain or microbial consortium is “engrafted” if evidence of its establishment, post-administration, can be obtained. In some embodiments, that evidence is obtained by molecular identification (e.g., Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS), 16S rRNA sequencing, or genomic sequencing) of a sample obtained from the animal. In some embodiments, the sample is a stool sample. In some embodiments, the sample is a biopsy sample taken from the gut of the animal (e.g., from a location along the gastrointestinal tract of the animal). Engraftment may be transient or may be persistent. In some embodiments, transient engraftment means that the microbial strain or microbial community can no longer be detected in an animal to which it has been administered after the lapse of about 1 week, about 2 weeks, about three weeks, about 1 month, about 2 months, about 3 months, about 4 months, about 6 months, about 8 month, about 10 months, about 1 year, about 1.5 years, or about 2 years.

For example, microbial consortia are designed to be capable of engrafting into one or more than one niche of the gastrointestinal tract whose composition varies according to a number of environmental factors including, but not limited to, the particular physical compartment of the gastrointestinal tract, the chemical and physicochemical properties of the niche environment (e.g., gastrointestinal motility, pH), the metabolic substrate composition of the niche environment, and other co-inhabiting commensal microbial species. To analyze engraftment of a designed microbial consortium described herein, an in vivo assay can be used as described in Example 8, wherein stool samples from treated mice are analyzed for the presence of specific microbial strains comprising the microbial consortium by whole genome shotgun sequencing of microbial DNA extracted from fecal pellets and sequence reads mapped against a comprehensive database of complete, sequenced genomes of all the defined microbial strains comprising the microbial consortium.

In some embodiments, a microbial consortium described herein is designed to include microbes that support the growth and increase the biomass of one or more than one other microbe in the consortium when engrafted in the GI tract of an animal (e.g., a human). For example, in some embodiments, microbial consortia are designed to promote co-culturability and/or ecological stability of one or more than one microbial strain of the consortium.

In some embodiments, a microbial consortium described herein is designed to include one or more than one microbe having longitudinal stability in the GI tract of an animal (e.g., a human) despite transient or long-term changes to the gastrointestinal niche due to modifications in diet, the presence or absence of disease, or other physiological or environmental factors. In some embodiments, longitudinal stability of a community refers to the ability of a microbial consortium to persist (i.e. remain engrafted) in the GI tract of an animal following microbial challenge. In some embodiments, when given sufficient time to permit colonization of microbial challenge strains in the GI tract of an animal engrafted with a microbial consortium, longitudinal stability can be defined as one where at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of the defined microbial strains are detectable by metagenomic analysis. For example, in some embodiments, metagenomic analysis comprises whole genome shotgun sequencing analysis.

In other embodiments, longitudinal stability of a community refers to the characteristic of microbial strains comprising a consortium to maintain a metabolic phenotype over a period of time or following microbial challenge. For example, in some embodiments, defined microbial strains comprising a consortium can maintain a metabolic phenotype for at least 1 week, at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 6 weeks, at least 8 weeks, at least 10 weeks, at least 12 weeks, at least 4 months, at least 6 months at least 8 months, at least 10 months, at least 1 year, at least 1.5 years, or at least 2 years.

In some embodiments, a longitudinal stability can be defined as one where the defined microbial strains comprising a consortium maintain the one or more metabolic phenotype of mucin degradation, polysaccharide fermentation, hydrogen utilization, succinate metabolism, butyrate production, amino acid metabolism, bile acid metabolism, CO₂fixation, formate metabolism, methanogenesis, acetogenesis, hydrogen production, or propionate production over a period of time or following microbial challenge.

In some embodiments, a microbial consortium is designed to include one or more than one microbe capable of increasing the flux of a precursor of the first metabolic substrate into a biochemical pathway that converts said precursor into a metabolite that is not the first metabolic substrate. For example, in some embodiments, a microbial consortium can be designed to include microbial strains having robust 7α-HSDH and 7β-HSDH activity, which direct precursors of DCA and LCA first metabolic substrates (CA and CDCA, respectively) down biochemical pathways producing 7betaCA and UDCA.

In some embodiments, microbial consortia described herein are designed to include representative microbial strains isolated from a healthy donor fecal sample, with the exception of species known to be associated with pathogenesis, which represent microbial species belonging to a diverse array of taxonomic phyla including, Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia and Euryarchaeota. In some embodiments, microbial consortia having phylogenetic diversity are less sensitive to perturbations in the GI environment and are more stably engrafted For example, in some embodiments, microbial consortia can be designed to include one or more than one microbial species from Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, or Euryarchaeota.

In some embodiments, microbial consortia can be designed to include one or more than one microbial species from Bacteroidetes and Firmicutes, Bacteroidetes and Actinobacteria, Bacteroidetes and Proteobacteria, Bacteroidetes and Verrucomicrobia, Bacteroidetes and Euryarchaeota, Firmicutes and Actinobacteria, Firmicutes and Proteobacteria, Firmicutes and Verrucomicrobia, Firmicutes and Euryarchaeota, Actinobacteria and Proteobacteria, Actinobacteria and Verrucomicrobia, Actinobacteria and Euryarchaeota, Proteobacteria and Verrucomicrobia, Proteobacteria and Euryarchaeota, or Verrucomicrobia and Euryarchaeota.

In some embodiments, microbial consortia can be designed to include one or more than one microbial species from: Bacteroidetes, Firmicutes, and Actinobacteria; Bacteroidetes, Firmicutes, and Proteobacteria; Bacteroidetes, Firmicutes, and Verrucomicrobia; Bacteroidetes, Firmicutes and Euryarchaeota; Bacteroidetes, Actinobacteria, and Proteobacteria; Bacteroidetes, Actinobacteria, and Verrucomicrobia; Bacteroidetes, Actinobacteria, and Euryarchaeota; Bacteroidetes, Proteobacteria, and Verrucomicrobia; Bacteroidetes, Proteobacteria, and Euryarchaeota; Bacteroidetes, Verrucomicrobia, and Euryarchaeota; Firmicutes, Actinobacteria, and Proteobacteria; Firmicuates, Actinobacteria, and Verrucomicrobia; Firmicuates, Actinobacteria, and Euryarchaeota; Firmicuates, Proteobacteria, and Verrucomicrobia; Firmicuates, Proteobacteria, and Euryarchaeota; Firmicutes, Verrucomicrobia, and Euryarchaeota; Actinobacteria, Proteobacteria, and Verrrucomicrobia; Actinobacteria, Proteobacteria, and Euryarchaeota; or Proteobacteria, Verrucomicrobia, and Euryarchaeota.

In some embodiments, microbial consortia can be designed to include one or more than one microbial species from: Bacteoidetes, Firmicutes, Actinobacteria, and Proteobacteria; Bacteoidetes, Firmicutes, Actinobacteria and Verrucomicrobia; Bacteoidetes, Firmicutes, Actinobacteria, and Euryarchaeota; Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia; Bacteroidetes, Actinobacteria, Proteobacteria, and Euryarchaeota; Bacteroidetes, Proteobacteria, Verrucomicrobia, and Euryarchaeota; Firmicutes, Actinobacteria, Proteobacteria, and Verrucomicrobia; Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota; Firmicuates, Proteobacteria, Verrucomicrobia, and Euryarchaeota; or Actinobacteria, Proteobacteria, Verrucomicrobia, and Euryarchaeota.

In some embodiments, microbial consortia can be designed to include one or more than one microbial species from: Bacteoidetes, Firmicutes, Actinobacteria, Proteobacteria, and Verrucomicrobia; Bacteoidetes, Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota; Bacteroidetes, Firmicutes, Actinobacteria, Verrucomicrobia, and Euryarchaeota; Bacteoidetes, Firmicutes, Proteobacteria, Verrucomicrobia, and Eurarchaeota; Bacteoidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, and Eurarchaeota; or Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, and Eurarchaeota.

In some embodiments, microbial consortia can be designed to include one or more than one microbial species from: Bacteoidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, and Euryarchaeota.

For example, in some embodiments, a microbial consortium can be designed to include one or more than one Bacteroidetes strain listed in Table 4. In some embodiments, a microbial consortium can be designed to include a Bacteroidetes strain comprising a 16S sequence 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% identical to any one of the Bacteroidetes microbes listed in Table 4. In some embodiments, a microbial consortium can be designed to include a Bacteroidetes strain comprising a 16S sequence at least 80% identical to any one of the Bacteroidetes microbes listed in Table 4.

In some embodiments, a microbial consortium can be designed to include one or more than one Firmicutes strain listed in Table 4. In some embodiments, a microbial consortium can be designed to include a Firmicutes strain comprising a 16S sequence 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% identical to any one of the Firmicutes microbes listed in Table 4. In some embodiments, a microbial consortium can be designed to include a Firmicutes strain comprising a 16S sequence at least 80% identical to any one of the Firmicutes microbes listed in Table 4.

In some embodiments, a microbial consortium can be designed to include one or more than one Actinobacteria strain listed in Table 4. In some embodiments, a microbial consortium can be designed to include a Actinobacteria strain comprising a 16S sequence 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% identical to any one of the Actinobacteria microbes listed in Table 4. In some embodiments, a microbial consortium can be designed to include a Actinobacteria strain comprising a 16S sequence at least 80% identical to any one of the Actinobacteria microbes listed in Table 4.

In some embodiments, a microbial consortium can be designed to include one or more than one Proteobacteria strain listed in Table 4. In some embodiments, a microbial consortium can be designed to include a Proteobacteria strain comprising a 16S sequence 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% identical to any one of the Proteobacteria microbes listed in Table 4. In some embodiments, a microbial consortium can be designed to include a Proteobacteria strain comprising a 16S sequence at least 80% identical to any one of the Proteobacteria microbes listed in Table 4.

In some embodiments, a microbial consortium can be designed to include one or more than one Verrucomicrobia strain listed in Table 4. In some embodiments, a microbial consortium can be designed to include a Verrucomicrobia strain comprising a 16S sequence 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% identical to any one of the Verrucomicrobia microbes listed in Table 4. In some embodiments, a microbial consortium can be designed to include a Verrucomicrobia strain comprising a 16S sequence at least 80% identical to any one of the Verrucomicrobia microbes listed in Table 4.

In some embodiments, a microbial consortium can be designed to include Methonobrevibacter smithii. In some embodiments, a microbial consortium can be designed to include a Methonobrevibacter smithii strain comprising a 16S sequence 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% identical to SEQ ID NO: 292. In some embodiments, a microbial consortium can be designed to include a Methonobrevibacter smithii strain comprising a 16S sequence at least 80% identical to SEQ ID NO: 292.

In some embodiments, a microbial consortium is designed such that when administered to a subject the plurality of active microbes and the supportive community of microbes have one or more than one synergistic effect. For example, in some embodiments administration of a microbial consortium comprising the plurality of active microbes in combination with the supportive community of microbes results in an enhanced metabolization of a first metabolic substrate than achieved by administration of either the plurality of active microbes or supportive community of microbes alone. For example, in some embodiments administration of a microbial consortium results in enhanced oxalate metabolism (e.g., as measured by urinary oxalate levels) in a subject as compared to a subject administered with either a plurality of active microbes or a supportive community of microbes alone. In other embodiments, administration of a microbial consortium results in enhanced conversion of primary bile acids (e.g., DCA and/or LCA) in a subject as compared to a subject administered with either a plurality of active microbes or a supportive community of microbes alone. In some embodiments, a microbial composition comprising the plurality of active microbes in combination with the supportive community of microbes results in enhanced GI engraftment than the engraftment achieved by administration of either the plurality of active microbes or supportive community of microbes alone. In some embodiments, a microbial composition comprising the plurality of active microbes in combination with the supportive community of microbes results in greater biomass in the GI tract than the biomass achieved by administration of either the plurality of active microbes or supportive community of microbes alone. In some embodiments, a microbial composition comprising the plurality of active microbes in combination with the supportive community of microbes results in enhanced longitudinal stability than the stability achieved by administration of either the plurality of active microbes or supportive community of microbes alone. In some embodiments, a microbial composition comprising the plurality of active microbes in combination with the supportive community of microbes results in enhanced clinical efficacy in the treatment of a disease than the efficacy achieved by administration of either the plurality of active microbes or supportive community of microbes alone.

In some embodiments, a microbial consortium is designed to comprise 20 to 300, 20 to 250, 20 to 200, 20 to 190, 20 to 180, 20 to 170, 20 to 160, 20 to 150, 20 to 140, 20 to 130, 20 to 120, 20 to 110, 20 to 100, 20 to 90, 20 to 80, 20 to 70, 20 to 60, 20 to 50, 50 to 300, 50 to 250, 50 to 200, 50 to 190, 50 to 180, 50 to 170, 50 to 160, 50 to 150, 50 to 140, 50 to 130, 50 to 120, 50 to 110, 50 to 100, 50 to 90, 50 to 80, 50 to 70, 50 to 60, 100 to 300, 100 to 250, 100 to 200, 100 to 190, 100 to 180, 100 to 170, 100 to 160, 100 to 150, 100 to 140, 100 to 130, 100 to 120, 100 to 110, 70 to 80, 80 to 90, or 150 to 160 microbial strains, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 4.

In some embodiments, a microbial consortium is designed to comprise 20 to 160, 30 to 160, 40 to 160, 50 to 160, 60 to 160, 70 to 160, 80 to 160, 90 to 160, 100 to 160, 110 to 160, 120 to 160, 130 to 160, 140 to 160, 150 to 160, 20 to 140, 30 to 140, 40 to 140, 50 to 140, 60 to 140, 70 to 140, 80 to 140, 90 to 140, 100 to 140, 110 to 140, 120 to 140, 130 to 140, 20 to 120, 30 to 120, 40 to 120, 50 to 120, 60 to 120, 70 to 120, 80 to 120, 90 to 120, 100 to 120, 110 to 120, 20 to 100, 30 to 100, 40 to 100, 50 to 100, 60 to 100, 70 to 100, 80 to 100, 90 to 100, 20 to 80, 30 to 80, 40 to 80, 50 to 80, 60 to 80, or 70 to 80 microbial strains, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 22.

In some embodiments, a microbial consortium is designed to comprise 20 to 104, 40 to 104, 60 to 104, 80 to 104, 100 to 104, 20 to 80, 40 to 80, 60 to 80, 20 to 60, or 40 to 60 microbial strains, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 23.

In some embodiments, a microbial consortium is designed to comprise 20 to 158, 30 to 158, 40 to 158, 50 to 158, 60 to 158, 70 to 158, 80 to 158, 90 to 158, 100 to 158, 110 to 158, 120 to 158, 130 to 158, 140 to 158, 150 to 158, 20 to 140, 30 to 140, 40 to 140, 50 to 140, 60 to 140, 70 to 140, 80 to 140, 90 to 140, 100 to 140, 110 to 140, 120 to 140, 130 to 140, 20 to 120, 30 to 120, 40 to 120, 50 to 120, 60 to 120, 70 to 120, 80 to 120, 90 to 120, 100 to 120, 110 to 120, 20 to 100, 30 to 100, 40 to 100, 50 to 100, 60 to 100, 70 to 100, 80 to 100, 90 to 100, 20 to 80, 30 to 80, 40 to 80, 50 to 80, 60 to 80, or 70 to 80 microbial strains, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 20.

In some embodiments, a microbial consortium is designed to comprise 20 to 152, 30 to 152, 40 to 152, 50 to 152, 60 to 152, 70 to 152, 80 to 152, 90 to 152, 100 to 152, 110 to 152, 120 to 152, 130 to 152, 140 to 152, 150 to 152, 20 to 140, 30 to 140, 40 to 140, 50 to 140, 60 to 140, 70 to 140, 80 to 140, 90 to 140, 100 to 140, 110 to 140, 120 to 140, 130 to 140, 20 to 120, 30 to 120, 40 to 120, 50 to 120, 60 to 120, 70 to 120, 80 to 120, 90 to 120, 100 to 120, 110 to 120, 20 to 100, 30 to 100, 40 to 100, 50 to 100, 60 to 100, 70 to 100, 80 to 100, 90 to 100, 20 to 80, 30 to 80, 40 to 80, 50 to 80, 60 to 80, or 70 to 80 microbial strains, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 16.

In some embodiments, a microbial consortium is designed to comprise 20 to 88, 40 to 88, 60 to 88, 80 to 88, 20 to 80, 40 to 80, 60 to 80, 20 to 60, or 40 to 60 microbial strains, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 17.

In some embodiments a microbial consortium is designed to comprise 20 to 89, 40 to 89, 60 to 89, 80 to 89, 20 to 80, 40 to 80, 60 to 80, 20 to 60, or 40 to 60 microbial strains, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 18.

In some embodiments, a microbial consortium is designed to comprise 20 to 75, 40 to 75, 60 to 75, 80 to 75, 20 to 60, or 40 to 60 microbial strains, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 19.

In some embodiments, a microbial consortium is designed to comprise 2 to 51, 5 to 51, 10 to 51, 20 to 51, 30 to 51, or 40 to 51 Actinobacteria; 10 to 102, 20 to 102, 30 to 102, 40 to 102, 50 to 102, 60 to 102, 70 to 102, 80 to 102, 90 to 102, 10 to 50, 20 to 50, 30 to 50, or 40 to 50 Bacteroidetes; 1 or 2 Euryacrchaeota; 20 to 197, 40 to 197, 60 to 197, 80 to 197, 100 to 197, 120 to 197, 140 to 197, 160 to 197, 180 to 197, 20 to 150, 40 to 150, 60 to 150, 80 to 150, 100 to 150, 120 to 150, 140 to 150, 20 to 100, 40 to 100, 60 to 100, or 80 to 100 Firmicutes; 2 to 24, 8 to 24, 12 to 24, 18 to 24, or 20 to 24 Proteobacteria; and 1 Verrucomicrobia, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 4.

In some embodiments, a microbial consortium is designed to comprise 2 to 20, 5 to 20, 10 to 20, or 15 to 20 Actinobacteria; 2 to 48, 10 to 48, 20 to 48, 30 to 48, 40 to 48 Bacteroidetes; 2 to 76, 10 to 76, 20 to 76, 30 to 76, 40 to 76, 50 to 76, 60 to 76, 70 to 76, 2 to 50, 10 to 50, 20 to 50, 30 to 50, 40 to 50 Firmicutes; 2 to 7 Proteobacteria; and 1 Verrucomicrobia, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 16.

In some embodiments, a microbial consortium is designed to comprise 2 to 22, 10 to 22, or 20 to 22 Actinobacteria; 2 to 27, 10 to 27, or 20 to 27 Bacteroidetes; 2 to 29, 10 to 29, or 20 to 29 Firmicutes; 1 to 9 Proteobacteria; and 1 Verrucomicrobia, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 17.

In some embodiments, a microbial consortium is designed to comprise 2 to 18 or 10 to 18 Actinobacteria; 2 to 27, 10 to 27, or 20 to 27 Bacteroidetes; 2 to 38, 10 to 38, 20 to 38, 30 to 38 Firmicutes; and 2 to 6 Proteobacteria, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 18.

In some embodiments, a microbial consortium is designed to comprise 2 to 7 Actinobacteria; 2 to 20 or 10 to 20 Bacteroidetes; 2 to 38, 10 to 38, 20 to 38, or 30 to 38 Firmicutes; 2 to 8 Proteobacteria; and 1 Verrucomicrobia, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 19.

In some embodiments, a microbial consortium is designed to comprise 2 to 20 or 10 to 20 Actinobacteria; 2 to 42, 10 to 42, 20 to 42, 30 to 42, or 40 to 42 Bacteroidetes; 2 to 84, 10 to 84, 20 to 84, 30 to 84, 40 to 84, 50 to 84, 60 to 84, 70 to 84, 80 to 84, 2 to 50, 10 to 50, 20 to 50, 30 to 50, or 40 to 50 Firmicutes; 2 to 11 Proteobacteria; and 1 Verrucomicrobia, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 20.

In some embodiments, a microbial consortium is designed to comprise 2 to 20 or 10 to 20 Actinobacteria; 2 to 44, 10 to 44, 20 to 44, 30 to 44, or 40 to 44 Bacteroidetes; 1 or 2 Euryarcheota; 2 to 83, 10 to 83, 20 to 83, 30 to 83, 40 to 83, 50 to 83, 60 to 83, 70 to 83, 80 to 83, 2 to 50, 10 to 50, 20 to 50, 30 to 50, or 40 to 50 Firmicutes; 2 to 10 Proteobacteria; and 1 Verrucomicrobia, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 22.

In some embodiments, a microbial consortium is designed to comprise 2 to 15 or 10 to 15 Actinobacteria; 2 to 25, 10 to 25, or 20 to 25 Bacteroidetes; 2 to 55, 10 to 55, 20 to 55, 30 to 55, 40 to 55, 50 to 55, 2 to 25, 10 to 25, or 20 to 25 Firmicutes; 2 to 8 Proteobacteria; and 1 Verrucomicrobia, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 23.

In some embodiments, a microbial consortium is designed to comprise 2 to 11 Actinobacteria; 2 to 28, 10 to 28, or 20 to 28 Bacteroidetes; 1 Euryarchaeota; 2 to 56, 10 to 56, 20 to 56, 30 to 56, 40 to 56, 50 to 56, 2 to 25, 10 to 25, or 20 to 25 Firmicutes; 2 to 7 Proteobacteria; and 1 Verrucomicrobia, each comprising a 16S sequence at least 80%, 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% identical to any one of the microbes listed in Table 24.

Isolation and Propagation of Microbial Strains

Active and supportive microbial strains can be derived from human donor fecal samples, or purchased from the American Type Culture Collection (ATCC; www.atcc.org), the Leibniz institute DSMZ (www.dsmz.de), or BEI Resources (www.beiresources.org). Microbial strains purchased from a depository can be cultured according to depository instructions and microbial strains derived from human donors can be cultured according to the media conditions described in Table 3, below.

Fecal donors can be selected based on multiple criteria, including a health and medical history questionnaire, physical exam, and blood and stool tests for assessing pathogen-free status. Upon collection of a stool sample from a donor, stool samples can cultured in an anaerobic chamber (5% CO₂, 5% H₂, 90% N₂) and microbial strains isolated by making serial dilution aliquots of the stool samples and plating said aliquots on a variety of microbial cultivation media suitable for growth of anaerobes. Specific enrichment techniques can be performed for species having particular metabolic capabilities, such as consumption or tolerance of oxalate or bile acids. In order to enrich for strains having oxalate metabolism capabilities, aliquots of the serially-diluted stool samples can be plated on agar growth media supplemented with varying concentrations of potassium oxalate (20 mM, 40 mM, 80 mM, 160 mM, or 200 mM). In order to enrich for species capable of metabolizing bile acids, aliquots of serially diluted stool samples can be plated on growth media supplemented with 2% bile. Archaea can be isolated by diluting fecal samples and plating on culture media containing a mixture of antibiotics that is lethal to both gram-positive and gram-negative bacteria. Microbial strain identification can be performed either by 16S rRNA gene sequencing or proteomic fingerprinting using high-throughput Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS).

In some embodiments, methods of producing a microbial consortium described herein comprise individually culturing each of a plurality of active microbes and supportive microbes prior to combining the microbes to form the consortium. In other embodiments, methods of producing a microbial consortium described herein comprise culturing all of a plurality of active microbes and supportive microbes together. In still other embodiments, methods of producing a microbial consortium comprise individually culturing one or more than one microbial strain and co-culturing two or more microbial strains having compatible culture growth conditions, then combining together the individually-cultured microbial strains and co-cultured defined microbial strains to form a microbial consortium. In other embodiments, methods of producing a microbial consortium comprise individually culturing one or more than one microbial strain and co-culturing two or more microbial strains having compatible culture growth conditions, then combining together the individually-cultured microbial strains and co-cultured defined microbial strains to form a microbial consortium.

Pharmaceutical Compositions

The present disclosure also provides pharmaceutical compositions that contain an effective amount of a microbial consortium described herein. The composition can be formulated for use in a variety of delivery systems. One or more physiologically acceptable buffer(s) or carrier(s) can also be included in the composition for proper formulation. Suitable formulations for use in the present disclosure are found in Remington's Pharmaceutical Sciences, Mack Publishing Company, Philadelphia, Pa., 17th ed., 1985. For a brief review of methods for drug delivery, see, e.g., Langer (Science 249:1527-1533, 1990).

In some embodiments, microbial cells of the present invention are harvested by microfiltration and centrifugation. In some embodiments, microfiltration is done with a membrane comprising a nonreactive polymer. For example, in some embodiments, said membrane comprises Polyvinylidene fluoride, Polysulfones, or nitrocellulose. In some embodiments, a membrane for microfiltration has a pore size of approximately 0.2 to 0.45 μm. In some embodiments, the cells are centrifuged at approximately 1000 to 30000, 5000 to 30000, 10000 to 30000, 15000 to 30000, 20000 to 30000, 25000 to 30000, 1000 to 25000, 5000 to 25000, 10000 to 25000, 15000 to 25000, 20000 to 25000, 1000 to 20000, 5000 to 20000, 10000 to 20000, 15000 to 20000, 1000 to 15000, 5000 to 15000, 10000 to 15000, 1000 to 10000, 5000 to 10000, 1000 to 5000 g force. In some embodiments, the cells are concentrated to approximately 1×10⁶to 1×10¹², 1×10⁷to 1×10¹², 1×10⁸to 1×10¹², 1×10⁹to 1×10¹², 1×10¹⁰to 1×10¹², 1×10¹¹to 1×10¹², 1×10⁶to 1×10¹¹, 1×10⁷to 1×10¹¹, 1×10⁸to 1×10¹¹, 1×10⁹to 1×10¹¹, 1×10¹⁰to 1×10¹¹, 1×10⁶to 1×10¹⁰, 1×10⁷to 1×10¹⁰, 1×10⁸to 1×10¹⁰, 1×10⁹to 1×10¹⁰, 1×10⁶to 1×10⁹, 1×10⁷to 1×10⁹, 1×10⁸to 1×10⁹, 1×10⁶to 1×10⁸, 1×10⁷to 1×10⁸1×10⁶to 1×10⁷CFUs per milliliter.

In some embodiments, microbial cells of the present invention are frozen. In some embodiments, the microbial cells of the present invention are mixed with one or more cryoprotective agents (CPAs) before freezing. In some embodiments, the ratio of cells to CPA is approximately 25:1, 10:1, 5:1, 4:1, 3:1, 2:1, 1:1, 1:2, 1:3, 1:4, 1:5, 1:10, or 1:25. In some embodiments, a CPA comprises one or more of glycerol, maltodextrin, sucrose, inulin, trehalose, and alginate. In some embodiments, a CPA further comprises one or more antioxidants. In some embodiments, an antioxidant is selected from the list of cysteine, ascorbic acid, and riboflavin.

In some embodiments, the microbial cells of the present invention are lyophilized. In some embodiments, the lyophilized cells are used to make an orally-administered dose of the invention. In some embodiments, primary drying is conducted below approximately −20° C. In some embodiments, primary drying is followed by a secondary drying at a higher temperature, e.g. greater than 0° C., greater than 5° C., or greater than 10° C.

In some embodiments a pharmaceutical composition disclosed herein may comprise a microbial consortium of the present invention and one or more than one agent selected from, but not limited to: carbohydrates (e.g., glucose, sucrose, galactose, mannose, ribose, arabinose, xylose, fructose, maltose, cellobiose, lactose, deoxyribose, hexose); lipids (e.g. 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)); minerals (e.g., chloride, sodium, calcium, iron, chromium, copper, iodine, zinc, magnesium, manganese, molybdenum, phosphorus, potassium, and selenium); vitamins (e.g., vitamin C, vitamin A, vitamin E, vitamin B 12, vitamin K, riboflavin, niacin, vitamin D, vitamin B6, folic acid, pyridoxine, thiamine, pantothenic acid, and biotin); buffering agents (e.g. sodium citrate, magnesium carbonate, magnesium bicarbonate, calcium carbonate, and calcium bicarbonate); preservatives (e.g., alpha-tocopherol, ascorbate, parabens, chlorobutanol, and phenol); binders (e.g., starches, pregelatinized starches, gelatin, polyvinylpyrolidone, cellulose, methylcellulose, sodium carboxymethylcellulose, ethylcellulose, polyacrylamides, polyvinyloxoazolidone, polyvinylalcohols, C₁₂-C₁₈fatty acid alcohol, polyethylene glycol, polyols, saccharides, oligosaccharides); lubricants (e.g. magnesium stearate, calcium stearate, zinc stearate, hydrogenated vegetable oils, sterotex, polyoxyethylene monostearate, talc, polyethyleneglycol, sodium benzoate, sodium lauryl sulfate, magnesium lauryl sulfate, and light mineral oil); dispersants (e.g., starch, alginic acid, polyvinylpyrrolidones, guar gum, kaolin, bentonite, purified wood cellulose, sodium starch glycolate, isoamorphous silicate, and microcrystalline cellulose); disintegrants (e.g., corn starch, potato starch, pregelatinized and modified starches thereof, sweeteners, clays, such as bentonite, micro-crystalline cellulose, alginates, sodium starch glycolate, gums such as agar, guar, locust bean, karaya, pecitin, tragacanth, sodium bicarbonate in combination with citric acid, and sodium bicarbonate in combination with tartaric acid); flavoring agents; sweeteners; and coloring agents. In some embodiments, additional nutrients such as oxalate or formate are added to support robust revival of specific strains from the capsule.

In certain embodiments, a microbial consortium of the present invention is administered orally as a lyophilized powder, capsule, tablet, troche, lozenge, granule, gel or liquid. In some embodiments, a microbial consortium of the present invention is administered as a tablet or pill and can be compressed, multiply compressed, multiply layered, and/or coated. For example, in some embodiments, a lyophilized powder is filled in “0”, “00”, or “000” size capsules to accommodate various strengths. In some embodiments the tablet or pill comprises an enteric coating.

Therapeutic Applications

The present invention provides microbial consortia capable of engrafting into one or more than one niche of a gastrointestinal tract where it is capable of metabolizing a first metabolic substrate that causes or contributes to disease in an animal. In some embodiments, the animal is a mouse. In some embodiments, the animal is a germ-free mouse. In some embodiments, the animal is a mouse engrafted with a human microbiome. In some embodiments, the animal is a human.

In some embodiments of the invention, when administered to an animal, the animal is pre-treated with one or more antibiotics prior to administration of the microbial consortium. In some embodiments, the one or more antibiotics is selected from ampicillin, enrofloxacin, clarithromycin, and metronidazole. In some embodiments, the animal is pre-treated with a polyethylene glycol bowel-preparation procedure.

In some embodiments, when administered to an animal, the microbial consortium of the present invention significantly reduces the concentration of a first metabolic substrate present in the blood, serum, bile, stool or urine as compared to samples collected pretreatment from the same animal or from corresponding control animal that have not been administered with the microbial consortium. For example, in some embodiments, when administered to an animal on a high oxalate diet, the microbial consortium of the present invention significantly reduces the concentration of oxalate present in a sample of blood, serum, bile, stool or urine as compared to samples collected pretreatment from the same animal or from a corresponding control animal that has not been administered with the microbial consortium. As used herein, a “high oxalate diet” refers to a diet that induces a hyperoxaluria phenotype in an animal. For example, in some embodiments, an animal may be maintained on a high oxalate diet for 7 days to 1 month. In some embodiments, an animal may be maintained on a high oxalate diet for 7 days, 14 days, 21 days, or 1 month. In some embodiments, a high oxalate diet can have a calcium to oxalate molar ratio of less than 2.0. For example, in some embodiments, a high oxalate diet can have a calcium to oxalate molar ratio of about 0.1 to about 0.8. In some embodiments, an animal may be maintained on a grain-based diet that is rich in complex polysaccharides and nutritionally complete and given ad libitum drinking water supplemented with about 0.5% to 1% oxalate. In some embodiments, a control animal may be maintained on a diet as shown in Table 1 or an animal may be maintained on a high oxalate diet as shown in Table 2.

TABLE 1

Control Diet

Casein
200
mg/g

DL-Methionine
3.0
mg/g

Sucrose
302.8
mg/g

Corn Starch
280.0
mg/g

Corn Oil
50.0
mg/g

Inulin
35.0
mg/g

Pectin
35.0
mg/g

Cellulose
25.0
mg/g

Mineral Mix, Ca—P Deficient (79055)
13.37
mg/g

Potassium phosphate, monobasic
11.4
mg/g

Calcium chloride
14.94
mg/g

Sodium chloride
19.48
mg/g

Vitamin Mix, Teklad (40060)
10.0
mg/g

Ethoxyquin, antioxidant
0.01
mg/g

TABLE 2

Oxalate Diet

Casein
200
mg/g

DL-Methionine
3.0
mg/g

Sucrose
316.2
mg/g

Corn Starch
280.0
mg/g

Corn Oil
50.0
mg/g

Inulin
35.0
mg/g

Pectin
35.0
mg/g

Cellulose
25.0
mg/g

Mineral Mix, Ca—P Deficient (79055)
13.37
mg/g

Potassium phosphate, monobasic
11.4
mg/g

Calcium chloride
1.05
mg/g

Sodium chloride
16.23
mg/g

Vitamin Mix, Teklad (40060)
10.0
mg/g

Ethoxyquin, antioxidant
0.01
mg/g

Sodium oxalate
3.72
mg/g

In some embodiments, a microbial consortium of the present invention is administered to an animal on a diet supplemented with one or more bile acids. In some embodiments, the diet is supplemented with one or more of TCDCA, GCDCA, TCA, GCA, CA, CDCA, LCA, or DCA. For example, in some embodiments, an animal may be maintained on a diet supplemented with one or more bile acids for 7 days to 1 month. In some embodiments, an animal may be maintained on a diet supplemented with bile acids for 7 days, 14 days, 21 days, or 1 month.

In some embodiments, a microbial consortium of the present invention is used to treat a subject having or at risk of developing a metabolic disease or condition. For example, in some embodiments, the metabolic disease is primary hyperoxaluria. In some embodiments, the metabolic disease is secondary hyperoxaluria. In some embodiments, the metabolic disease is secondary hyperoxaluria associated with bowel resection surgery or IBD. In some embodiments, a microbial consortium of the present invention significantly reduces the concentration of oxalate present in a sample of blood, serum, bile, stool, or urine when administered to a subject by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, or by at least 80% as compared to untreated subjects or pre-administration concentrations.

In some embodiments, a microbial consortium of the present invention significantly alters the profile and/or concentration of bile acids present in an animal. For example, in some embodiments, a microbial consortium of the present invention significantly alters the profile and/or concentration of Tβ-MCA, Tα-MCA, TUDCA, THDCA, TCA, 7β-CA, 7-oxo-CA, TCDCA, Tω-MCA, TDCA, α-MCA, β-MCA, ω-MCA, Muro-CA, d4-CA, CA, TLCA, UDCA, HDCA, CDCA, DCA, and LCA in an animal.

In some embodiments, a high-complexity defined gut microbial community of the present invention can be used to treat an animal having a cholestatic disease, such as, for example, primary sclerosing cholangitis, primary biliary cholangitis, progressive familial intrahepatic cholestasis, or nonalcoholic steatohepatitis. For example in some embodiments, the animal may be a mammal, and more particularly a human.

In some embodiments, a microbial consortium of the present invention can be administered via an enteric route. For example, in some embodiments, a microbial consortium is administered orally, rectally (e.g., by enema, suppository, or colonoscope), or by oral or nasal tube.

In some embodiments, a microbial consortium of the present invention can be administered to a specific location along the gastrointestinal tract. For example, in some embodiments, a microbial consortium can be administered into one or more than one gastrointestinal location including the mouth, esophagus, stomach, small intestine (duodenum, jejunum, ileum), large intestine (cecum, ascending colon, transverse colon, descending colon), or rectum. In some embodiments, a microbial consortium can be administered in all regions of the gastrointestinal tract.

Dosages

In some embodiments, a microbial consortium of the present invention is administered in a dosage form having a total amount of microbial consortium of at least 1×10⁶colony forming units (CFU) or above, at least 2×10⁶CFU or above, at least 3×10⁶CFU or above, at least 4×10⁶CFU or above, at least 5×10⁶CFU or above, at least 6×10⁶CFU or above, at least 7×10⁶CFU or above, at least 8×10⁶CFU or above, at least 9×10⁶CFU or above, at least 1×10⁷CFU or above, at least 2×10⁷CFU or above, at least 3×10⁷CFU or above, at least 4×10⁷CFU or above, at least 5×10⁷CFU or above, at least 6×10⁷CFU or above, at least 7×10⁷CFU or above, at least 8×10⁷CFU or above, at least 9×10⁷CFU or above, 1×10⁸CFU or above, at least 2×10⁸CFU or above, at least 3×10⁸CFU or above, at least 4×10⁸CFU or above, at least 5×10⁸CFU or above, at least 6×10⁸CFU or above, at least 7×10⁸CFU or above, at least 8×10⁸CFU or above, at least 9×10⁸CFU or above, 1×10⁹CFU or above, at least 2×10⁹CFU or above, at least 3×10⁹CFU or above, at least 4×10⁹CFU or above, at least 5×10⁹CFU or above, at least 6×10⁹CFU or above, at least 7×10⁹CFU or above, at least 8×10⁹CFU or above, at least 9×10⁹CFU or above, 1×10¹⁰CFU or above, at least 2×10¹⁰CFU or above, at least 3×10¹⁰CFU or above, at least 4×10¹⁰CFU or above, at least 5×10¹⁰CFU or above, at least 6×10¹⁰CFU or above, at least 7×10¹⁰CFU or above, at least 8×10¹⁰CFU or above, at least 9×10¹⁰CFU or above, 1×10¹¹CFU or above, at least 2×10¹¹CFU or above, at least 3×10¹¹CFU or above, at least 4×10¹¹CFU or above, at least 5×10¹¹CFU or above, at least 6×10¹¹CFU or above, at least 7×10¹¹CFU or above, at least 8×10¹¹CFU or above, at least 9×10¹¹CFU or above, 1×10¹²CFU or above, at least 2×10¹²CFU or above, at least 3×10¹²CFU or above, at least 4×10¹²CFU or above, at least 5×10¹²CFU or above, at least 6×10¹²CFU or above, at least 7×10¹²CFU or above, at least 8×10¹²CFU or above, or at least 9×10¹²CFU or above.

In some embodiments, a microbial consortium of the present invention is administered in a dosage form having a total amount of microbial consortium of 0.1 ng to 500 mg, 0.5 ng to 500 mg, 1 ng to 500 mg, 5 ng to 500 mg, 10 ng to 500 mg, 50 ng to 500 mg, 100 ng to 500 mg, 500 ng to 500 mg, 1 μg to 500 mg, 5 μg to 500 mg, 10 μg to 500 mg, 50 μg to 500 mg, 100 μg to 500 mg, 500 μg to 500 mg, 1 mg to 500 mg, 5 mg to 500 mg, 10 mg to 500 mg, 50 mg to 500 mg, 100 mg to 500 mg, 0.1 ng to 100 mg, 0.5 ng to 100 mg, 1 ng to 100 mg, 5 ng to 100 mg, 10 ng to 100 mg, 50 ng to 100 mg, 100 ng to 100 mg, 500 ng to 500 mg, 1 μg to 100 mg, 5 μg to 100 mg, 10 us to 100 mg, 50 us to 100 mg, 100 μg to 100 mg, 500 μg to 100 mg, 1 mg to 500 mg, 5 mg to 100 mg, 10 mg to 100 mg, 50 mg to 100 mg, 0.1 ng to 50 mg, 0.5 ng to 50 mg, 1 ng to 50 mg, 5 ng to 50 mg, 10 ng to 50 mg, 50 ng to 50 mg, 100 ng to 50 mg, 500 ng to 500 mg, 1 μg to 50 mg, 5 μg to 50 mg, 10 μg to 50 mg, 50 us to 50 mg, 100 μg to 50 mg, 500 μg to 50 mg, 1 mg to 500 mg, 5 mg to 50 mg, 10 mg to 50 mg, 0.1 ng to 10 mg, 0.5 ng to 10 mg, 1 ng to 10 mg, 5 ng to 10 mg, 10 ng to 10 mg, 50 ng to 10 mg, 100 ng to 10 mg, 500 ng to 500 mg, 1 μg to 10 mg, 5 μg to 10 mg, 10 us to 10 mg, 50 μg to 10 mg, 100 μg to 10 mg, 500 μg to 10 mg, 1 mg to 500 mg, 5 mg to 10 mg, 0.1 ng to 5 mg, 0.5 ng to 5 mg, 1 ng to 5 mg, 5 ng to 5 mg, 10 ng to 5 mg, 50 ng to 5 mg, 100 ng to 5 mg, 500 ng to 500 mg, 1 μg to 5 mg, 5 μg to 5 mg, 10 μg to 5 mg, 50 us to 5 mg, 100 us to 5 mg, 500 μg to 5 mg, 1 mg to 500 mg, 0.1 ng to 1 mg, 0.5 ng to 1 mg, 1 ng to 1 mg, 5 ng to 1 mg, 10 ng to 1 mg, 50 ng to 1 mg, 100 ng to 1 mg, 500 ng to 500 mg, 1 μg to 1 mg, 5 μg to 1 mg, 10 μg to 1 mg, 50 μg to 1 mg, 100 μg to 1 mg, 500 us to 1 mg, 0.1 ng to 500 μg, 0.5 ng to 500 μg, 1 ng to 500 μg, 5 ng to 500 μg, 10 ng to 500 μg, 50 ng to 500 μg, 100 ng to 500 μg, 500 ng to 500 μg, 1 μg to 500 μg, 5 us to 500 μg, 10 us to 500 μg, 50 us to 500 μg, 100 μg to 500 μg, 0.1 ng to 100 μg, 0.5 ng to 100 μg, 1 ng to 100 μg, 5 ng to 100 μg, 10 ng to 100 μg, 50 ng to 100 μg, 100 ng to 100 μg, 500 ng to 100 μg, 1 μg to 100 μg, 5 μg to 100 μg, 10 μg to 100 μg, 50 μg to 100 μg, 0.1 ng to 50 μg, 0.5 ng to 50 μg, 1 ng to 50 μg, 5 ng to 50 μg, 10 ng to 50 μg, 50 ng to 50 μg, 100 ng to 50 μg, 500 ng to 50 μg, 1 μg to 50 μg, 5 μg to 50 μg, 10 μg to 50 μg, 0.1 ng to 10 μg, 0.5 ng to 10 μg, 1 ng to 10 μg, 5 ng to 10 μg, 10 ng to 10 μg, 50 ng to 10 μg, 100 ng to 10 μg, 500 ng to 10 μg, 1 μg to 10 μg, 5 μg to 10 μg, 0.1 ng to 5 μg, 0.5 ng to 5 μg, 1 ng to 5 μg, 5 ng to 5 μg, 10 ng to 5 μg, 50 ng to 5 μg, 100 ng to 5 μg, 500 ng to 5 μg, 1 μg to 5 μg, 0.1 ng to 1 μg, 0.5 ng to 1 μg, 1 ng to 1 μg, 5 ng to 1 μg, 10 ng to 1 μg, 50 ng to 1 μg, 100 ng to 1 μg, 500 ng to 1 μg, 0.1 ng to 500 ng, 0.5 ng to 500 ng, 1 ng to 500 ng, 5 ng to 500 ng, 10 ng to 500 ng, 50 ng to 500 ng, 100 ng to 500 ng, 0.1 ng to 100 ng, 0.5 ng to 100 ng, 1 ng to 100 ng, 5 ng to 100 ng, 10 ng to 100 ng, 50 ng to 100 ng, 0.1 ng to 50 ng, 0.5 ng to 50 ng, 1 ng to 50 ng, 5 ng to 50 ng, 10 ng to 50 ng, 0.1 ng to 10 ng, 0.5 ng to 10 ng, 1 ng to 10 ng, 5 ng to 10 ng, 0.1 ng to 5 ng, 0.5 ng to 5 ng, 1 ng to 5 ng, 0.1 ng to 1 ng, 0.1 ng to 1 ng, or 0.1 ng to 0.5 ng total dry weight.

In other embodiments, a microbial consortium of the present invention is consumed at a rate of 0.1 ng to 500 mg a day, 0.5 ng to 500 mg a day, 1 ng to 500 mg a day, 5 ng to 500 mg a day, 10 ng to 500 mg a day, 50 ng to 500 mg a day, 100 ng to 500 mg a day, 500 ng to 500 mg a day, 1 μg to 500 mg a day, 5 μg to 500 mg a day, 10 μg to 500 mg a day, 50 μg to 500 mg a day, 100 μg to 500 mg a day, 500 μg to 500 mg a day, 1 mg to 500 mg a day, 5 mg to 500 mg a day, 10 mg to 500 mg a day, 50 mg to 500 mg a day, 100 mg to 500 mg a day, 0.1 ng to 100 mg a day, 0.5 ng to 100 mg a day, 1 ng to 100 mg a day, 5 ng to 100 mg a day, 10 ng to 100 mg a day, 50 ng to 100 mg a day, 100 ng to 100 mg a day, 500 ng to 500 mg a day, 1 μg to 100 mg a day, 5 μg to 100 mg a day, 10 μg to 100 mg a day, 50 μg to 100 mg a day, 100 μg to 100 mg a day, 500 μg to 100 mg a day, 1 mg to 500 mg a day, 5 mg to 100 mg a day, 10 mg to 100 mg a day, 50 mg to 100 mg a day, 0.1 ng to 50 mg a day, 0.5 ng to 50 mg a day, 1 ng to 50 mg a day, 5 ng to 50 mg a day, 10 ng to 50 mg a day, 50 ng to 50 mg a day, 100 ng to 50 mg a day, 500 ng to 500 mg a day, 1 μg to 50 mg a day, 5 μg to 50 mg a day, 10 μg to 50 mg a day, 50 μg to 50 mg a day, 100 μg to 50 mg a day, 500 μg to 50 mg a day, 1 mg to 500 mg a day, 5 mg to 50 mg a day, 10 mg to 50 mg a day, 0.1 ng to 10 mg a day, 0.5 ng to 10 mg a day, 1 ng to 10 mg a day, 5 ng to 10 mg a day, 10 ng to 10 mg a day, 50 ng to 10 mg a day, 100 ng to 10 mg a day, 500 ng to 500 mg a day, 1 μg to 10 mg a day, 5 μg to 10 mg a day, 10 μg to 10 mg a day, 50 μg to 10 mg a day, 100 μg to 10 mg a day, 500 μg to 10 mg a day, 1 mg to 500 mg a day, 5 mg to 10 mg a day, 0.1 ng to 5 mg a day, 0.5 ng to 5 mg a day, 1 ng to 5 mg a day, 5 ng to 5 mg a day, 10 ng to 5 mg a day, 50 ng to 5 mg a day, 100 ng to 5 mg a day, 500 ng to 500 mg a day, 1 μg to 5 mg a day, 5 μg to 5 mg a day, 10 μg to 5 mg a day, 50 μg to 5 mg a day, 100 μg to 5 mg a day, 500 μg to 5 mg a day, 1 mg to 500 mg a day, 0.1 ng to 1 mg a day, 0.5 ng to 1 mg a day, 1 ng to 1 mg a day, 5 ng to 1 mg a day, 10 ng to 1 mg a day, 50 ng to 1 mg a day, 100 ng to 1 mg a day, 500 ng to 500 mg a day, 1 μg to 1 mg a day, 5 μg to 1 mg a day, 10 μg to 1 mg a day, 50 μg to 1 mg a day, 100 μg to 1 mg a day, 500 μg to 1 mg a day, 0.1 ng to 500 μg a day, 0.5 ng to 500 μg a day, 1 ng to 500 μg a day, 5 ng to 500 μg a day, 10 ng to 500 μg a day, 50 ng to 500 μg a day, 100 ng to 500 μg a day, 500 ng to 500 μg a day, 1 μg to 500 μg a day, 5 μg to 500 μg a day, 10 μg to 500 μg a day, 50 μg to 500 μg a day, 100 μg to 500 μg a day, 0.1 ng to 100 μg a day, 0.5 ng to 100 μg a day, 1 ng to 100 μg a day, 5 ng to 100 μg a day, 10 ng to 100 μg a day, 50 ng to 100 μg a day, 100 ng to 100 μg a day, 500 ng to 100 μg a day, 1 μg to 100 μg a day, 5 μg to 100 μg a day, 10 μg to 100 μg a day, 50 μg to 100 μg a day, 0.1 ng to 50 μg a day, 0.5 ng to 50 μg a day, 1 ng to 50 μg a day, 5 ng to 50 μg a day, 10 ng to 50 μg a day, 50 ng to 50 μg a day, 100 ng to 50 μg a day, 500 ng to 50 μg a day, 1 μg to 50 μg a day, 5 μg to 50 μg a day, 10 μg to 50 μg a day, 0.1 ng to 10 μg a day, 0.5 ng to 10 μg a day, 1 ng to 10 μg a day, 5 ng to 10 μg a day, 10 ng to 10 μg a day, 50 ng to 10 μg a day, 100 ng to 10 μg a day, 500 ng to 10 μg a day, 1 μg to 10 μg a day, 5 μg to 10 μg a day, 0.1 ng to 5 μg a day, 0.5 ng to 5 μg a day, 1 ng to 5 μg a day, 5 ng to 5 μg a day, 10 ng to 5 μg a day, 50 ng to 5 μg a day, 100 ng to 5 μg a day, 500 ng to 5 μg a day, 1 μg to 5 μg a day, 0.1 ng to 1 μg a day, 0.5 ng to 1 μg a day, 1 ng to 1 μg a day, 5 ng to 1 μg a day, 10 ng to 1 μg a day, 50 ng to 1 μg a day, 100 ng to 1 μg a day, 500 ng to 1 μg a day, 0.1 ng to 500 ng a day, 0.5 ng to 500 ng a day, 1 ng to 500 ng a day, 5 ng to 500 ng a day, 10 ng to 500 ng a day, 50 ng to 500 ng a day, 100 ng to 500 ng a day, 0.1 ng to 100 ng a day, 0.5 ng to 100 ng a day, 1 ng to 100 ng a day, 5 ng to 100 ng a day, 10 ng to 100 ng a day, 50 ng to 100 ng a day, 0.1 ng to 50 ng a day, 0.5 ng to 50 ng a day, 1 ng to 50 ng a day, 5 ng to 50 ng a day, 10 ng to 50 ng a day, 0.1 ng to 10 ng a day, 0.5 ng to 10 ng a day, 1 ng to 10 ng a day, 5 ng to 10 ng a day, 0.1 ng to 5 ng a day, 0.5 ng to 5 ng a day, 1 ng to 5 ng a day, 0.1 ng to 1 ng a day, 0.1 ng to 1 ng a day, or 0.1 ng to 0.5 ng a day.

In some embodiments, the microbial composition of the present invention is administered for a period of at least 1 day to 1 week, 1 week to 1 month, 1 month to 3 months, 3 months to 6 months, 6 months to 1 year, or more than 1 year. For example, in some embodiments, the microbial composition of the present invention is administered for a period of at least 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, or 1 year.

In some embodiments, a microbial consortium of the present invention is administered as a single dose or as multiple doses. For example, in some embodiments, a microbial consortium of the present invention is administered once a day for 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, or 1 year. In some embodiments, a microbial consortium of the present invention is administered multiple times daily. For example, in some embodiments, a microbial consortium of the present invention is administered twice daily, three times daily, 4 times daily, or 5 times daily. In some embodiments, a microbial consortium of the present invention is administered intermittently. For example, in some embodiments, a microbial consortium of the present invention is administered once weekly, once monthly, or when a subject is in need thereof.

Combination Therapy

In some embodiments, a microbial consortium of the present invention can be administered in combination with other agents. For example, in some embodiments, a microbial consortium of the present invention can be administered with an antimicrobial agent, an antifungal agent, an antiviral agent, an antiparasitic agent or a prebiotic. In some embodiments, a microbial consortium of the present invention can be administered subsequent to administration of an antimicrobial agent, an antifungal agent, an antiviral agent, an antiparasitic agent or a prebiotic. In some embodiments, administration may be sequential over a period of hours or days, or simultaneously.

For example, in some embodiments, a microbial consortium can be administered with, or pre-administered with, one or more than one antibacterial agent selected from fluoroquinolone antibiotics (ciprofloxacin, Levaquin, floxin, tequin, avelox, and norflox); cephalosporin antibiotics (cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cefamandole, cefoxitin, cefprozil, and ceftobiprole); penicillin antibiotics (amoxicillin, ampicillin, penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin); tetracycline antibiotics (tetracycline, minocycline, oxytetracycline, and doxycycline); and carbapenem antibiotics (ertapenem, doripenem, imipenem/cilastatin, and meropenem).

For example, in some embodiments, a microbial consortium can be administered with one or more than one antiviral agent selected from Abacavir, Acyclovir, Adefovir, Amprenavir, Atazanavir, Cidofovir, Darunavir, Delavirdine, Didanosine, Docosanol, Efavirenz, Elvitegravir, Emtricitabine, Enfuviltide, Etravirine, Famciclovir, Foscamet, Fomivirsen, Ganciclovir, Indinavir, Idoxuridine, Lamivudine, Lopinavir Maraviroc, MK-2048, Nelfinavir, Nevirapine, Penciclovir, Raltegravir, Rilpivirine, Ritonavir, Saquinavir, Stavudine, Tenofovir Trifluridine, Valaciclovir, Valganciclovir, Vidarabine, Ibacitabine, Amantadine, Oseltamivir, Rimantidine, Tipranavir, Zalcitabine, Zanamivir, and Zidovudine.

In some embodiments, a microbial consortium can be administered with one or more than one antifungal agent selected from miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxiconazole, sertaconazole, sulconazole, and tioconazole; triazole antifungals such as fluconazole, itraconazole, isavuconazole, ravuconazole, posaconazole, voriconazok, terconazole, and albaconazole; thiazole antifungals such as abafungin; allylamine antifungals such as terbinafine, naftifine, and butenafine; and echinocandin antifungals such as anidulafungin, caspofungin, and micafungin; polygodial; benzoic acid; ciclopirox; tolnaftate; undecylenic acid; flucytosine or 5-fluorocytosine; griseofulvin; and haloprogin.

In some embodiments, a microbial consortium can be administered with one or more than one anti-inflammatory and/or immunosuppressive agent selected from cyclophosphamide, mycophenolate mofetil, corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, cyclosporin A, mercaptopurine, azathiopurine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anticholinergics, monoclonal anti-IgE, immunomodulatory peptides, immunomodulatory small molecules, immunomodulatory cytokines, immunomodulatory antibodies, and vaccines.

In some embodiments, a microbial consortium of the present invention can be administered with one or more than one prebiotic selected from, but not limited to, amino acids, biotin, fructooligosaccharides, galactooligosaccharides, inulin, lactulose, mannan oligosaccharides, oligofructose-enriched inulin, oligofructose, oligodextrose, tagatose, trans-galactooligosaccharide, and xylooligosaccharides.

EXAMPLES

The disclosure now being generally described, will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present disclosure, and are not intended to limit the scope of the disclosure in any way.

Example 1: Sourcing and Identification of Active and Supportive Microbial Strains

Active and supportive microbial strains were derived from human donor fecal samples, or were purchased from one of three depositories: the American Type Culture Collection (ATCC; www.atcc.org), the Leibniz institute DSMZ (www.dsmz.de), or BEI Resources (www.beiresources.org).

Microbial strains purchased from a depository were cultured according to depository instructions.

Isolation of Donor-Derived Active and Supportive Microbial Strains

Fecal donors were selected based on multiple criteria, including a health and medical history questionnaire, physical exam, and blood and stool tests for assessing pathogen-free status. Stool samples from donors who did not meet the inclusion criteria based on any of the above-mentioned assessment were discarded from quarantine.

Donors provided a stool sample sealed in a plastic container. Upon collection, stool samples were immediately transferred to an anaerobic chamber (5% CO₂, 5% H₂, 90% N₂) within 15 minutes of collection.

Once transferred to the anaerobic chamber, the fresh stool sample was labeled, weighed, evaluated for anomalies (presence of urine, toilet paper, etc.), and scored according to the Bristol scale. A stool sample weighing less than 45 g, or that failed to conform to a Bristol Stool Scale type 2, 3, 4 or 5, was rejected. Stool samples that met the acceptance criteria were processed and aliquoted. 45 g of the stool sample was transferred into a sterile container for specific pathogen testing. The remainder of the sample was mixed with cryopresertative, homogenized, and aliquoted into cryovials (approximately 2 g of sample per vial; 6 vials per stool sample). These vials were transferred from the anaerobic chamber to a −80° C. freezer for storage until shipping on dry ice.

Microbial strain isolation was performed by making serial dilution aliquots of the stool samples and plating said aliquots on a variety of microbial cultivation media suitable for growth of anaerobes. All cultures were grown under anaerobic conditions for the duration of culturing. Approximately 20 different media/culture conditions were used to isolate a variety of gut microbial species. Specific enrichment techniques were performed for species having particular metabolic capabilities, such as consumption or tolerance of oxalate or bile acids. In order to enrich for strains having oxalate metabolism capabilities, aliquots of the serially-diluted stool samples were plated on agar growth media supplemented with varying concentrations of potassium oxalate (20 mM, 40 mM, 80 mM, 160 mM, or 200 mM). In order to enrich for species capable of metabolizing bile acids, aliquots of serially diluted stool samples were plated on growth media supplemented with 2% bile. In order to isolate archaea, diluted fecal samples were plated on culture media containing a mixture of antibiotics that is lethal to both gram-positive and gram-negative bacteria. This archaeal isolation plate was co-incubated in a small enclosed container together with a separate plate containing a heterogenous population of microbes derived from a fecal sample; the heterogenous population contained hydrogen-producing microbes, thereby providing hydrogen (through diffusion within the small container) to allow archaea on the archaeal isolation plate to grow.

Single colonies from isolation or enrichment plates were picked for further isolation on appropriate microbial cultivation agar media plates (passage 2). After incubation at 37° C., if the single colony plating resulted in uniformly isolated colony morphology, the culture was further investigated for strain identification. Preliminary strain identification was performed either by 16S rRNA gene sequencing or by creating and analyzing proteomic fingerprinting using high-throughput Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS). If the single-colony plating resulted in multiple colony morphologies, each unique colony type was picked for further isolation on an appropriate cultivation agar plate until uniform colony morphology was achieved (passage 3 or more). Monoculture identity was confirmed by 16S rRNA gene sequencing.

Isolated colonies of strains purified to monocultures for species of interest, as well as novel strains of unknown species, were inoculated into culture tubes containing appropriate broth media and incubated under anaerobic conditions at 37° C. For most strains, sufficient growth was visualized during this first broth passaging as indicated by turbidity. However, some strains required more than one broth passaging to achieve sufficient growth. Sterile glycerol solution was added to the microbial culture to achieve a final glycerol concentration of 25% prior to mixing and aliquoting into cryovials. The cryovials were removed from the anaerobic gas chambers and were promptly transferred to −80° C.

After at least 10 hours of freezing, one vial of each purified frozen strain isolate was retrieved from the freezer and thawed under anaerobic conditions followed by plating on agar plates containing appropriate growth media. The plates were incubated under anaerobic conditions at 37° C. Growth on the plate was observed to confirm revival and uniform morphology for each purified isolate. Individual colonies of the isolates were subsequently analyzed by 16S rRNA gene sequencing to confirm the identity and colony purity of each frozen strain against the National Center for Biotechnology Information (NCBI) 16S rRNA gene databases.

A list of donor-derived isolates and a summary of their corresponding isolation media and growth/banking media is reported in Table 3. Additional identifying information for the isolates is reported in Table 4.

in vitro activity-based assays, bioinformatic screens to identify strains with the genetic capability to metabolize oxalate, and identification of target species with known oxalate metabolizing activity based on scientific literature, were utilized to identify candidate active strains. Active oxalate-metabolizing strains obtained from depositories (“commercial strains”) include those listed in Table 5. Supportive commercial strains include those listed in Table 6. Strains in Table 5 and Table 6 are identified by their genus/species and by the depository catalog number. “ATCC” strains were obtained from ATCC, “DSM” strains were obtained from the Liebniz Institute DSMZ, and “HM” strains were obtained from BEI Resources.

MALDI-TOF MS

MALDI-TOF mass spectrometry was used for preliminary identification of bacterial strains (genus and/or species) using a BD Bruker MALDI Biotyper. Briefly, an α-cyano-4-hydroxycinnamic acid (HCCA) matrix was prepared in Bruker standard solvent (acetonitrile 50%, water 47.5% and trifluoroacetic acid 2.5%). A disposable MALDI Biotyper Biotarget plate was loaded with a smear of the sample bacterial colony, overlaid with HCCA matrix and allowed to dry. For strains that required extended extraction, 70% formic acid was added to the sample smear prior to adding HCCA matrix. Bruker Bacterial Testing Standards (BTS) were also loaded onto the Biotarget for quality control analysis. The Biotarget as then loaded into a Biotyper MALDI-TOF machine, and the sample was analyzed. The machine was configured to perform the quality control analysis of the BTS quality control samples first and aborted the run if the BTS quality control analysis failed. The generated spectrum of the test sample was then compared to a database of the reference proteomics spectra containing strains belonging to species which were previously characterized by their proteomic fingerprinting.

DNA Extraction

DNA was extracted from fecal samples using a Qiagen DNeasy Power Soil Kit (Qiagen, Germantown, Md.) in accordance with the manufacturer's instructions. Alternative methods for extracting DNA from fecal samples are well-known and routinely practiced in the art (e.g., described by Sambrook and Russell, Molecular Cloning: A Laboratory Manual, 3d ed., 2001).

Whole Genome Shotgun Sequencing

Sequencing of DNA samples was carried out using the TruSeq Nano DNA Library Preparation kit (Illumina, San Diego, Calif., US) and a NextSeq platform (Illumina, San Diego, Calif., US). In brief, sequencing libraries were prepared from DNA extracted from each sample. DNA was mechanically fragmented using an ultrasonicator. The fragmented DNA was subjected to end repair and size selection of fragments, adenylation of 3′ ends, linked with adaptors, and DNA fragments enriched according to the TruSeq Nano DNA Library Preparation kit manual (Illumina, San Diego, Calif., US). Samples were sequenced to generate more than 50 million paired-end reads of 150, 250, or 300 bp length.

16S rRNA Gene Sequencing and Species Identification

Microbial species identification was performed by full-length Sanger sequencing of the 16S rRNA gene using the 27F and 1492 primers (PMID 18296538). Species were identified by performing a bidirectional best-BLAST search against a database of curated 16S rRNA gene sequences of type species. To refine species identities, 16S rRNA gene sequences were inserted into a phylogenetic tree of curated 16S rRNA gene sequences of type species. If the sequence formed a monophyletic cluster with a known species, the strain was assigned to that species. Otherwise, the strain was assigned to a novel species. Optionally, isolates were additionally characterized by whole-genome sequencing. Genome assemblies were inserted into a phylogenetic tree of curated genomes of type species. If the sequence formed a monophyletic cluster with a known species, the strain was assigned to that species. Otherwise, the strain was assigned to a novel species.

TABLE 3

Summary of Isolation/Growth Media for Donor-Derived Isolates

Isolated from
Isolated from

media
media

Stool plating agar media
Additives
containing
containing
Glycerol

Strain #
Species ID
type (Vendor, Cat #)
information
oxalate
2% Ox bile
stock media

FBI00001

Clostridium citroniae

Bifidobacterium Selective
40 mM
40 mM
NO
YCFAC + 40 mM

agar (Anaerobe Systems,
Potassium

oxalate

AS-6423)
oxalate

FBI00002

Bacteroides salyersiae

Bifidobacterium Selective
40 mM
40 mM
NO
YCFAC + 40 mM

agar (Anaerobe Systems,
Potassium

oxalate

AS-6423)
oxalate

FBI00003

Enterococcus faecalis

Bifidobacterium Selective
40 mM
40 mM
NO
YCFAC + 40 mM

agar (Anaerobe Systems,
Potassium

oxalate

AS-6423)
oxalate

FBI00004

Neglecta timonensis

YCFAC-B (Anaerobe
80 mM
80 mM
NO
YCFAC + 80 mM

Systems, AS-677)
Potassium

oxalate

oxalate

FBI00005

Enterococcus

YCFAC-B (Anaerobe
80 mM
80 mM
NO
YCFAC + 80 mM

casseliflavus

Systems, AS-677)
Potassium

oxalate

oxalate

FBI00006

Enterobacter

YCFAC-B (Anaerobe
80 mM
80 mM
NO
YCFAC + 80 mM

himalayensis

Systems, AS-677)
Potassium

oxalate

oxalate

FBI00007

Enterococcus

YCFAC-B (Anaerobe
80 mM
80 mM
NO
YCFAC + 80 mM

casseliflavus

Systems, AS-677)
Potassium

oxalate

oxalate

FBI00008

Blautia luti

YCFAC-B (Anaerobe
20 mM
20 mM
NO
YCFAC + 20 mM

Systems, AS-677)
Potassium

oxalate

oxalate

FBI00009

Bifidobacterium

YCFAC-B (Anaerobe

NO
NO
YCFAC

adolescentis

Systems, AS-677)

FBI00010

Blautia obeum

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00011

Bifidobacterium longum

Bifidobacterium Selective

NO
NO
YCFAC

agar (Anaerobe Systems,

AS-6423)

FBI00012

Alistipes onderdonkii

Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00013

Parabacteroides merdae

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00014

Blautia luti

YCFAC-B (Anaerobe
20 mM
20 mM
NO
YCFAC + 20 mM

Systems, AS-677)
Potassium

oxalate

oxalate

FBI00015

Bacteroides uniformis

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00016

Bifidobacterium

YCFAC-B (Anaerobe

NO
NO
YCFAC

pseudocatenulatum

Systems, AS-677)

FBI00017

Blautia obeum

YCFAC-B (Anaerobe
20 mM
20 mM
NO
YCFAC + 20 mM

Systems, AS-677)
Potassium

oxalate

oxalate

FBI00018

Eubacterium rectale

Bifidobacterium Selective

NO
NO
YCFAC

agar (Anaerobe Systems,

AS-6423)

FBI00019

Alistipes timonensis

Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00020

Bacteroides

Bifidobacterium Selective
40 mM
40 mM
NO
YCFAC + 40 mM

thetaiotaomicron

agar (Anaerobe Systems,
Potassium

oxalate

AS-6423)
oxalate

FBI00021

Bacteroides kribbi/

YCFAC-B (Anaerobe
80 mM
80 mM
NO
YCFAC + 80 mM

Bacteroides koreensis

Systems, AS-677)
Potassium

oxalate

species cluster

oxalate

FBI00022

Alistipes putredinrs

Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00023

Enterococcus

Strain Isolation Media 1

NO
NO
YCFAC

casseliflavus

(SL1)

FBI00024

Bacteroides kribbi/

Chocolate Agar (Teknova,

NO
NO
YCFAC

Bacteroides koreensis

C4900)

species cluster

FBI00025

Coprococcus comes

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00026

Enterobacter

YCFAC-BO 200 mM

200 mM
NO
YCFAC + 80 mM

hormaechei

(Anaerobe Systems, AS-

oxalate

7529)

FBI00027

Fusicatenibacter

Brain Heart Infusion

NO
NO
YCFAC

saccharivorans

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00028

Oscillibacter sp.
Brain Heart Infusion

NO
NO
YCFAC

FBI00028
(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00029

Parabacteroides

Brain Heart Infusion

NO
NO
YCFAC

distasonis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00030

Eggerthella lenta

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00031

Enterobacter

YCFAC-BO 200 mM

200 mM
NO
YCFAC + 80 mM

hormaechei

(Anaerobe Systems, AS-

oxalate

7529)

FBI00032

Anaerostipes hadrus

Bifidobacterium Selective

NO
NO
YCFAC

agar (Anaerobe Systems,

AS-6423)

FBI00033

Lachnospiraceae sp.
YCFAC-B (Anaerobe
20 mM
20 mM
NO
YCFAC + 20 mM

FBI00033
Systems, AS-677)
Potassium

oxalate

oxalate

FBI00034

Eubacterium eligens

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00035

Enterococcus

YCFAC-BO 200 mM

200 mM
NO
YCFAC + 80 mM

casseliflavus

(Anaerobe Systems, AS-

oxalate

7529)

FBI00036

Blautia faecis

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00037

Enterococcus

YCFAC-BO 200 mM

200 mM
NO
YCFAC + 80 mM

casseliflavus

(Anaerobe Systems, AS-

oxalate

7529)

FBI00038

Coprococcus eutactus

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00039

Bacteroides vulgatus

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00040

Bilophila wadsworthia

Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00041

Phascolarctobacterium

YCFAC-B (Anaerobe
80 mM
80 mM
NO
YCFAC + 80 mM

faecium

Systems, AS-677)
Potassium

oxalate

oxalate

FBI00042

Bacteroides

Strain Isolation Media 1

NO
NO
YCFAC

xylani solvens

(SL1)

FBI00043

Bifidobacterium

Reinforced Clostridial

NO
NO
YCFAC

dentium

Agar (RCA) (Teknova,

C0205)

FBI00044

Blautia wexlerae

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00045

Bifidobacterium

Reinforced Clostridial

NO
NO
YCFAC

adolescentis

Agar (RCA) (Teknova,

C0205)

FBI00046

Bacteroides caccae

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00047

Eubacterium eligens

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00048

Fusicatenibacter

YCFAC-B (Anaerobe

NO
NO
YCFAC

saccharivorans

Systems, AS-677)

FBI00049

Dialister succinatiphilus

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00050

Bacteroides nordii

Bifidobacterium Selective
40 mM
40 mM
NO
YCFAC + 40 mM

agar (Anaerobe Systems,
Potassium

oxalate

AS-6423)
oxalate

FBI00051

Dorea formicigenerans

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00052

Bacteroides

YCFAC-BO 40 mM

40 mM
NO
YCFAC + 40 mM

xylanisolvens

(Anaerobe Systems, AS-

oxalate

7523)

FBI00053

Lactobacillus rogosae

YCFAC-BO 40 mM

40 mM
NO
YCFAC + 40 mM

(Anaerobe Systems, AS-

oxalate

7523)

FBI00054

Escherichia flexneri

YCFAC-BO 80 mM

80 mM
NO
YCFAC + 80 mM

(Anaerobe Systems, AS-

oxalate

7524)

FBI00055

Bacteroides kribbi/

YCFAC-BO 80 mM

80 mM
NO
YCFAC + 80 mM

Bacteroides koreensis

(Anaerobe Systems, AS-

oxalate

species cluster

7524)

FBI00056

Clostridium citroniae

YCFAC-BO 80 mM

80 mM
NO
YCFAC + 80 mM

(Anaerobe Systems, AS-

oxalate

7524)

FBI00057

Dorea longicatena

Reinforced Clostridial

NO
NO
YCFAC

Agar (RCA) (Teknova,

C0205)

FBI00058

Eubacterium rectale

Lactobacillus MRS
40 mM
40 mM
NO
YCFAC

(Anaerobe Systems, AS-
Potassium

6429)
oxalate

FBI00059

Bacteroides

Columbia agar, 5% sheep

NO
NO
YCFAC

stercorirosoris

blood (BD, 221165)

FBI00060

Bifidobacterium longum

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00061

Alistipes shahii

Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00062

Collinsella aerofaciens

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00063

Lachnospira sp.
YCFAC-B (Anaerobe

NO
NO
YCFAC

FBI00063 FBI00285
Systems, AS-677)

FBI00364

FBI00064

Dorea sp. FBI00064
YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00065

Sutterellaceae sp.
Bacteroides Bile Esculin

NO
YES
YCFAC

FBI00065
(BBE) (Anaerobe Systems,

AS-144)

FBI00066

Parasutterella

Bacteroides Bile Esculin

NO
YES
YCFAC

excrementihominis

(BBE) (Anaerobe Systems,

AS-144)

FBI00067

Oxalobacter formigenes

YCFAC-BO 40 mM

40 mM
NO
YCFAC + 100

(Anaerobe Systems, AS-

mM oxalate

7523)

FBI00068

Akkermansia

Strain Isolation Media 1

NO
NO
YCFAC

muciniphila

(SL1)

FBI00069

Ruminococcus bromii

Bifidobacterium Selective
40 mM
40 mM
NO
YCFAC

agar (Anaerobe Systems,
Potassium

AS-6423)
oxalate

FBI00070

Bacteroides kribbi/

YCFAC-BO 40 mM

40 mM
NO
YCFAC + 40 mM

Bacteroides koreensis

(Anaerobe Systems, AS-

oxalate

species cluster

7523)

FBI00071

Lachnospiraceae sp.
YCFAC-B (Anaerobe

NO
NO
YCFAC

FBI00071
Systems, AS-677)

FBI00072

Coprococcus eutactus

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00073

Parabacteroides

YCFAC-BO 40 mM

40 mM
NO
YCFAC

distasonis

(Anaerobe Systems, AS-

7523)

FBI00074

Clostridium fessum

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00075

Paraprevotella clara

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00076

Bacteroides

YCFAC-BO 80 mM

80 mM
NO
YCFAC

thetaiotaomicron

(Anaerobe Systems, AS-

7524)

FBI00077

Sutterella

Lactobacillus MRS
20 mM
20 mM
NO
YCFAC

wadsworthensis

(Anaerobe Systems, AS-
Potassium

6429)
oxalate

FBI00078

Blautia obeum

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00079

Clostridium

Chocolate Agar (Teknova,

NO
NO
YCFAC

clostridioforme

C4900)

FBI00080

Sutterella massiliensis

Lactobacillus MRS
40 mM
40 mM
NO
YCFAC

(Anaerobe Systems, AS-
Potassium

6429)
oxalate

FBI00081

Porphyromonas

Columbia agar, 5% sheep

NO
NO
YCFAC

asaccharolytica

blood (BD, 221165)

FBI00082

Ruminococcaceae sp.
Brain Heart Infusion

NO
NO
YCFAC

FBI00082 FBI00097
(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00083

Alistipes shahii

Columbia agar, 5% sheep
Antibiotics
NO
NO
YCFAC

blood (BD, 221165)

FBI00084

Bifidobacterium longum

Bifidobacterium Selective

NO
NO
YCFAC

agar (Anaerobe Systems,

AS-6423)

FBI00085

Ruminococcus bromii

Reinforced Clostridial

NO
NO
YCFAC

Agar (RCA) (Teknova,

C0205)

FBI00086

Ruminococcus bromii

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00087

Clostridium scindens

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00088

Lactobacillus rogosae

Reinforced Clostridial

NO
NO
YCFAC

Agar (RCA) (Teknova,

C0205)

FBI00089

Bifidobacterium longum

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00090

Eubacterium eligens

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00091

Eubacterium rectale

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00092

Monoglobus

YCFAC-BO 40 mM

40 mM
NO
YCFAC

pectinilyticus

(Anaerobe Systems, AS-

7523)

FBI00093

Roseburia hominis

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00094

Enterococcus faecium

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00095

Ruminococcus bromii

Reinforced Clostridial

NO
NO
YCFAC

Agar (RCA) (Teknova,

C0205)

FBI00096

Eggerthella lenta

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00097

Ruminococcaceae sp.
Brain Heart Infusion

NO
NO
YCFAC

FBI00082 FBI00097
(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00098

Bacteroides dorei

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00099

Gordonibacter

Chocolate Agar (Teknova,

NO
NO
YCFAC

pamelaeae

C4900)

FBI00100

Lachnospira sp.
Brain Heart Infusion

NO
NO
YCFAC

FBI00063 FBI00285
(BHI), hemin, vitamin K

FBI00364
(Teknova, B1093)

FBI00101

Faecalibacterium

Brain Heart Infusion

NO
NO
YCFAC

prausnitzii

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00102

Clostridium fessum

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00103

Bacteroides massiliensis

Bifidobacterium Selective

NO
NO
YCFAC

agar (Anaerobe Systems,

AS-6423)

FBI00104

Blautia wexlerae

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00105

Ruminococcaceae sp.
Chocolate Agar (Teknova,

NO
NO
YCFAC

FBI00105 FBI00160
C4900)

FBI00106

Enterococcus durans

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00107

Enterococcus durans

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00108

Ruminococcaceae sp.
YCFAC-B (Anaerobe

NO
NO
YCFAC

FBI00108
Systems, AS-677)

FBI00109

Coprococcus comes

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00110

Lachnoclostridium

YCFAC-BO 80 mM

80 mM
NO
YCFAC

pacaense

(Anaerobe Systems, AS-

7524)

FBI00111

Bacteroides vulgatus

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00112

Bacteroides uniformis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00113

Parabacteroides merdae

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00114

Dorea formicigenerans

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00115

Dorea formicigenerans

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00116

Ruminococcus faecis

Bifidobacterium Selective
40 mM
40 mM
NO
YCFAC

agar (Anaerobe Systems,
Potassium

AS-6423)
oxalate

FBI00117

Blautia faecis

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00118

Blautia faecis

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00119

Blautia obeum

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00120

Hungatella effluvii

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00121

Bacteroides vulgatus

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00122

Bacteroides uniformis

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00123

Roseburia hominis

YCFAC-BO 160 mM

160 mM
NO
YCFAC

(Anaerobe Systems, AS-

7527)

FBI00124

Anaerostipes hadrus

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00125

Bacteroides stercoris

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00126

Bifidobacterium

YCFAC-BO 40 mM

40 mM
NO
YCFAC

adolescentis

(Anaerobe Systems, AS-

7523)

FBI00127

Collinsella aerofaciens

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00128

Hungatella effluvii

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00129

Escherichia flexneri

YCFAC-BO 200 mM

200 mM
NO
YCFAC

(Anaerobe Systems, AS-

7529)

FBI00130

Coprococcus comes

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00131

Fusicatenibacter

YCFAC-B (Anaerobe

NO
NO
YCFAC

saccharivorans

Systems, AS-677)

FBI00132

Gordonibacter

YCFAC-BO 80 mM

80 mM
NO
YCFAC

pamelaeae

(Anaerobe Systems, AS-

7524)

FBI00133

Oxalobacter formigenes

YCFAC-BO 80 mM

80 mM
NO
YCFAC + 100

(Anaerobe Systems, AS-

mM oxalate

7524)

FBI00134

Bifidobacterium

YCFAC-B (Anaerobe

NO
NO
YCFAC

adolescentis

Systems, AS-677)

FBI00135

Bifidobacterium

YCFAC-B (Anaerobe

NO
NO
YCFAC

pseudocatenulatum

Systems, AS-677)

FBI00136

Eisenbergiella tayi

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00137

Bacteroides fragilis

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00138

Blautia massiliensis

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00139

Bacteroides

YCFAC-BO 80 mM

80 mM
NO
YCFAC

thetaiotaomicron

(Anaerobe Systems, AS-

7524)

FBI00140

Phascolarctobacterium

YCFAC-BO 160 mM

160 mM
NO
YCFAC + 80 mM

faecium

(Anaerobe Systems, AS-

oxalate

7527)

FBI00141

Phascolarctobacterium

YCFAC-BO 80 mM

80 mM
NO
YCFAC + 80 mM

faecium

(Anaerobe Systems, AS-

oxalate

7524)

FBI00142

Clostridium fessum

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00143

Parabacteroides merdae

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00144

Holdemanella biformis

Brain Heart Infusion

NO
NO
YCFAC +

(BHI), hemin, vitamin K

hemin/vitamin K

(Teknova, B1093)

FBI00145

Bifidobacterium

YCFAC-B (Anaerobe

NO
NO
YCFAC

adolescentis

Systems, AS-677)

FBI00146

Blautia faecis

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00147

Clostridium bolteae

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00148

Oscillibacter sp.
Brain Heart Infusion

NO
NO
YCFAC

FBI00028
(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00149

Monoglobus

YCFAC-BO 80 mM

80 mM
NO
YCFAC

pectinilyticus

(Anaerobe Systems, AS-

7524)

FBI00150

Lachnospiraceae sp.
YCFAC-B (Anaerobe

NO
NO
YCFAC

FBI00033
Systems, AS-677)

FBI00151

Clostridium aldenense

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00152

Dialister invisus

YCFAC-B (Anaerobe

NO
NO
YCFAC +

Systems, AS-677)

hemin/vitamin K

FBI00153

Dialister succinatiphilus

YCFAC-BO 80 mM

80 mM
NO
YCFAC + 3 mM

(Anaerobe Systems, AS-

succinate + 7.3

7524)

mM formate

FBI00154

Bacteroides dorei

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00155

Blautia obeum

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00156

Enterococcus durans

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00157

Lachnospiraceae sp.
Bifidobacterium Selective

NO
NO
YCFAC

FBI00157
agar (Anaerobe Systems,

AS-6423)

FBI00158

Butyricimonas sp.
Columbia agar, 5% sheep
Antibiotics
NO
NO
YCFAC

FBI00158
blood (BD, 221165)

FBI00159

Eisenbergiella tayi

YCFAC-BO 160 mM

160 mM
NO
YCFAC

(Anaerobe Systems, AS-

7527)

FBI00160

Ruminococcaceae sp.
Brain Heart Infusion

NO
NO
YCFAC

FBI00105 FBI00160
(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00161

Bacteroides

Brain Heart Infusion

NO
NO
YCFAC

cellulosilyticus

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00162

Bifidobacterium

Reinforced Clostridial

NO
NO
YCFAC

catenulatum

Agar (RCA) (Teknova,

C0205)

FBI00163

Acidaminococcus

Reinforced Clostridial

NO
NO
YCFAC

intestini

Agar (RCA) (Teknova,

C0205)

FBI00164

Bacteroides stercoris

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00165

Bacteroides massiliensis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00166

Blautia massiliensis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00167

Dorea longicatena

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00168

Collinsella aerofaciens

Reinforced Clostridial

NO
NO
YCFAC

Agar (RCA) (Teknova,

C0205)

FBI00169

Parabacteroides

Brain Heart Infusion

NO
NO
YCFAC

distasonis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00170

Eggerthella lenta

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00171

Bilophila wadsworthia

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00172

Bifidobacterium longum

Reinforced Clostridial

NO
NO
YCFAC

Agar (RCA) (Teknova,

C0205)

FBI00173

Bacteroides vulgatus

Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00174

Lactobacillus rogosae

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00175

Holdemanella biformis

YCFAC-B (Anaerobe

NO
NO
YCFAC +

Systems, AS-677)

hemin/vitamin K

FBI00176

Ruthenibacterium

Brain Heart Infusion

NO
NO
YCFAC

lactatiformans

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00177

Parasutterella

Bacteroides Bile Esculin

NO
YES
YCFAC

excrementihominis

(BBE) (Anaerobe Systems,

AS-144)

FBI00178

Bifidobacterium

YCFAC-B (Anaerobe

NO
NO
YCFAC

adolescentis

Systems, AS-677)

FBI00179

Bifidobacterium

Reinforced Clostridial

NO
NO
YCFAC

adolescentis

Agar (RCA) (Teknova,

C0205)

FBI00180

Alistipes sp. FBI00180
Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00181

Blautia wexlerae

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00182

Bacteroides coprocola

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00183

Bacteroides dorei

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00184

Bacteroides faecis

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00185

Eisenbergiella tayi

YCFAC-BO 160 mM

160 mM
NO
YCFAC

(Anaerobe Systems, AS-

7527)

FBI00186

Coprococcus comes

OxyPras Plus Brucella

NO
NO
YCFAC

Blood Agar (Oxyrase, P-

BRU-BA)

FBI00187

Eubacterium rectale

OxyPras Plus Brucella

NO
NO
YCFAC

Blood Agar (Oxyrase, P-

BRU-BA)

FBI00188

Blautia faecis

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00189

Bacteroides ovatus

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00190

Bacteroides finegoldii

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00191

Clostridiaceae sp.
OxyPras Plus Brucella

NO
NO
YCFAC +

FBI00191
Blood Agar (Oxyrase, P-

hemin/vitamin K

BRU-BA)

FBI00192

Sutterella

YCFAC-B (Anaerobe

NO
NO
YCFAC

wadsworthensis

Systems, AS-677)

FBI00193

Alistipes onderdonkii

OxyPras Plus Brucella

NO
NO
YCFAC

Blood Agar (Oxyrase, P-

BRU-BA)

FBI00194

Ruminococcus faecis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00195

Parasutterella

YCFAC-B (Anaerobe

NO
NO
YCFAC

excrementihominis

Systems, AS-677)

FBI00196

Blautia obeum

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00197

Bifidobacterium

YCFAC-B (Anaerobe

NO
NO
YCFAC

bifidum

Systems, AS-677)

FBI00198

Lachnoclostridium

YCFAC-BO 40 mM

40 mM
NO
YCFAC

pacaense

(Anaerobe Systems, AS-

7523)

FBI00199

Clostridium bolteae

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00200

Longicatena caecimuris

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00201

Eggerthella lenta

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00202

Erysipelotrichaceae sp.
YCFAC-B (Anaerobe

NO
NO
YCFAC

FBI00202
Systems, AS-677)

FBI00203

Bacteroides kribbi/

YCFAC-BO 40 mM

40 mM
NO
YCFAC

Bacteroides koreensis

(Anaerobe Systems, AS-

species cluster
7523)

FBI00204

Escherichia flexneri

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00205

Blautia massiliensis

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00206

Bacteroides

YCFAC-BO 40 mM

40 mM
NO
YCFAC

xylanisolvens

(Anaerobe Systems, AS-

7523)

FBI00207

Parabacteroides merdae

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00208

Anaerotruncus

YCFAC-BO 40 mM

40 mM
NO
YCFAC

massiliensis

(Anaerobe Systems, AS-

7523)

FBI00209

Bacteroides salyersiae

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00210

Bifidobacterium

YCFAC-B (Anaerobe

NO
NO
YCFAC

bifidum

Systems, AS-677)

FBI00211

Bacteroides vulgatus

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00212

Clostridium aldenense

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00213

Ruminococcus bromii

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00214

Blautia obeum

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00215

Eubacterium rectale

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00216

Blautia faecis

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00217

Alistipes shahii

Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00218

Bacteroides uniformis

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00219

Roseburia hominis

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00220

Megasphaera

Brain Heart Infusion

NO
NO
YCFAC

massiliensis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00221

Butyricimonas

Brain Heart Infusion

NO
NO
YCFAC

faecihominis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00222

Alistipes onderdonkii

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00223

Alistipes onderdonkii

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00224

Sutterella

YCFAC-BO 40 mM

40 mM
NO
YCFAC

wadsworthensis

(Anaerobe Systems, AS-

7523)

FBI00225

Phascolarctobacterium

YCFAC-BO 40 mM

40 mM
NO
YCFAC + 80 mM

faecium

(Anaerobe Systems, AS-

oxalate

7523)

FBI00226

Catabacter

YCFAC-BO 40 mM

40 mM
NO
YCFAC +

hongkongensis

(Anaerobe Systems, AS-

hemin/vitamin K

7523)

FBI00227

Bacteroides

Brain Heart Infusion

NO
NO
YCFAC

cellulosilyticus

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00228

Collinsella aerofaciens

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00229

Alistipes senegalensis

Brain Heart Infusion

NO
NO
Thioglycollate

(BHI), hemin, vitamin K

with

(Teknova, B1093)

hemin/vitamin K

FBI00230

Eisenbergiella tayi

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00231

Parabacteroides

Brain Heart Infusion

NO
NO
YCFAC

distasonis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00232

Bacteroides stercoris

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00233

Ruminococcaceae sp.
Brain Heart Infusion

NO
NO
YCFAC +

FBI00233
(BHI), hemin, vitamin K

hemin/vitamin K

(Teknova, B1093)

FBI00234

Faecalicatena contorta

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00235

Alistipes shahii

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00236

Eisenbergiella tayi

YCFAC-BO 40 mM

40 mM
NO
YCFAC

(Anaerobe Systems, AS-

7523)

FBI00237

Dielma fastidiosa

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00238

Alistipes sp. FBI00238
Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00239

Lactonifactor

Brain Heart Infusion

NO
NO
YCFAC

longoviformis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00240

Clostridium citroniae

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00241

Collinsella aerofaciens

YCFAC-B (Anaerobe

NO
NO
YCFAC +

Systems, AS-677)

hemin/vitamin K

FBI00242

Clostridium aldenense

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00243

Eubacterium siraeum

Brain Heart Infusion

NO
NO
YCFAC, pH 6

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00244

Faecalibacterium

YCFAC-BO 40 mM

40 mM
NO
YCFAC, pH 6

prausnitzii

(Anaerobe Systems, AS-

7523)

FBI00245

Acidaminococcus

Columbia agar, 5% sheep

NO
NO
YCFAC +

intestini

blood (BD, 221165)

hemin/vitamin K

FBI00246

Bifidobacterium longum

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00247

Phascolarctobacterium

YCFAC-BO 80 mM

80 mM
NO
YCFAC + 80 mM

faecium

(Anaerobe Systems, AS-

oxalate

7524)

FBI00248

Neglecta timonensis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00249

Citrobacter

Strain Isolation Media 3

NO
NO
YCFAC

portucalensis

(SL3)

FBI00250

Bifidobacterium

Reinforced Clostridial

NO
NO
YCFAC

adolescentis

Agar (RCA) (Teknova,

C0205)

FBI00251

Bifidobacterium

Reinforced Clostridial

NO
NO
YCFAC

pseudocatenulatum

Agar (RCA) (Teknova,

C0205)

FBI00252

Oscillibacter sp.
Columbia agar, 5% sheep

NO
NO
BHI + hemin/vitK

FBI00028
blood (BD, 221165)

FBI00253

Roseburia hominis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00254

Eubacterium hallii

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00255

Hungatella effluvii

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00256

Blautia faecis

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00257

Eubacterium eligens

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00258

Turicibacter sanguinis

Strain Isolation Media 3

NO
NO
Thioglycollate

(SL3)

with

hemin/vitamin K

FBI00259

Dorea longicatena

Reinforced Clostridial

NO
NO
YCFAC

Agar (RCA) (Teknova,

C0205)

FBI00260

Eubacterium rectale

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00261

Bacteroides uniformis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00262

Bacteroides massiliensis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00263

Bacteroides caccae

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00264

Bifidobacterium

Reinforced Clostridial

NO
NO
YCFAC

adolescentis

Agar (RCA) (Teknova,

C0205)

FBI00265

Bacteroides

YCFAC-BO 80 mM

80 mM
NO
YCFAC

cellulosilyticus

(Anaerobe Systems, AS-

7524)

FBI00266

Coprococcus eutactus

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00267

Anaerofustis

YCFAC-BO 80 mM

80 mM
NO
YCFAC

stercorihominis

(Anaerobe Systems, AS-

7524)

FBI00268

Clostridiales sp.
Brain Heart Infusion

NO
NO
Thioglycollate

FBI00268
(BHI), hemin, vitamin K

with

(Teknova, B1093)

hemin/vitamin K

FBI00269

Alistipes putredinis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00270

Methanobrevibacter

Columbia agar, 5% sheep
Antibiotics
NO
NO
SAB

smithii

blood (BD, 221165)

FBI00271

Bacteroides

Brain Heart Infusion

NO
NO
YCFAC

xylanisolvens

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00272

Clostridiales XIII sp.
Columbia agar, 5% sheep

NO
NO
Thioglycollate

FBI00272
blood (BD, 221165)

with

hemin/vitamin K

FBI00273

Barnesiella

Brain Heart Infusion

NO
NO
YCFAC

intestinihominis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00274

Eubacterium

YCFAC-BO 80 mM

80 mM
NO
YCFAC, pH 6

xylanophilum

(Anaerobe Systems, AS-

7524)

FBI00275

Holdemanella biformis

Brain Heart Infusion

NO
NO
YCFAC +

(BHI), hemin, vitamin K

hemin/vitamin K

(Teknova, B1093)

FBI00276

Dorea formicigenerans

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00277

Alistipes onderdonkii

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00278

Eubacterium ventriosum

Brain Heart Infusion

NO
NO
YCFAC, pH 6

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00279

Coprococcus comes

YCFAC-BO 80 mM

80 mM
NO
YCFAC

(Anaerobe Systems, AS-

7524)

FBI00280

Bacteroides

YCFAC-BO 80 mM

80 mM
NO
YCFAC

thetaiotaomicron

(Anaerobe Systems, AS-

7524)

FBI00281

Senegalimassilia

Reinforced Clostridial

NO
NO
YCFAC

anaerobia

Agar (RCA) (Teknova,

C0205)

FBI00282

Porphyromonas

Columbia agar, 5% sheep

NO
NO
YCFAC

asaccharolytica

blood (BD, 221165)

FBI00283

Ruminococcus bromii

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00284

Blautia obeum

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00285

Lachnospira sp.
Brain Heart Infusion

NO
NO
YCFAC

FBI00063 FBI00285
(BHI), hemin, vitamin K

FBI00364
(Teknova, B1093)

FBI00286

Fusicatenibacter

Brain Heart Infusion

NO
NO
YCFAC

saccharivorans

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00287

Alistipes shahii

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00288

Blautia

Brain Heart Infusion

NO
NO
YCFAC

hydrogenotrophica

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00289

Oxalobacter formigenes

YCFAC-BO 80 mM

80 mM
NO
YCFAC + 80 mM

(Anaerobe Systems, AS-

oxalate

7524)

FBI00290

Lachnospiraceae sp.
Brain Heart Infusion

NO
NO
YCFAC

FBI00290
(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00291

Oribacterium sp.
Strain Isolation Media 3

NO
NO
YCFAC

FBI00291
(SL3)

FBI00292

Methanobrevibacter

Columbia agar, 5% sheep

NO
NO
SAB

smithii

blood (BD, 221165)

FBI00293

Bifidobacterium

Reinforced Clostridial

NO
NO
YCFAC

adolescentis

Agar (RCA) (Teknova,

C0205)

FBI00294

Bacteroides stercoris

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00295

Bifidobacterium

Reinforced Clostridial

NO
NO
YCFAC

adolescentis

Agar (RCA) (Teknova,

C0205)

FBI00296

Dorea longicatena

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00297

Alistipes obesi

Strain Isolation Media 3

NO
NO
YCFAC +

(SL3)

hemin/vitamin K

FBI00298

Faecalibacterium

Brain Heart Infusion

NO
NO
YCFAC

prausnitzii

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00299

Streptococcus

Lactobacillus MRS

NO
NO
YCFAC

pasteurianus

(Anaerobe Systems, AS-

6429)

FBI00300

Collinsella aerofaciens

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00301

Bifidobacterium

Brain Heart Infusion

NO
NO
YCFAC

adolescentis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00302

Blautia faecis

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00303

Parabacteroides merdae

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00304

Dorea longicatena

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00305

Alistipes onderdonkii

Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00306

Parasutterella

Strain Isolation Media 3

NO
NO
BHI + hemin/vitK

excrementihominis

(SL3)

FBI00307

Parasutterella

Bacteroides Bile Esculin

NO
YES
BHI + hemin/vitK

excrementihominis

(BBE) (Anaerobe Systems,

AS-144)

FBI00308

Bacteroides vulgatus

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00309

Eubacterium rectale

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00310

Butyricimonas

Brain Heart Infusion

NO
NO
YCFAC

faecihominis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00311

Anaerostipes hadrus

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00312

Alistipes shahii

Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00313

Collinsella aerofaciens

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00314

Anaerotignum

Brain Heart Infusion

NO
NO
YCFAC

lactatifermentans

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00315

Blautia obeum

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00316

Collinsella aerofaciens

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00317

Bifidobacterium longum

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00318

Collinsella aerofaciens

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00319

Collinsella aerofaciens

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00320

Dorea formicigenerans

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00321

Bacteroides vulgatus

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00322

Bifidobacterium

Brain Heart Infusion

NO
NO
YCFAC

adolescentis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00323

Blautia wexlerae

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00324

Bilophila wadsworthia

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00325

Alistipes indistinctus

Brain Heart Infusion

NO
NO
YCFAC +

(BHI), hemin, vitamin K

hemin/vitamin K

(Teknova, B1093)

FBI00326

Bacteroides vulgatus

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00327

Coprococcus comes

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00328

Blautia luti

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00329

Alistipes indistinctus

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00330

Bifidobacterium longum

Lactobacillus MRS

NO
NO
YCFAC

(Anaerobe Systems, AS-

6429)

FBI003 31

Bacillus circulans

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00332

Clostridium intestinale

YCFAC-B (Anaerobe

NO
NO
YCFAC

Systems, AS-677)

FBI00333

Alistipes onderdonkii

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00334

Bacteroides caccae

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00335

Anaerostipes hadrus

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00336

Staphylococcus

Brain Heart Infusion

NO
NO
YCFAC

epidermidis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00337

Coprococcus comes

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00338

Blautia obeum

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00339

Eubacterium rectale

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00340

Lachnospiraceae sp.
Brain Heart Infusion

NO
NO
YCFAC

FBI00033
(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00341

Lachnospiraceae sp.
Columbia agar, 5% sheep

NO
NO
YCFAC

FBI00071
blood (BD, 221165)

FBI00342

Alistipes indistinctus

Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00343

Sutterella massiliensis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00344

Alistipes putredinis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00345

Roseburia inulinivorans

Strain Isolation Media 1

NO
NO
YCFAC

(SL1)

FBI00346

Coriobacteriia sp.
Brain Heart Infusion

NO
NO
YCFAC

FBI00346
(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00347

Bacteroides uniformis

Strain Isolation Media 1

NO
NO
YCFAC

(SL1)

FBI00348

Parabacteroides merdae

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00349

Holdemanella biformis

Brain Heart Infusion

NO
NO
BHI + hemin/vitK

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00350

Alistipes putredinis

Bacteroides Bile Esculin

NO
YES
YCFAC

(BBE) (Anaerobe Systems,

AS-144)

FBI00351

Alistipes obesi

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00352

Collinsella aerofaciens

Columbia agar, 5% sheep

NO
NO
YCFAC

blood (BD, 221165)

FBI00353

Bifidobacterium

Brain Heart Infusion

NO
NO
YCFAC

adolescentis

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00354

Bifidobacterium

Strain Isolation Media 3

NO
NO
YCFAC

adolescentis

(SL3)

FBI00355

Blautia massiliensis

Strain Isolation Media 1

NO
NO
YCFAC

(SL1)

FBI00356

Eubacterium eligens

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00357

Bacteroides kribbi/

Strain Isolation Media 1

NO
NO
YCFAC

Bacteroides koreensis

(SL1)

species cluster

FBI00358

Eubacterium hallii

Strain Isolation Media 1

NO
NO
YCFAC

(SL1)

FBI00359

Eubacterium rectale

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00360

Bacteroides massiliensis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00361

Bacteroides stercoris

Strain Isolation Media 3

NO
NO
YCFAC

(SL3)

FBI00362

Prevotella copri

Chocolate Agar (Teknova,

NO
NO
Thioglycollate

C4900)

with

hemin/vitamin K

FBI00363

Roseburia intestinalis

Strain Isolation Media 1

NO
NO
YCFAC

(SL1)

FBI00364

Lachnospira sp.
Brain Heart Infusion

NO
NO
YCFAC

FBI00063 FBI00285
(BHI), hemin, vitamin K

FBI00364
(Teknova, B1093)

FBI00365

Paraprevotella clara

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00366

Eubacterium eligens

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00367

Phascolarctobacterium

Strain Isolation Media 1

NO
NO
YCFAC

faecium

(SL1)

FBI00368

Alistipes putredinis

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00369

Clostridiales sp.
Brain Heart Infusion

NO
NO
BHI + hemin/vitK

FBI00369
(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00370

Bifidobacterium

Columbia agar, 5% sheep

NO
NO
YCFAC

adolescentis

blood (BD, 221165)

FBI00371

Bacteroides stercoris

Brain Heart Infusion

NO
NO
YCFAC

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00372

Dorea longicatena

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00373

Coriobacteriaceae sp.
Columbia agar, 5% sheep

NO
NO
Thioglycollate

FBI00373 FBI00374
blood (BD, 221165)

with

hemin/vitamin K

FBI00374

Coriobacteriaceae sp.
Columbia agar, 5% sheep

NO
NO
Thioglycollate

FBI00373 FBI00374
blood (BD, 221165)

with

hemin/vitamin K

FBI00375

Dorea longicatena

Chocolate Agar (Teknova,

NO
NO
YCFAC

C4900)

FBI00376

Dialister succinatiphilus

Brain Heart Infusion

NO
NO
BHI + hemin/vitK

(BHI), hemin, vitamin K

(Teknova, B1093)

FBI00377

Clostridiales sp.
Brain Heart Infusion

NO
NO
Thioglycollate

FBI00377
(BHI), hemin, vitamin K

with

(Teknova, B1093)

hemin/vitamin K

TABLE 4

NCBI

Taxonomy
Closest 16S
% Match
SEQ ID

Strain #
Species ID
Kingdom
Phylum
ID
Species
(16S)
NO: X

FBI00001

Clostridium citroniae

bacteria

firmicutes
358743

Clostridium citroniae

99.64
1

FBI00002

Bacteroides salyersiae

bacteria

bacteroidetes
291644

Bacteroides salyersiae

99.5
2

FBI00003

Enterococcus faecalis

bacteria

firmicutes
1351

Enterococcus faecalis

99.93
3

FBI00004

Neglecta timonensis

bacteria

firmicutes
1776382

Neglecta timonensis

99.14
4

FBI00005

Enterococcus casseliflavus

bacteria

firmicutes
37734

Enterococcus gallinarum

99.65
5

FBI00006

Enterobacter himalayensis

bacteria

proteobacteria
547

Enterobacter hormaechei

99
6

FBI00007

Enterococcus casseliflavus

bacteria

firmicutes
37734

Enterococcus

99.05
7

casseliflavus

FBI00008

Blautia luti

bacteria

firmicutes
89014

Blautia luti

97.02
8

FBI00009

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium faecale

98.6
9

FBI00010

Blautia obeum

bacteria

firmicutes
40520

Blautia obeum

98.12
10

FBI00011

Bifidobacterium longum

bacteria

actinobacteria
216816

Bifidobacterium longum

99.28
11

FBI00012

Alistipes onderdonkii

bacteria

bacteroidetes
328813

Alistipes onderdonkii

99.71
12

FBI00013

Parabacteroides merdae

bacteria

bacteroidetes
46503

Parabacteroides merdae

99.5
13

FBI00014

Blautia luti

bacteria

firmicutes
89014

Blautia luti

97.02
14

FBI00015

Bacteroides uniformis

bacteria

bacteroidetes
820

Bacteroides uniformis

99.78
15

FBI00016

Bifidobacterium

bacteria

actinobacteria
28026

Bifidobacterium

99.64
16

pseudocatenulatum

pseudocatenulatum

FBI00017

Blautia obeum

bacteria

firmicutes
40520

Blautia obeum

98.34
17

FBI00018

Eubacterium rectale

bacteria

firmicutes
39491

Eubacterium rectale

99.71
18

FBI00019

Alistipes timonensis

bacteria

bacteroidetes
1465754

Alistipes timonensis

99.78
19

FBI00020

Bacteroides thetaiotaomicron

bacteria

bacteroidetes
818

Bacteroides

99.57
20

thetaiotaomicron

FBI00021

Bacteroides kribbi/

bacteria

bacteroidetes
816

Bacteroides kribbi

99.07
21

Bacteroides koreensis species

cluster

FBI00022

Alistipes putredinis

bacteria

bacteroidetes
28117

Alistipes putredinis

99.93
22

FBI00023

Enterococcus casseliflavus

bacteria

firmicutes
37734

Enterococcus gallinarum

99.65
23

FBI00024

Bacteroides kribbi/

bacteria

bacteroidetes
816

Bacteroides koreensis

99.07
24

Bacteroides koreensis species

cluster

FBI00025

Coprococcus comes

bacteria

firmicutes
410072

Coprococcus comes

99.21
25

FBI00026

Enterobacter hormaechei

bacteria

proteobacteria
158836

Enterobacter hormaechei

99.14
26

FBI00027

Fusicatenibacter

bacteria

firmicutes
1150298

Fusicatenibacter

97.6
27

saccharivorans

saccharivorans

FBI00028

Oscillibacter sp. FBI00028

bacteria

firmicutes
459786

Oscillibacter

93.85
28

valericigenes

FBI00029

Parabacteroides distasonis

bacteria

bacteroidetes
823

Parabacteroides

99.26
29

distasonis

FBI00030

Eggerthella lenta

bacteria

firmicutes
84112

Eggerthella lenta

98.47
30

FBI00031

Enterobacter hormaechei

bacteria

proteobacteria
158836

Enterobacter hormaechei

99.43
31

FBI00032

Anaerostipes hadrus

bacteria

firmicutes
649756

Anaerostipes hadrus

99.64
32

FBI00033

Lachnospiraceae sp.

bacteria

firmicutes
186803

Clostridium

93.56
33

FBI00033

amygdalinum

FBI00034

Eubacterium eligens

bacteria

firmicutes
39485

Eubacterium eligens

98.78
34

FBI00035

Enterococcus casseliflavus

bacteria

firmicutes
37734

Enterococcus

98.24
35

casseliflavus

FBI00036

Blautia faecis

bacteria

firmicutes
871665

Blautia faecis

99.53
36

FBI00037

Enterococcus casseliflavus

bacteria

firmicutes
37734

Enterococcus gallinarum

99.65
37

FBI00038

Coprococcus eutactus

bacteria

firmicutes
33043

Coprococcus eutactus

95.96
38

FBI00039

Bacteroides vulgatus

bacteria

bacteroidetes
821

Bacteroides vulgatus

99.71
39

FBI00040

Bilophila wadsworthia

bacteria

proteobacteria
35833

Desulfovibrio

91.38
40

desulfuricans

FBI00041

Phascolarctobacterium

bacteria

firmicutes
33025

Phascolarctobacterium

99.23
41

faecium

faecium

FBI00042

Bacteroides xylanisolvens

bacteria

bacteroidetes
371601

Bacteroides

99.71
42

xylanisolvens

FBI00043

Bifidobacterium dentium

bacteria

actinobacteria
1689

Bifidobacterium

99.35
43

dentium

FBI00044

Blautia wexlerae

bacteria

firmicutes
418240

Blautia wexlerae

98.69
44

FBI00045

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium faecale

99.56
45

FBI00046

Bacteroides caccae

bacteria

bacteroidetes
47678

Bacteroides caccae

99.71
46

FBI00047

Eubacterium eligens

bacteria

firmicutes
39485

Eubacterium eligens

98.79
47

FBI00048

Fusicatenibacter

bacteria

firmicutes
1150298

Fusicatenibacter

97.95
48

saccharivorans

saccharivorans

FBI00049

Dialister succinatiphilus

bacteria

firmicutes
487173

Dialister succinatiphilus

95.74
49

FBI00050

Bacteroides nordii

bacteria

bacteroidetes
291645

Bacteroides nordii

98.63
50

FBI00051

Dorea formicigenerans

bacteria

firmicutes
39486

Dorea formicigenerans

98.07
51

FBI00052

Bacteroides xylanisolvens

bacteria

bacteroidetes
371601

Bacteroides

99.14
52

xylanisolvens

FBI00053

Lactobacillus rogosae

bacteria

firmicutes
706562

Lachnospira

97.36
53

pectinoschiza

FBI00054

Escherichia flexneri

bacteria

proteobacteria
623

Escherichia fergusonii

99.71
54

FBI00055

Bacteroides kribbi/

bacteria

bacteroidetes
816

Bacteroides kribbi

99.64
55

Bacteroides koreensis species

cluster

FBI00056

Clostridium citroniae

bacteria

firmicutes
358743

Clostridium citroniae

99.2
56

FBI00057

Dorea longicatena

bacteria

firmicutes
88431

Dorea longicatena

99.7
57

FBI00058

Eubacterium rectale

bacteria

firmicutes
39491

Eubacterium rectale

99.71
58

FBI00059

Bacteroides stercorirosoris

bacteria

bacteroidetes
871324

Bacteroides oleiciplenus

98.81
59

FBI00060

Bifidobacterium longum

bacteria

actinobacteria
216816

Bifidobacterium longum

99.49
60

FBI00061

Alistipes shahii

bacteria

bacteroidetes
328814

Alistipes shahii

99.19
61

FBI00062

Collinsella aerofaciens

bacteria

actinobacteria
74426

Collinsella aerofaciens

99.48
62

FBI00063

Lachnospira sp. FBI00063

bacteria

firmicutes
28050

Lactobacillus rogosae

95.3
63

FBI00285 FBI00364

FBI00064

Dorea sp. FBI00064

bacteria

firmicutes
189330

Ruminococcus gnavus

95.58
64

FBI00065

Sutterellaceae sp. FBI00065

bacteria

proteobacteria
995019

Turicimonas muris

91.55
65

FBI00066

Parasutterella

bacteria

proteobacteria
487175

Parasutterella

99.13
66

excrementihominis

excrementihominis

FBI00067

Oxalobacter formigenes

bacteria

proteobacteria
847

Oxalobacter formigenes

98.84
67

FBI00068

Akkermansia muciniphila

bacteria

vemicomicrobia
239935

Akkermansia

99.42
68

muciniphila

FBI00069

Ruminococcus bromii

bacteria

firmicutes
40518

Ruminococcus bromii

98.84
69

FBI00070

Bacteroides kribbi/

bacteria

bacteroidetes
816

Bacteroides koreensis

99.71
70

Bacteroides koreensis species

cluster

FBI00071

Lachnospiraceae sp.

bacteria

firmicutes
186803

Roseburia faecis

94.92
71

FBI00071

FBI00072

Coprococcus eutactus

bacteria

firmicutes
33043

Coprococcus eutactus

96.17
72

FBI00073

Parabacteroides distasonis

bacteria

bacteroidetes
823

Parabacteroides

98.99
73

distasonis

FBI00074

Clostridium fessum

bacteria

firmicutes
2126740

Clostridium symbiosum

94.03
74

FBI00075

Paraprevotella clara

bacteria

bacteroidetes
454154

Paraprevotella clara

98.85
75

FBI00076

Bacteroides thetaiotaomicron

bacteria

bacteroidetes
818

Bacteroides

99.78
76

thetaiotaomicron

FBI00077

Sutterella wadsworthensis

bacteria

proteobacteria
40545

Sutterella

99.86
77

wadsworthensis

FBI00078

Blautia obeum

bacteria

firmicutes
40520

Blautia obeum

98.34
78

FBI00079

Clostridium clostridioforme

bacteria

firmicutes
1531

Clostridium

99.14
79

clostridioforme

FBI00080

Sutterella massiliensis

bacteria

proteobacteria
1816689

Sutterella massiliensis

99.78
80

FBI00081

Porphyromonas

bacteria

bacteroidetes
28123

Porphyromonas

99.35
81

asaccharolytica

asaccharolytica

FBI00082

Ruminococcaceae sp.

bacteria

firmicutes
541000

Phocea massiliensis

93.08
82

FBI00082 FBI00097

FBI00083

Alistipes shahii

bacteria

bacteroidetes
328814

Alistipes shahii

99.64
83

FBI00084

Bifidobacterium longum

bacteria

actinobacteria
216816

Bifidobacterium longum

98.07
84

FBI00085

Ruminococcus bromii

bacteria

firmicutes
40518

Ruminococcus bromii

98.62
85

FBI00086

Ruminococcus bromii

bacteria

firmicutes
40518

Ruminococcus bromii

98.77
86

FBI00087

Clostridium scindens

bacteria

firmicutes
29347

Clostridium scindens

98.28
87

FBI00088

Lactobacillus rogosae

bacteria

firmicutes
706562

Lactobacillus rogosae

99.64
88

FBI00089

Bifidobacterium longum

bacteria

actinobacteria
216816

Bifidobacterium longum

98.49
89

FBI00090

Eubacterium eligens

bacteria

firmicutes
39485

Eubacterium eligens

98.71
90

FBI00091

Eubacterium rectale

bacteria

firmicutes
39491

Eubacterium rectale

99.86
91

FBI00092

Monoglobus pectinilyticus

bacteria

firmicutes
1981510

Monoglobus

99.5
92

pectinilyticus

FBI00093

Roseburia hominis

bacteria

firmicutes
301301

Roseburia hominis

99.71
93

FBI00094

Enterococcus faecium

bacteria

firmicutes
1352

Enterococcus faecium

99.38
94

FBI00095

Ruminococcus bromii

bacteria

firmicutes
40518

Ruminococcus bromii

98.7
95

FBI00096

Eggerthella lenta

bacteria

actinobacteria
84112

Eggerthella lenta

98.76
96

FBI00097

Ruminococcaceae sp.

bacteria

firmicutes
541000

Phocea massiliensis

93.07
97

FBI00082 FBI00097

FBI00098

Bacteroides dorei

bacteria

bacteroidetes
357276

Bacteroides dorei

99.93
98

FBI00099

Gordonibacter pamelaeae

bacteria

actinobacteria
471189

Gordonibacter

99.56
99

pamelaeae

FBI00100

Lachnospira sp. FBI00063

bacteria

firmicutes
28050

Lactobacillus rogosae

95.35
100

FBI00285 FBI00364

FBI00101

Faecalibacterium prausnitzii

bacteria

firmicutes
853

Faecalibacterium

97.97
101

prausnitzii

FBI00102

Clostridium fessum

bacteria

firmicutes
2126740

Clostridium symbiosum

94.31
102

FBI00103

Bacteroides massiliensis

bacteria

bacteroidetes
204516

Bacteroides massiliensis

99.86
103

FBI00104

Blautia wexlerae

bacteria

firmicutes
418240

Blautia luti

97.18
104

FBI00105

Ruminococcaceae sp.

bacteria

firmicutes
541000

Pseudoflavonifractor

95.06
105

FBI00105 FBI00160

phocaeensis

FBI00106

Enterococcus durans

bacteria

firmicutes
53345

Enterococcus lactis

96.68
106

FBI00107

Enterococcus durans

bacteria

firmicutes
53345

Enterococcus faecium

98.83
107

FBI00108

Ruminococcaceae sp.

bacteria

firmicutes
541000

Gemmiger formicilis

96.96
108

FBI00108

FBI00109

Coprococcus comes

bacteria

firmicutes
410072

Coprococcus comes

98.39
109

FBI00110

Lachnoclostridium pacaense

bacteria

firmicutes
1917870

Lachnoclostridium

98.92
110

pacaense

FBI00111

Bacteroides vulgatus

bacteria

bacteroidetes
821

Bacteroides vulgatus

99.43
111

FBI00112

Bacteroides uniformis

bacteria

bacteroidetes
820

Bacteroides uniformis

99.78
112

FBI00113

Parabacteroides merdae

bacteria

bacteroidetes
46503

Parabacteroides merdae

99.79
113

FBI00114

Dorea formicigenerans

bacteria

firmicutes
39486

Dorea formicigenerans

97.83
114

FBI00115

Dorea formicigenerans

bacteria

firmicutes
39486

Dorea formicigenerans

97.98
115

FBI00116

Ruminococcus faecis

bacteria

firmicutes
592978

Ruminococcus faecis

99.57
116

FBI00117

Blautia faecis

bacteria

firmicutes
871665

Blautia faecis

99.52
117

FBI00118

Blautia faecis

bacteria

firmicutes
871665

Blautia faecis

99.84
118

FBI00119

Blautia obeum

bacteria

firmicutes
40520

Blautia obeum

98.02
119

FBI00120

Hungatella effluvii

bacteria

firmicutes
154046

Hungatella hathewayi

98.78
120

FBI00121

Bacteroides vulgatus

bacteria

bacteroidetes
821

Bacteroides vulgatus

99.86
121

FBI00122

Bacteroides uniformis

bacteria

bacteroidetes
820

Bacteroides uniformis

99.57
122

FBI00123

Roseburia hominis

bacteria

firmicutes
301301

Roseburia hominis

100
123

FBI00124

Anaerostipes hadrus

bacteria

firmicutes
649756

Anaerostipes hadrus

99.86
124

FBI00125

Bacteroides stercoris

bacteria

bacteroidetes
46506

Bacteroides stercoris

99.64
125

FBI00126

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium

98.98
126

adolescentis

FBI00127

Collinsella aerofaciens

bacteria

actinobacteria
74426

Collinsella aerofaciens

98.81
127

FBI00128

Hungatella effluvii

bacteria

firmicutes
1096246

Hungatella effluvii

98.71
128

FBI00129

Escherichia flexneri

bacteria

proteobacteria
623

Escherichia fergusonii

99.43
129

FBI00130

Coprococcus comes

bacteria

firmicutes
410072

Coprococcus comes

99.35
130

FBI00131

Fusicatenibacter

bacteria

firmicutes
1150298

Fusicatenibacter

99.2
131

saccharivorans

saccharivorans

FBI00132

Gordonibacter pamelaeae

bacteria

actinobacteria
471189

Gordonibacter

99.48
132

pamelaeae

FBI00133

Oxalobacter formigenes

bacteria

proteobacteria
847

Oxalobacter formigenes

99.21
133

FBI00134

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium faecale

98.92
134

FBI00135

Bifidobacterium

bacteria

actinobacteria
28026

Bifidobacterium

99.57
135

pseudocatenulatum

pseudocatenulatum

FBI00136

Eisenbergiella tayi

bacteria

firmicutes
1432052

Eisenbergiella tayi

99.77
136

FBI00137

Bacteroides fragilis

bacteria

bacteroidetes
817

Bacteroides fragilis

99.71
137

FBI00138

Blautia massiliensis

bacteria

firmicutes
1737424

Blautia luti

97.94
138

FBI00139

Bacteroides thetaiotaomicron

bacteria

bacteroidetes
818

Bacteroides

99.5
139

thetaiotaomicron

FBI00140

Phascolarctobacterium

bacteria

firmicutes
33025

Phascolarctobacterium

99.58
140

faecium

faecium

FBI00141

Phascolarctobacterium

bacteria

firmicutes
33025

Phascolarctobacterium

99.15
141

faecium

faecium

FBI00142

Clostridium fessum

bacteria

firmicutes
2126740

Clostridium symbiosum

94.07
142

FBI00143

Parabacteroides merdae

bacteria

bacteroidetes
46503

Parabacteroides merdae

99.07
143

FBI00144

Holdemanella biformis

bacteria

firmicutes
1735

Holdemanella biformis

97.73
144

FBI00145

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium

99.14
145

adolescentis

FBI00146

Blautia faecis

bacteria

firmicutes
871665

Blautia faecis

99.68
146

FBI00147

Clostridium bolteae

bacteria

firmicutes
208479

Clostridium bolteae

99.28
147

FBI00148

Oscillibacter sp. FBI00028

bacteria

firmicutes
459786

Oscillibacter

94.28
148

ruminantium

FBI00149

Monoglobus pectinilyticus

bacteria

firmicutes
1981510

Monoglobus

99.5
149

pectinilyticus

FBI00150

Lachnospiraceae sp.

bacteria

firmicutes
186803

Clostridium

93.55
150

FBI00033

amygdalinum

FBI00151

Clostridium aldenense

bacteria

firmicutes
358742

Clostridium aldenense

98.55
151

FBI00152

Dialister invisus

bacteria

firmicutes
218538

Dialister invisus

99.58
152

FBI00153

Dialister succinatiphilus

bacteria

firmicutes
487173

Dialister succinatiphilus

95.72
153

FBI00154

Bacteroides dorei

bacteria

bacteroidetes
357276

Bacteroides dorei

100
154

FBI00155

Blautia obeum

bacteria

firmicutes
40520

Blautia obeum

98.7
155

FBI00156

Enterococcus durans

bacteria

firmicutes
53345

Enterococcus sp.
96.45
156

FBI00157

Lachnospiraceae sp.

bacteria

firmicutes
186803

Cuneatibacter

91.24
157

FBI00157

caecimuris

FBI00158

Butyricimonas sp. FBI00158

bacteria

bacteroidetes
574697

Butyricimonas sp.
97.54
158

FBI00159

Eisenbergiella tayi

bacteria

firmicutes
1432052

Eisenbergiella tayi

99.03
159

FBI00160

Ruminococcaceae sp.

bacteria

firmicutes
541000

Pseudoflavonifractor

97.17
160

FBI00105 FBI00160

capillosus

FBI00161

Bacteroides cellulosilyticus

bacteria

bacteroidetes
246787

Bacteroides

99.14
161

cellulosilyticus

FBI00162

Bifidobacterium catenulatum

bacteria

actinobacteria
1686

Bifidobacterium

99.14
162

catenulatum

FBI00163

Acidaminococcus intestini

bacteria

firmicutes
187327

Acidaminococcus

99.72
163

intestini

FBI00164

Bacteroides stercoris

bacteria

bacteroidetes
46506

Bacteroides stercoris

98.56
164

FBI00165

Bacteroides massiliensis

bacteria

bacteroidetes
204516

Bacteroides massiliensis

99.71
165

FBI00166

Blautia massiliensis

bacteria

firmicutes
1737424

Blautia luti

97.55
166

FBI00167

Dorea longicatena

bacteria

firmicutes
88431

Dorea longicatena

99.39
167

FBI00168

Collinsella aerofaciens

bacteria

actinobacteria
74426

Collinsella aerofaciens

99.26
168

FBI00169

Parabacteroides distasonis

bacteria

bacteroidetes
823

Parabacteroides

98.7
169

distasonis

FBI00170

Eggerthella lenta

bacteria

actinobacteria
84112

Eggerthella lenta

98.61
170

FBI00171

Bilophila wadsworthia

bacteria

proteobacteria
35833

Desulfovibrio

91.45
171

desulfuricans

FBI00172

Bifidobacterium longum

bacteria

actinobacteria
216816

Bifidobacterium longum

99.05
172

FBI00173

Bacteroides vulgatus

bacteria

bacteroidetes
821

Bacteroides vulgatus

100
173

FBI00174

Lactobacillus rogosae

bacteria

firmicutes
706562

Lachnospira

97.92
174

pectinoschiza

FBI00175

Holdemanella biformis

bacteria

firmicutes
1735

Holdemanella biformis

98.19
175

FBI00176

Ruthenibacterium

bacteria

firmicutes
1550024

Ruthenibacterium

99.71
176

lactatiformans

lactatiformans

FBI00177

Parasutterella

bacteria

proteobacteria
487175

Parasutterella

99.71
177

excrementihominis

excrementihominis

FBI00178

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium faecale

98.99
178

FBI00179

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium faecale

98.91
179

FBI00180

Alistipes sp. FBI00180

bacteria

bacteroidetes
239759

Alistipes senegalensis

97.56
180

FBI00181

Blautia wexlerae

bacteria

firmicutes
418240

Blautia wexlerae

97.17
181

FBI00182

Bacteroides coprocola

bacteria

bacteroidetes
310298

Bacteroides coprocola

99.64
182

FBI00183

Bacteroides dorei

bacteria

bacteroidetes
357276

Bacteroides dorei

99.86
183

FBI00184

Bacteroides faecis

bacteria

bacteroidetes
674529

Bacteroides faecis

99.78
184

FBI00185

Eisenbergiella tayi

bacteria

firmicutes
1432052

Eisenbergiella tayi

98.96
185

FBI00186

Coprococcus comes

bacteria

firmicutes
410072

Coprococcus comes

99.06
186

FBI00187

Eubacterium rectale

bacteria

firmicutes
39491

Eubacterium rectale

99.57
187

FBI00188

Blautia faecis

bacteria

firmicutes
871665

Blautia faecis

99.05
188

FBI00189

Bacteroides ovatus

bacteria

bacteroidetes
28116

Bacteroides koreensis

99.93
189

FBI00190

Bacteroides finegoldii

bacteria

bacteroidetes
338188

Bacteroides finegoldii

98.91
190

FBI00191

Clostridiaceae sp. FBI00191

bacteria

firmicutes
31979

Clostridium

96.24
191

swellfunianum

FBI00192

Sutterella wadsworthensis

bacteria

proteobacteria
40545

Sutterella

99.71
192

wadsworthensis

FBI00193

Alistipes onderdonkii

bacteria

bacteroidetes
328813

Alistipes onderdonkii

99.64
193

FBI00194

Ruminococcus faecis

bacteria

firmicutes
592978

Ruminococcus faecis

98.41
194

FBI00195

Parasutterella

bacteria

proteobacteria
487175

Parasutterella

99.06
195

excrementihominis

excrementihominis

FBI00196

Blautia obeum

bacteria

firmicutes
40520

Blautia obeum

98.3
196

FBI00197

Bifidobacterium bifidum

bacteria

actinobacteria
1681

Bifidobacterium bifidum

99.85
197

FBI00198

Lachnoclostridium pacaense

bacteria

firmicutes
1917870

Lachnoclostridium

99.71
198

pacaense

FBI00199

Clostridium bolteae

bacteria

firmicutes
208479

Clostridium bolteae

99.28
199

FBI00200

Longicatena caecimuris

bacteria

firmicutes
1796635

Longicatena caecimuris

99.71
200

FBI00201

Eggerthella lenta

bacteria

actinobacteria
84112

Eggerthella lenta

98.83
201

FBI00202

Erysipelotrichaceae sp.

bacteria

firmicutes
128827

Longibaculum muris

92.85
202

FBI00202

FBI00203

Bacteroides kribbi/

bacteria

bacteroidetes
816

Bacteroides koreensis

100
203

Bacteroides koreensis species

cluster

FBI00204

Escherichia flexneri

bacteria

proteobacteria
623

Escherichia fergusonii

98.98
204

FBI00205

Blautia massiliensis

bacteria

firmicutes
1737424

Blautia luti

97.55
205

FBI00206

Bacteroides xylanisolvens

bacteria

bacteroidetes
371601

Bacteroides

99.56
206

xylanisolvens

FBI00207

Parabacteroides merdae

bacteria

bacteroidetes
46503

Parabacteroides merdae

99.49
207

FBI00208

Anaerotruncus massiliensis

bacteria

firmicutes
1673720

Anaerotruncus

96.52
208

colihominis

FBI00209

Bacteroides salyersiae

bacteria

bacteroidetes
291644

Bacteroides salyersiae

99.63
209

FBI00210

Bifidobacterium bifidum

bacteria

actinobacteria
1681

Bifidobacterium bifidum

99.93
210

FBI00211

Bacteroides vulgatus

bacteria

bacteroidetes
821

Bacteroides vulgatus

99.78
211

FBI00212

Clostridium aldenense

bacteria

firmicutes
358742

Clostridium aldenense

99.1
212

FBI00213

Ruminococcus bromii

bacteria

firmicutes
40518

Ruminococcus bromii

98.99
213

FBI00214

Blautia obeum

bacteria

firmicutes
40520

Blautia obeum

98.67
214

FBI00215

Eubacterium rectale

bacteria

firmicutes
39491

Eubacterium rectale

99.78
215

FBI00216

Blautia faecis

bacteria

firmicutes
871665

Blautia faecis

99.76
216

FBI00217

Alistipes shahii

bacteria

bacteroidetes
328814

Alistipes shahii

98.77
217

FBI00218

Bacteroides uniformis

bacteria

bacteroidetes
820

Bacteroides uniformis

99.42
218

FBI00219

Roseburia hominis

bacteria

firmicutes
301301

Roseburia hominis

99.78
219

FBI00220

Megasphaera massiliensis

bacteria

firmicutes
1232428

Megasphaera

98.8
220

massiliensis

FBI00221

Butyricimonas faecihominis

bacteria

bacteroidetes
1472416

Butyricimonas

98.61
221

faecihominis

FBI00222

Alistipes onderdonkii

bacteria

bacteroidetes
328813

Alistipes onderdonkii

99.78
222

FBI00223

Alistipes onderdonkii

bacteria

bacteroidetes
328813

Alistipes onderdonkii

99.7
223

FBI00224

Sutterella wadsworthensis

bacteria

proteobacteria
40545

Sutterella

99.71
224

wadsworthensis

FBI00225

Phascolarctobacterium

bacteria

firmicutes
33025

Phascolarctobacterium

99.37
225

faecium

faecium

FBI00226

Catabacter hongkongensis

bacteria

firmicutes
270498

Catabacter

99.71
226

hongkongensis

FBI00227

Bacteroides cellulosilyticus

bacteria

bacteroidetes
246787

Bacteroides

99.2
227

cellulosilyticus

FBI00228

Collinsella aerofaciens

bacteria

actinobacteria
74426

Collinsella aerofaciens

99.27
228

FBI00229

Alistipes senegalensis

bacteria

bacteroidetes
1288121

Alistipes senegalensis

99.19
229

FBI00230

Eisenbergiella tayi

bacteria

firmicutes
1432052

Eisenbergiella tayi

99.48
230

FBI00231

Parabacteroides distasonis

bacteria

bacteroidetes
823

Parabacteroides

99.11
231

distasonis

FBI00232

Bacteroides stercoris

bacteria

bacteroidetes
46506

Bacteroides stercoris

98.84
232

FBI00233

Ruminococcaceae sp.

bacteria

firmicutes
474960

Anaerotruncus

91.63
233

FBI00233

colihominis

FBI00234

Faecalicatena contorta

bacteria

firmicutes
39482

Faecalicatena contorta

99.21
234

FBI00235

Alistipes shahii

bacteria

bacteroidetes
328814

Alistipes shahii

99.86
235

FBI00236

Eisenbergiella tayi

bacteria

firmicutes
1432052

Eisenbergiella tayi

99.41
236

FBI00237

Dielma fastidiosa

bacteria

firmicutes
1034346

Dielma fastidiosa

99.78
237

FBI00238

Alistipes sp. FBI00238

bacteria

bacteroidetes
239759

Alistipes finegoldii

95.84
238

FBI00239

Lactonifactor longoviformis

bacteria

firmicutes
341220

Lactonifactor

98.99
239

longoviformis

FBI00240

Clostridium citroniae

bacteria

firmicutes
358743

Clostridium citroniae

99.57
240

FBI00241

Collinsella aerofaciens

bacteria

actinobacteria
74426

Collinsella aerofaciens

99.34
241

FBI00242

Clostridium aldenense

bacteria

firmicutes
358742

Clostridium aldenense

99.05
242

FBI00243

Eubacterium siraeum

bacteria

firmicutes
39492

Eubacterium siraeum

98.53
243

FBI00244

Faecalibacterium prausnitzii

bacteria

firmicutes
853

Faecalibacterium

98.69
244

prausnitzii

FBI00245

Acidaminococcus intestini

bacteria

firmicutes
187327

Acidaminococcus

99.72
245

intestini

FBI00246

Bifidobacterium longum

bacteria

actinobacteria
216816

Bifidobacterium longum

99.7
246

FBI00247

Phascolarctobacterium

bacteria

firmicutes
33025

Phascolarctobacterium

99.79
247

faecium

faecium

FBI00248

Neglecta timonensis

bacteria

firmicutes
1776382

Emergencia timonensis

99.64
248

FBI00249

Citrobacter portucalensis

bacteria

proteobacteria
1639133

Citrobacter freundii

99.79
249

FBI00250

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium faecale

99.24
250

FBI00251

Bifidobacterium

bacteria

actinobacteria
28026

Bifidobacterium

99.85
251

pseudocatenulatum

pseudocatenulatum

FBI00252

Oscillibacter sp. FBI00028

bacteria

firmicutes
459786

Oscillibacter

95.79
252

ruminantium

FBI00253

Roseburia hominis

bacteria

firmicutes
301301

Roseburia hominis

99.71
253

FBI00254

Eubacterium hallii

bacteria

firmicutes
39488

Eubacterium hallii

99.08
254

FBI00255

Hungatella effluvii

bacteria

firmicutes
1096246

Hungatella hathewayi

98.56
255

FBI00256

Blautia faecis

bacteria

firmicutes
871665

Blautia faecis

97.86
256

FBI00257

Eubacterium eligens

bacteria

firmicutes
39485

Eubacterium eligens

99.28
257

FBI00258

Turicibacter sanguinis

bacteria

firmicutes
154288

Turicibacter sanguinis

99.93
258

FBI00259

Dorea longicatena

bacteria

firmicutes
88431

Dorea longicatena

99.7
259

FBI00260

Eubacterium rectale

bacteria

firmicutes
39491

Eubacterium rectale

99.64
260

FBI00261

Bacteroides uniformis

bacteria

bacteroidetes
820

Bacteroides uniformis

99.21
261

FBI00262

Bacteroides massiliensis

bacteria

bacteroidetes
204516

Bacteroides massiliensis

99.71
262

FBI00263

Bacteroides caccae

bacteria

bacteroidetes
47678

Bacteroides caccae

99.56
263

FBI00264

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium faecale

99.2
264

FBI00265

Bacteroides cellulosilyticus

bacteria

bacteroidetes
246787

Bacteroides

99.21
265

cellulosilyticus

FBI00266

Coprococcus eutactus

bacteria

firmicutes
33043

Coprococcus eutactus

99.2
266

FBI00267

Anaerofustis stercorihominis

bacteria

firmicutes
214853

Anaerofustis

97.29
267

stercorihominis

FBI00268

Clostridiales sp. FBI00268

bacteria

firmicutes
186802

Catabacter

86.05
268

hongkongensis

FBI00269

Alistipes putredinis

bacteria

bacteroidetes
28117

Alistipes putredinis

100
269

FBI00270

Methanobrevibacter smithii

archaea

euryarchaeota
2173

Methanobrevibacter

99.69
270

smithii

FBI00271

Bacteroides xylanisolvens

bacteria

bacteroidetes
371601

Bacteroides

98.42
271

xylanisolvens

FBI00272

Clostridiales XIII sp.

bacteria

firmicutes
543314

Anaerovorax

93.12
272

FBI00272

odorimutans

FBI00273

Barnesiella intestinihominis

bacteria

bacteroidetes
487174

Barnesiella

99.43
273

intestinihominis

FBI00274

Eubacterium xylanophilum

bacteria

firmicutes
39497

Eubacterium

93.5
274

xylanophilum

FBI00275

Holdemanella biformis

bacteria

firmicutes
1735

Holdemanella biformis

98.99
275

FBI00276

Dorea formicigenerans

bacteria

firmicutes
39486

Dorea formicigenerans

98.19
276

FBI00277

Alistipes onderdonkii

bacteria

bacteroidetes
328813

Alistipes onderdonkii

99.63
277

FBI00278

Eubacterium ventriosum

bacteria

firmicutes
39496

Eubacterium ventriosum

94.14
278

FBI00279

Coprococcus comes

bacteria

firmicutes
410072

Coprococcus comes

98.48
279

FBI00280

Bacteroides thetaiotaomicron

bacteria

bacteroidetes
818

Bacteroides

100
280

thetaiotaomicron

FBI00281

Senegalimassilia anaerobia

bacteria

actinobacteria
1473216

Senegalimassilia

99.45
281

anaerobia

FBI00282

Porphyromonas

bacteria

bacteroidetes
28123

Porphyromonas

99.35
282

asaccharolytica

asaccharolytica

FBI00283

Ruminococcus bromii

bacteria

firmicutes
40518

Ruminococcus bromii

96.02
283

FBI00284

Blautia obeum

bacteria

firmicutes
40520

Blautia obeum

98.67
284

FBI00285

Lachnospira sp. FBI00063

bacteria

firmicutes
28050

Lactobacillus rogosae

95.3
285

FBI00285 FBI00364

FBI00286

Fusicatenibacter

bacteria

firmicutes
1150298

Fusicatenibacter

96.32
286

saccharivorans

saccharivorans

FBI00287

Alistipes shahii

bacteria

bacteroidetes
328814

Alistipes shahii

98.47
287

FBI00288

Blautia hydrogenotrophica

bacteria

firmicutes
53443

Blautia

99.57
288

hydrogenotrophica

FBI00289

Oxalobacter formigenes

bacteria

proteobacteria
847

Oxalobacter formigenes

99.21
289

FBI00290

Lachnospiraceae sp.

bacteria

firmicutes
186803

Eubacterium

94.81
290

FBI00290

ruminantium

FBI00291

Oribacterium sp. FBI00291

bacteria

firmicutes
265975

Lactobacillus rogosae

91.63
291

FBI00292

Methanobrevibacter smithii

archaea

euryarchaeota
2173

Methanobrevibacter

99.44
292

smithii

FBI00293

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium

98.77
293

adolescentis

FBI00294

Bacteroides stercoris

bacteria

bacteroidetes
46506

Bacteroides stercoris

99.35
294

FBI00295

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium

98.48
295

adolescentis

FBI00296

Dorea longicatena

bacteria

firmicutes
88431

Dorea longicatena

99.21
296

FBI00297

Alistipes obesi

bacteria

bacteroidetes
2585118

Alistipes obesi

99.49
297

FBI00298

Faecalibacterium prausnitzii

bacteria

firmicutes
853

Faecalibacterium

97.24
298

prausnitzii

FBI00299

Streptococcus pasteurianus

bacteria

firmicutes
197614

Streptococcus

100
299

pasteurianus

FBI00300

Collinsella aerofaciens

bacteria

actinobacteria
74426

Collinsella aerofaciens

99.49
300

FBI00301

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium

98.64
301

adolescentis

FBI00302

Blautia faecis

bacteria

firmicutes
871665

Blautia faecis

99.6
302

FBI00303

Parabacteroides merdae

bacteria

bacteroidetes
46503

Parabacteroides merdae

98.78
303

FBI00304

Dorea longicatena

bacteria

firmicutes
88431

Dorea longicatena

99.7
304

FBI00305

Alistipes onderdonkii

bacteria

bacteroidetes
328813

Alistipes onderdonkii

99.85
305

FBI00306

Parasutterella

bacteria

proteobacteria
487175

Parasutterella

98.53
306

excrementihominis

excrementihominis

FBI00307

Parasutterella

bacteria

proteobacteria
487175

Parasutterella

98.53
307

excrementihominis

excrementihominis

FBI00308

Bacteroides vulgatus

bacteria

bacteroidetes
821

Bacteroides vulgatus

99.64
308

FBI00309

Eubacterium rectale

bacteria

firmicutes
39491

Eubacterium rectale

99.71
309

FBI00310

Butyricimonas faecihominis

bacteria

bacteroidetes
1472416

Butyricimonas

99.13
310

faecihominis

FBI00311

Anaerostipes hadrus

bacteria

firmicutes
649756

Anaerostipes hadrus

99.07
311

FBI00312

Alistipes shahii

bacteria

bacteroidetes
328814

Alistipes shahii

99.35
312

FBI00313

Collinsella aerofaciens

bacteria

actinobacteria
74426

Collinsella aerofaciens

99.56
313

FBI00314

Anaerotignum

bacteria

firmicutes
160404

Anaerotignum

99.57
314

lactatifermentans

lactatifermentans

FBI00315

Blautia obeum

bacteria

firmicutes
40520

Blautia obeum

98.82
315

FBI00316

Collinsella aerofaciens

bacteria

actinobacteria
74426

Collinsella aerofaciens

99.26
316

FBI00317

Bifidobacterium longum

bacteria

actinobacteria
216816

Bifidobacterium longum

99.49
317

FBI00318

Collinsella aerofaciens

bacteria

actinobacteria
74426

Collinsella aerofaciens

99.41
318

FBI00319

Collinsella aerofaciens

bacteria

actinobacteria
74426

Collinsella aerofaciens

99.56
319

FBI00320

Dorea formicigenerans

bacteria

firmicutes
39486

Dorea formicigenerans

98.13
320

FBI00321

Bacteroides vulgatus

bacteria

bacteroidetes
821

Bacteroides vulgatus

97.63
321

FBI00322

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium

98.7
322

adolescentis

FBI00323

Blautia wexlerae

bacteria

firmicutes
418240

Blautia wexlerae

99.28
323

FBI00324

Bilophila wadsworthia

bacteria

proteobacteria
35833

Desulfovibrio

91.52
324

desulfuricans

FBI00325

Alistipes indistinctus

bacteria

bacteroidetes
626932

Alistipes indistinctus

99.93
325

FBI00326

Bacteroides vulgatus

bacteria

bacteroidetes
821

Bacteroides vulgatus

98.63
326

FBI00327

Coprococcus comes

bacteria

firmicutes
410072

Coprococcus comes

99.34
327

FBI00328

Blautia luti

bacteria

firmicutes
89014

Blautia luti

97.78
328

FBI00329

Alistipes indistinctus

bacteria

bacteroidetes
626932

Alistipes indistinctus

99.93
329

FBI00330

Bifidobacterium longum

bacteria

actinobacteria
216816

Bifidobacterium longum

99.28
330

FBI00331

Bacillus circulans

bacteria

firmicutes
1397

Bacillus circulans

96.84
331

FBI00332

Clostridium intestinale

bacteria

firmicutes
36845

Clostridium intestinale

99.13
332

FBI00333

Alistipes onderdonkii

bacteria

bacteroidetes
328813

Alistipes onderdonkii

99.93
333

FBI00334

Bacteroides caccae

bacteria

bacteroidetes
47678

Bacteroides caccae

99.56
334

FBI00335

Anaerostipes hadrus

bacteria

firmicutes
649756

Anaerostipes hadrus

99.64
335

FBI00336

Staphylococcus epidermidis

bacteria

firmicutes
1282

Staphylococcus

99.93
336

epidermidis

FBI00337

Coprococcus comes

bacteria

firmicutes
410072

Coprococcus comes

99.21
337

FBI00338

Blautia obeum

bacteria

firmicutes
40520

Blautia obeum

97.75
338

FBI00339

Eubacterium rectale

bacteria

firmicutes
39491

Eubacterium rectale

99.86
339

FBI00340

Lachnospiraceae sp.

bacteria

firmicutes
186803

Clostridium

93.57
340

FBI00033

amygdalinum

FBI00341

Lachnospiraceae sp.

bacteria

firmicutes
186803

Roseburia faecis

95.06
341

FBI00071

FBI00342

Alistipes indistinctus

bacteria

bacteroidetes
626932

Alistipes indistinctus

100
342

FBI00343

Sutterella massiliensis

bacteria

proteobacteria
1816689

Sutterella massiliensis

99.86
343

FBI00344

Alistipes putredinis

bacteria

bacteroidetes
28117

Alistipes putredinis

99.93
344

FBI00345

Roseburia inulinivorans

bacteria

firmicutes
360807

Roseburia inulinivorans

97.35
345

FBI00346

Coriobacteriia sp. FBI00346

bacteria

actinobacteria
84998

Paraeggerthella

93.84
346

hongkongensis

FBI00347

Bacteroides uniformis

bacteria

bacteroidetes
820

Bacteroides uniformis

99.85
347

FBI00348

Parabacteroides merdae

bacteria

bacteroidetes
46503

Parabacteroides merdae

99.93
348

FBI00349

Holdemanella biformis

bacteria

firmicutes
1735

Holdemanella biformis

98.14
349

FBI00350

Alistipes putredinis

bacteria

bacteroidetes
28117

Alistipes putredinis

100
350

FBI00351

Alistipes obesi

bacteria

bacteroidetes
2585118

Alistipes obesi

99.78
351

FBI00352

Collinsella aerofaciens

bacteria

actinobacteria
74426

Collinsella aerofaciens

99.56
352

FBI00353

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium

98.85
353

adolescentis

FBI00354

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium

98.7
354

stercoris

FBI00355

Blautia massiliensis

bacteria

firmicutes
1737424

Blautia luti

98.09
355

FBI00356

Eubacterium eligens

bacteria

firmicutes
39485

Eubacterium eligens

98.5
356

FBI00357

Bacteroides kribbi/

bacteria

bacteroidetes
816

Bacteroides koreensis

99.71
357

Bacteroides koreensis species

cluster

FBI00358

Eubacterium hallii

bacteria

firmicutes
39488

Eubacterium hallii

98.26
358

FBI00359

Eubacterium rectale

bacteria

firmicutes
39491

Eubacterium rectale

99.79
359

FBI00360

Bacteroides massiliensis

bacteria

bacteroidetes
204516

Bacteroides massiliensis

99.93
360

FBI00361

Bacteroides stercoris

bacteria

bacteroidetes
46506

Bacteroides stercoris

99.36
361

FBI00362

Prevotella copri

bacteria

bacteroidetes
165179

Prevotella copri

98.5
362

FBI00363

Roseburia intestinalis

bacteria

firmicutes
166486

Roseburia intestinalis

99.78
363

FBI00364

Lachnospira sp. FBI00063

bacteria

firmicutes
28050

Lactobacillus rogosae

95.2
364

FBI00285 FBI00364

FBI00365

Paraprevotella clara

bacteria

bacteroidetes
454154

Paraprevotella clara

98.78
365

FBI00366

Eubacterium eligens

bacteria

firmicutes
39485

Eubacterium eligens

99
366

FBI00367

Phascolarctobacterium

bacteria

firmicutes
33025

Phascolarctobacterium

99.58
367

faecium

faecium

FBI00368

Alistipes putredinis

bacteria

bacteroidetes
28117

Alistipes putredinis

99.86
368

FBI00369

Clostridiales sp. FBI00369

bacteria

firmicutes
186802

Catabacter

86
369

hongkongensis

FBI00370

Bifidobacterium adolescentis

bacteria

actinobacteria
1680

Bifidobacterium

97.11
370

adolescentis

FBI00371

Bacteroides stercoris

bacteria

bacteroidetes
46506

Bacteroides stercoris

99.21
371

FBI00372

Dorea longicatena

bacteria

firmicutes
88431

Dorea longicatena

99.7
372

FBI00373

Coriobacteriaceae sp.

bacteria

actinobacteria
84107

Parolsenella catena

96.58
373

FBI00373 FBI00374

FBI00374

Coriobacteriaceae sp.

bacteria

actinobacteria
84107

Parolsenella catena

97.11
374

FBI00373 FBI00374

FBI00375

Dorea longicatena

bacteria

firmicutes
88431

Dorea longicatena

99.62
375

FBI00376

Dialister succinatiphilus

bacteria

firmicutes
487173

Dialister succinatiphilus

95.82
376

FBI00377

Clostridiales sp. FBI00377

bacteria

firmicutes
186802

Christensenella

88.69
377

massiliensis

TABLE 5

Commercial Oxalate-metabolizing strains

Bifidobacterium dentium ATCC 27678

Bifidobacterium dentium ATCC 27680

Bifidobacterium dentium DSM 20221

Bifidobacterium dentium DSM 20436

Bifidobacterium sp. HM-868

Dialister invisus DSM 15470

Eggerthella lenta ATCC 43055

Eggerthella lenta DSM 2243

Enterococcus faecalis HM-202

Enterococcus faecalis HM-432

Lactobacillus acidophilus ATCC 4357

Lactobacillus acidophilus DSM 20079

Lactobacillus acidophilus DSM 20242

Lactobacillus gasseri ATCC 33323

Lactobacillus gasseri DSMZ 107525

Lactobacillus gasseri DSMZ 20077

Lactobacillus gasseri HM-104

Lactobacillus gasseri HM-644

Lactobacillus helveticus DSM 20075

Lactobacillus reuteri HM-102

Lactobacillus rhamnosus ATCC 53103

Lactobacillus rhamnosus DSM 20245

Lactobacillus rhamnosus DSM 8746

Lactobacillus rhamnosus HM-106

Oxalobacter formigenes ATCC 35274

Oxalobacter formigenes DSM 4420

Oxalobacter formigenes HM-1

TABLE 6

Commercial Supportive strains

Absiella dolichum DSM 3991

Acidaminococcus fermentans DSM 20731

Acidaminococcus sp. HM-81

Adlercreutzia equolifaciens DSM 19450

Akkermansia muciniphila ATCC BAA-835

Alistipes finegoldii DSM 17242

Alistipes indistinctus DSM 22520

Alistipes onderdonkii DSM 19147

Alistipes putredinis DSM 17216

Alistipes senegalensis DSM 25460

Alistipes shahii DSM 19121

Anaerobutyricum hallii DSM 3353

Anaerococcus lactolyticus DSM 7456

Anaerofustis stercorihominis DSM 17244

Anaerostipes caccae DSM 14662

Anaerotruncus colihominis DSM 17241

Bacteroides caccae ATCC 43185

Bacteroides caccae HM-728

Bacteroides cellulosilyticus DSM 14838

Bacteroides cellulosilyticus HM-726

Bacteroides coprocola DSM 17136

Bacteroides coprophilus DSM 18228

Bacteroides dorei DSM 17855

Bacteroides dorei HM-29

Bacteroides dorei HM-718

Bacteroides eggerthii DSM 20697

Bacteroides eggerthii HM-210

Bacteroides finegoldii DSM 17565

Bacteroides finegoldii HM-727

Bacteroides fragilis HM-20

Bacteroides fragilis HM-709

Bacteroides fragilis HM-710

Bacteroides intestinalis DSM 17393

Bacteroides ovatus ATCC 8483

Bacteroides ovatus HM-222

Bacteroides pectinophilus ATCC 43243

Bacteroides plebeius DSM 17135

Bacteroides rodentium DSM 26882

Bacteroides salyersiae HM-725

Bacteroides sp. HM-18

Bacteroides sp. HM-19

Bacteroides sp. HM-23

Bacteroides sp. HM-27

Bacteroides sp. HM-28

Bacteroides sp. HM-58

Bacteroides stercoris DSM 19555

Bacteroides stercoris HM-1036

Bacteroides thetaiotaomicron ATCC 29148

Bacteroides uniformis ATCC 8492

Bacteroides vulgatus ATCC 8482

Bacteroides vulgatus HM-720

Bacteroides xylanisolvens DSM 18836

Bifidobacterium adolescentis HM-633

Bifidobacterium angulatum HM-1189

Bifidobacterium animalis DSM 20104

Bifidobacterium animalis subsp. Lactis DSMZ 10140

Bifidobacterium bifidum ATCC 11863

Bifidobacterium breve DSM 20213

Bifidobacterium catenulatum DSM 16992

Bifidobacterium longum infantis ATCC 55813

Bifidobacterium longum subsp. longum HM-845

Bifidobacterium longum subsp. longum HM-846

Bifidobacterium longum subsp. longum HM-847

Bifidobacterium longum subsp. longum HM-848

Bifidobacterium pseudocatenulatum DSM 20438

Bilophila wadsworthia ATCC 49260

Bilophila wadsworthia DSM 11045

Blautia hansenii DSM 20583

Blautia hydrogenotrophica DSM 10507

Blautia obeum DSMZ 25238

Blautia sp. HM-1032

Blautia wexlerae DSM 19850

Butyricimonas virosa DSM 23226

Butyrivibrio crossotus DSM 2876

Catenibacterium mitsuokai DSM 15897

Cetobacterium somerae DSM 23941

Clostridium asparagiforme DSM 15981

Clostridium bolteae DSM 15670

Clostridium bolteae HM-1038

Clostridium bolteae HM-318

Clostridium cadaveris HM-1040

Clostridium citroniae HM-315

Clostridium hiranonis DSM 13275

Clostridium hylemonae DSM 15053

Clostridium innocuum HM-173

Clostridium leptum DSM 753

Clostridium methylpentosum DSM 5476

Clostridium saccharolyticum DSM 2544

Clostridium scindens DSM 5676

Clostridium scindens VPI 12708

Clostridium sp. ATCC 29733

Clostridium sp. DSM 4029

Clostridium sp. HM-634

Clostridium sp. HM-635

Clostridium spiroforme DSM 1552

Clostridium sporogenes ATCC 15579

Clostridium sporogenes ATCC 17889

Clostridium sporogenes DSM 767

Clostridium symbiosum HM-309

Clostridium symbiosum HM-319

Collinsella aerofaciens ATCC 25986

Collinsella stercoris DSM 13279

Coprococcus catus ATCC 27761

Coprococcus comes ATCC 27758

Coprococcus eutactus ATCC 27759

Coprococcus eutactus ATCC 51897

Coprococcus sp. DSM 21649

Desulfovibrio piger ATCC 29098

Dialister pneumosintes ATCC 51894

Dorea formicigenerans ATCC 27755

Dorea longicatena DSM 13814

Eggerthella sp. DSM 11767

Eggerthella sp. DSM 11863

Eggerthella sp. HM-1099

Ethanoligenens harbinense DSM 18485

Eubacterium eligens ATCC 27750

Eubacterium rectale ATCC 33656

Eubacterium siraeum DSM 15702

Eubacterium ventriosum ATCC 27560

Faecalibacterium prausnitzii ATCC 27766

Faecalibacterium prausnitzii ATCC 27768

Faecalibacterium prausnitzii DSM 17677

Faecalibacterium prausnitzii HM-473

Flavonifractor plautii HM-1044

Flavonifractor plautii HM-303

Granulicatella adiacens ATCC 49175

Holdemanella biformis DSM 3989

Holdemania filiformis DSM 12042

Hungatella (prev. Clostridium) hathewayi HM-308

Hungatella hathewayi DSM 13479

Intestinibacter bartlettii DSM 16795

Intestinimonas butyriciproducens DSM 26588

Lactobacillus amylovorus DSM 20552

Lactobacillus casei subsp. casei ATCC 393

Lactobacillus casei subsp. casei ATCC 39539

Lactobacillus crispatus HM-370

Lactobacillus johnsonii HM-643

Lactobacillus parafarraginis HM-478

Lactobacillus plantarum ATCC 14917

Lactobacillus plantarum ATCC 202195

Lactobacillus ruminis ATCC 25644

Lactobacillus ruminis DSM 20404

Lactobacillus ultunensis DSM 16048

Lactococcus lactis Berridge DSM 20729

Marvinbryantia formatexigens DSM 14469

Megasphaera indica DSM 25562

Megasphaera sp. DSM 102144

Methanobrevibacter smithii DSM 11975

Methanobrevibacter smithii DSM 2374

Methanobrevibacter smithii DSM 2375

Methanobrevibacter smithii DSM 861

Methanomassiliicoccus luminyensis DSM 25720

Methanosphaera stadtmanae DSMZ 3091

Mitsuokella multacida DSM 20544

Odoribacter splanchnicus DSM 20712

Olsenella uli DSM 7084

Oscillibacter sp. HM-1030

Parabacteroides distasonis ATCC 8503

Parabacteroides goldsteinii HM-1050

Parabacteroides johnsonii DSM 18315

Parabacteroides johnsonii HM-731

Parabacteroides merdae DSM 19495

Parabacteroides merdae HM-729

Parabacteroides merdae HM-730

Parabacteroides sp. HM-77

Peptostreptococcus anaerobius DSM 2949

Prevotella buccae HM-45

Prevotella buccalis DSM 20616

Prevotella copri DSM 18205

Proteocatella sphenisci DSM 23131

Providencia rettgeri ATCC BAA-2525

Roseburia intestinalis DSM 14610

Roseburia inulinivorans DSM 16841

Ruminococcaceae sp. HM-79

Ruminococcus albus ATCC 27210

Ruminococcus bromii ATCC 27255

Ruminococcus bromii ATCC 51896

Ruminococcus gauvreauii DSM 19829

Ruminococcus gnavus ATCC 29149

Ruminococcus gnavus DSM 108212

Ruminococcus gnavus HM-1056

Ruminococcus lactaris ATCC 29176

Ruminococcus lactaris HM-1057

Ruminococcus torques ATCC 27756

Slackia exigua DSM 15923

Slackia heliotrinireducens DSM 20476

Solobacterium moorei DSM 22971

Streptococcus salivarius subsp. thermophilus ATCC BAA-491

Streptococcus thermophilus ATCC 14485

Subdoligranulum variabile DSM 15176

Turicibacter sanguinis DSM 14220

Tyzzerella nexilis DSM 1787

Veillonella dispar ATCC 17748

Veillonella sp. HM-49

Veillonella sp. HM-64

Example 2: Commercial Microbial Strain Sensitivities to Oxalate Concentration

To determine the effect of the presence of oxalate on growth of commercial microbial strains, cultures were grown in their respective banking media (e.g., Mega Media, or Chopped Meat Media) to saturation and back-diluted into the same respective banking media containing no oxalate, 0.5% oxalate, or 0.125% oxalate. FIG. 1 shows % growth inhibition of microbial strains in the presence of 0.5% oxalate (closed bars) or 0.125% oxalate (open bars). % growth inhibition was calculated by determining the ratio of background-subtracted optical density (O.D.) of a microbial strain in the presence of oxalate to the O.D. of the same microbial strain grown in the absence of oxalate.

Example 3: In Vitro Oxalate Metabolization by Commercial Microbial Strains

48-well deep well plates were filled with 2.5 mL of banking media per commercial microbial strain, per condition. Potassium oxalate was added to achieve final oxalate concentrations of 7.5 mM or 750 μM. 50 μl of each microbial strain in banking media was added to the appropriate well and mixed by trituration. 1 mL of each sample was transferred to an appropriate well of a 96-well collection plate containing 25 μl of 6N HCl and mixed by trituration. The collection plate was covered and incubated at 37° C. for 0, 24, or 72 hours under anaerobic conditions.

The oxalate metabolizing activity of the microbial strains was measured using a commercial colorimetric enzyme kit (Sigma Aldrich Oxalate Assay kit, Catalog No. MAK315) in accordance with the manufacturer's instructions.

In brief, acidified microbial suspensions were centrifuged for 1 minute at >10,000×g to pellet intact cells and cellular debris. 10 μl of sample supernatant was transferred into each of three separate wells of a multiwell plate designated as a “Sample Blank,” “Sample,” or “Internal Standard.” 10 μl of dH₂O was added to Sample Blank and Sample wells, and 10 μl of oxalate standard was added to the Internal Standard well. Blank reagent was prepared for all Sample Blank wells by mixing 155 μl of Reagent B and 1 μl of Horseradish peroxidase (“HRP”) enzyme per Sample Blank well. 157 μl of Working Reagent (155 μl of Reagent B, 1 μl of oxalate oxidase enzyme, and 1 μl of HRP) was prepared for each Sample and Internal Standard well. 150 μl of Blank Reagent was added to each Sample Blank well and 150 μl of Working Reagent was added to each Sample and Internal Standard Well. Solutions were mixed and incubated for 10 minutes at room temperature. Following incubation, optical density was measured for each sample well at 595 nm using a BioTek Epoch 2 plate reader. Sample and Internal Standard values were corrected by subtracting the measured OD₅₉₅of the Sample Blank well from the measured OD₅₉₅of the Sample and Internal Standard wells. The proportion of oxalate remaining in each sample after 24 or 72 hour incubation was determined by dividing the corrected OD₅₉₅value from the Sample well for the initial timepoint (i.e., t=0 hours).

FIG. 2 shows % oxalate remaining in microbial strain cultures in Mega Media (FIG. 2A) or Chopped Meat Media (FIG. 2B) seeded with 7.5 mM oxalate (closed bars) or 750 μM oxalate (open bars) after 72 hours incubation at 37° C. under anaerobic conditions.

In Vitro Oxalate Metabolizing Activities of Microbial Strains Cultured Under Different pH

To determine the effect of pH on oxalate metabolization, the in vitro oxalate metabolization assay as described above was performed at an oxalate concentration of 7.5 mM, in culture media at pH 7.2 or adjusted to pH 4.5 with NaOH.

FIG. 3 shows % oxalate remaining in microbial strain cultures in Mega Media (FIG. 3A) or Chopped Meat Media (FIG. 3B) seeded with 7.5 mM oxalate at pH 4.5 (closed bars) or pH 7.2 (open bars) after 72 hours incubation at 37° C. under anaerobic conditions.

In Vitro Oxalate-Metabolizing Activity of Microbial Consortia

To determine the oxalate-metabolizing activity of a microbial consortium, the in vitro oxalate metabolization assay was performed at an oxalate concentration of 7.5 mM.

FIG. 4 shows the Absorbance (595 nm) of cultures comprising O. formigenes only, active microbial strains only, supportive microbial strains only, or a complete microbial consortium (i.e. both active and supportive microbial strains) in Mega Media (FIG. 4A) or Chopped Meat Media (FIG. 4B) at the time of oxalate addition (t=0, closed bars) or after 72 hours (open bars).

Example 4: Oxalate Analysis by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS)

In order to quantify oxalate levels in incubation medium, an aliquot of medium was transferred to a polypropylene tube containing 60 μL of 6N HCl/ml medium, vortex mixed, snap frozen, and then stored at −70° C. On the day of analysis, samples were thawed and vortexed to mix, and then 50 μL of media or media diluted with 0.1% formic acid were transferred with mixing to a polypropylene tube containing 20 μL of internal standard (1 mM ¹³C₂-oxalate in 0.1% formic acid) and vortex mixed. A 500 μL aliquot of 2% formic acid was added and vortex mixed. The entire sample was passed through a conditioned Strata-X-AW solid phase extraction plate (Phenomenex, 10 mg, 8E-S038-AGB), washed, and then eluted with 5% ammonium hydroxide in methanol. The eluent was then dried under nitrogen gas, re-constituted in 0.1% formic acid, and then placed on an API6500 autosampler and 5 μL were injected into a 2.1×50 mm Waters XBridge HILIC 3.5 μm particle size column. LC-MS/MS parameters were as indicated in Table 7.

In order to quantify oxalate levels in urine, urine samples were collected and immediately snap frozen and stored at −70° C. On the day of analysis, samples were thawed and vortexed, and then 50 μL of urine or urine diluted with 0.1% formic acid was transferred with mixing to a polypropylene tube containing 20 μL of internal standard (1 mM ¹³C₂-oxalate+5 mM ²H₃-creatinine in 0.1% formic acid) and vortex mixed. A 500 μL aliquot of 2% formic acid was added and vortex mixed. The entire sample was passed through a conditioned Strata-X-AW solid phase extraction plate (Phenomenex, 10 mg, 8E-5038-AGB), washed, and then eluted with 5% ammonium hydroxide in methanol. The eluent was then dried under nitrogen gas, re-constituted in 0.1% formic acid, and then placed on an API6500 autosampler and 5 μL were injected into a 2.1×50 mm Waters XBridge HILIC 3.5 μm particle size column. LC-MS/MS parameters were as indicated in Table 7.

TABLE 7

Time (min)
% Eluent B

Initial
89.5

1
89.5

2.5
0

4.20
0

4.21
89.5

6.69
89.5

6.70
End

Eluent A: 95:5 20 mM Ammonium Acetate pH 8:Acetonitrile

Eluent B: Acetonitrile

Autosampler Wash: 50% methanol

Flow rate: 500 μL/min

Column temperature: 50° C.

Divert output to waste from initial to 1.5 min and after 4.5 min

Example 5: In Vivo Oxalate Metabolization in Balb/c Male Mice Treated with a Microbial Consortium Containing Commercial Strains of Microbes

This example describes a study testing the ability of a microbial consortium, containing commercial strains of microbes, to degrade oxalate in vivo in Balb/c male mice.

To determine the in vivo oxalate degrading activity of a microbial consortium described herein, 30 gnotobiotic (n=3 per condition) Balb/c male mice were weighed on Day 0 and colonized by oral gavage with either a plurality of active microbes alone, a supportive community alone, O. formigenes alone, or a complete microbial consortium (active and supportives). The plurality of active microbes and the supportive community of microbes contained the strains in Table 8 marked with an ‘X’ in the indicated column. Colonized mice were fed either a defined, low-complexity diet supplemented with excess oxalate in order to induce hyperoxaluria (see Table 2 above) or a nutritionally equivalent control diet lacking oxalate (see Table 1 above).

After a two-week period, mice were sacrificed and a variety of samples were collected including terminal urine, feces, serum, kidneys, liver, gall bladder, cecum and spleen.

TABLE 8

Catalog
Active or
Examples 5 and 8
Examples 6, 7, 12, 13, 14

Species
Number
Supportive
Active
Supportive
Active
Supportive

Acidaminococcus fermentans

DSM 20731
Supportive

X

Acidaminococcus intestini

HM-81
Supportive

X

X

Adlercreutzia equolifaciens

DSM 19450
Supportive

X

X

Akkermansia muciniphila

ATCC BAA-835
Supportive

X

X

Alistipes finegoldii

DSM 17242
Supportive

X

X

Alistipes indistinctus

DSM 22520
Supportive

X

X

Alistipes onderdonkii

DSM 19147
Supportive

X

X

Alistipes putredinis

DSM 17216
Supportive

X

Alistipes senegalensis

DSM 25460
Supportive

X

X

Alistipes shahii

DSM 19121
Supportive

X

X

Anaerobutyricum hallii

DSM 3353
Supportive

X

Anaerococcus lactolyticus

DSM 7456
Supportive

Anaerofustis stercorihominis

DSM 17244
Supportive

X

Anaerostipes caccae

DSM 14662
Supportive

X

X

Anaerotruncus colihominis

DSM 17241
Supportive

X

X

Bacteroides caccae

ATCC 43185
Supportive

X

X

Bacteroides caccae

HM-728
Supportive

Bacteroides cellulosilyticus

DSM 14838
Supportive

X

X

Bacteroides cellulosilyticus

HM-726
Supportive

Bacteroides coprocola

DSM 17136
Supportive

X

X

Bacteroides coprophilus

DSM 18228
Supportive

X

X

Bacteroides dorei

DSM 17855
Supportive

X

X

Bacteroides dorei

HM-27
Supportive

X

X

Bacteroides dorei

HM-29
Supportive

X

X

Bacteroides dorei

HM-718
Supportive

Bacteroides eggerthii

DSM 20697
Supportive

X

X

Bacteroides eggerthii

HM-210
Supportive

Bacteroides finegoldii

DSM 17565
Supportive

X

X

Bacteroides finegoldii

HM-727
Supportive

Bacteroides fragilis

HM-20
Supportive

X

X

Bacteroides fragilis

HM-58
Supportive

X

X

Bacteroides fragilis

HM-709
Supportive

Bacteroides fragilis

HM-710
Supportive

Bacteroides intestinalis

DSM 17393
Supportive

X

X

Bacteroides ovatus

ATCC 8483
Supportive

X

X

Bacteroides ovatus

HM-222
Supportive

Bacteroides pectinophilus

ATCC 43243
Supportive

X

Bacteroides plebeius

DSM 17135
Supportive

X

Bacteroides rodentium

DSM 26882
Supportive

X

X

Bacteroides salyersiae

HM-725
Supportive

Bacteroides sp.
HM-28
Supportive

X

X

Bacteroides stercoris

DSM 19555
Supportive

X

X

Bacteroides stercoris

HM-1036
Supportive

Bacteroides thetaiotaomicron

ATCC 29148
Supportive

X

X

Bacteroides thetaiotaomicron

HM-23
Supportive

X

Bacteroides uniformis

ATCC 8492
Supportive

X

X

Bacteroides vulgatus

ATCC 8482
Supportive

X

X

Bacteroides vulgatus

HM-720
Supportive

Bacteroides xylanisolvens

DSM 18836
Supportive

X

X

Bacteroides xylanisolvens

HM-18
Supportive

X

X

Bifidobacterium adolescentis

HM-633
Supportive

Bifidobacterium angulatum

HM-1189
Supportive

Bifidobacterium animalis

DSM 20104
Supportive

Bifidobacterium animalis

DSMZ 10140
Supportive

Bifidobacterium bifidum

ATCC 11863
Supportive

Bifidobacterium breve

DSM 20213
Supportive

X

X

Bifidobacterium catenulatum

DSM 16992
Supportive

X

X

Bifidobacterium dentium

ATCC 27678
Active
X

X

Bifidobacterium dentium

ATCC 27680
Active
X

X

Bifidobacterium dentium

DSM 20221
Active
X

X

Bifidobacterium dentium

DSM 20436
Active
X

X

Bifidobacterium dentium

HM-868
Active
X

X

Bifidobacterium infantis

ATCC 55813
Supportive

Bifidobacterium longum

HM-845
Supportive

Bifidobacterium longum

HM-846
Supportive

Bifidobacterium longum

HM-847
Supportive

Bifidobacterium longum

HM-848
Supportive

Bifidobacterium pseudocatenulatum

DSM 20438
Supportive

X

X

Bilophila wadsworthia

ATCC 49260
Supportive

X

X

Bilophila wadsworthia

DSM 11045
Supportive

Bittarella massiliensis

ATCC 29733
Supportive

X

X

Bittarella massiliensis

DSM 4029
Supportive

Blautia hansenii

DSM 20583
Supportive

X

X

Blautia hydrogenotrophica

DSM 10507
Supportive

X

Blautia massiliensis

HM-1032
Supportive

X

X

Blautia obeum

DSMZ 25238
Supportive

X

X

Blautia wexlerae

DSM 19850
Supportive

X

Butyricimonas virosa

DSM 23226
Supportive

X

X

Butyrivibrio crossotus

DSM 2876
Supportive

X

Catenibacterium mitsuokai

DSM 15897
Supportive

X

X

Cetobacterium somerae

DSM 23941
Supportive

Clostridium asparagiforme

DSM 15981
Supportive

X

X

Clostridium bolteae

DSM 15670
Supportive

X

Clostridium bolteae

HM-1038
Supportive

Clostridium bolteae

HM-318
Supportive

Clostridium cadaveris

HM-1040
Supportive

Clostridium citroniae

HM-315
Supportive

Clostridium hiranonis

DSM 13275
Supportive

X

X

Clostridium hylemonae

DSM 15053
Supportive

X

X

Clostridium innocuum

HM-173
Supportive

Clostridium leptum

DSM 753
Supportive

X

X

Clostridium methylpentosum

DSM 5476
Supportive

X

Clostridium nexile

DSM 1787
Supportive

X

X

Clostridium orbiscindens

HM-303
Supportive

X

Clostridium orbiscindens

HM-1044
Supportive

Clostridium saccharolyticum

DSM 2544
Supportive

X

X

Clostridium saccharolyticum

HM-635
Supportive

X

Clostridium scindens

DSM 5676
Supportive

X

X

Clostridium scindens

VPI 12708
Supportive

Clostridium sp.
HM-634
Supportive

X

X

Clostridium spiroforme

DSM 1552
Supportive

X

Clostridium sporogenes

ATCC 15579
Supportive

Clostridium sporogenes

ATCC 17889
Supportive

Clostridium sporogenes

DSM 767
Supportive

Clostridium symbiosum

HM-309
Supportive

Clostridium symbiosum

HM-319
Supportive

Collinsella aerofaciens

ATCC 25986
Supportive

X

X

Collinsella stercoris

DSM 13279
Supportive

X

X

Coprococcus catus

ATCC 27761
Supportive

Coprococcus comes

ATCC 27758
Supportive

X

X

Coprococcus eutactus

ATCC 27759
Supportive

X

Coprococcus eutactus

ATCC 51897
Supportive

Coprococcus sp.
DSM 21649
Supportive

Desulfovibrio piger

ATCC 29098
Supportive

X

X

Dialister invisus

DSM 15470
Active
X

X

Dialister pneumosintes

ATCC 51894
Supportive

Dorea formicigenerans

ATCC 27755
Supportive

X

X

Dorea longicatena

DSM 13814
Supportive

X

X

Eggerthella lenta

ATCC 43055
Active
X

X

Eggerthella lenta

DSM 2243
Active
X

X

Eggerthella lenta

DSM 11767
Supportive

Eggerthella lenta

DSM 11863
Supportive

Eggerthella lenta

EIM-1099
Supportive

Enterococcus faecalis

HM-202
Active
X

X

Enterococcus faecalis

HM-432
Active

X

Ethanoligenens harbinense

DSM 18485
Supportive

X

Eubacterium dolichum

DSM 3991
Supportive

X

X

Eubacterium eligens

ATCC 27750
Supportive

Eubacterium rectale

ATCC 33656
Supportive

X

X

Eubacterium siraeum

DSM 15702
Supportive

X

X

Eubacterium ventriosum

ATCC 27560
Supportive

X

X

Faecalibacterium prausnitzii

DSM 17677
Supportive

X

X

Faecalibacterium prausnitzii

ATCC 27766
Supportive

Faecalibacterium prausnitzii

ATCC 27768
Supportive

Faecalibacterium prausnitzii

HM-473
Supportive

Granulicatella adiacens

ATCC 49175
Supportive

X

X

Holdemanella biformis

DSM 3989
Supportive

X

X

Holdemania filiformis

DSM 12042
Supportive

X

X

Hungatella hathewayi

DSM 13479
Supportive

X

X

Hungatella hathewayi

HM-308
Supportive

Intestinibacter bartlettii

DSM 16795
Supportive

X

Intestinimonas butyriciproducens

DSM 26588
Supportive

X

Lactobacillus acidophilus

DSM 20079
Active
X

X

Lactobacillus acidophilus

ATCC 4357
Active

Lactobacillus acidophilus

DSM 20242
Active

Lactobacillus amylovorus

DSM 20552
Supportive

Lactobacillus casei

ATCC 393
Supportive

Lactobacillus casei

ATCC 39539
Supportive

Lactobacillus crispatus

HM-370
Supportive

Lactobacillus gasseri

ATCC 33323
Active
X

X

Lactobacillus gasseri

DSMZ 107525
Active

Lactobacillus gasseri

DSMZ 20077
Active

Lactobacillus gasseri

HM-104
Active

Lactobacillus gasseri

HM-644
Active

Lactobacillus helveticus

DSM 20075
Active
X

X

Lactobacillus johnsonii

HM-643
Supportive

Lactobacillus parafarraginis

HM-478
Supportive

Lactobacillus plantarum

ATCC 14917
Supportive

Lactobacillus plantarum

ATCC 202195
Supportive

Lactobacillus reuteri

HM-102
Active
X

X

Lactobacillus rhamnosus

DSM 20245
Active
X

X

Lactobacillus rhamnosus

HM-106
Active
X

X

Lactobacillus rhamnosus

ATCC 53103
Active

Lactobacillus rhamnosus

DSM 8746
Active

Lactobacillus ruminis

ATCC 25644
Supportive

X

X

Lactobacillus ruminis

DSM 20404
Supportive

Lactobacillus ultunensis

DSM 16048
Supportive

Lactococcus lactis

DSM 20729
Supportive

Marvinbryantia formatexigens

DSM 14469
Supportive

X

X

Megasphaera indica

DSM 25562
Supportive

Megasphaera stantonii

DSM 102144
Supportive

X

X

Methanobrevibacter smithii

DSM 11975
Supportive

Methanobrevibacter smithii

DSM 2374
Supportive

Methanobrevibacter smithii

DSM 2375
Supportive

Methanobrevibacter smithii

DSM 861
Supportive

Methanomassiliicoccus luminyensis

DSM 25720
Supportive

Methanosphaera stadtmanae

DSM 3091
Supportive

Mitsuokella multacida

DSM 20544
Supportive

X

X

Odoribacter splanchnicus

DSM 20712
Supportive

X

X

Olsenella uli

DSM 7084
Supportive

X

X

Oscillibacter welbionis

HM-1030
Supportive

X

Oxalobacter formigenes

ATCC 35274
Active
X

X

Oxalobacter formigenes

HM-1
Active
X

X

Oxalobacter formigenes

DSM 4420
Active

Oxalobacter vibrioformis

DSM 5502
Supportive

Oxalophagus oxalicus

ATCC 49686
Supportive

Parabacteroides distasonis

HM-19
Supportive

X

X

Parabacteroides distasonis

HM-77
Supportive

X

X

Parabacteroides goldsteinii

HM-1050
Supportive

Parabacteroides johnsonii

DSM 18315
Supportive

X

X

Parabacteroides johnsonii

HM-731
Supportive

Parabacteroides merdae

DSM 19495
Supportive

X

Parabacteroides merdae

HM-729
Supportive

Parabacteroides merdae

HM-730
Supportive

Peptostreptococcus anaerobius

DSM 2949
Supportive

Prevotella buccae

HM-45
Supportive

Prevotella buccalis

DSM 20616
Supportive

X

X

Prevotella copri

DSM 18205
Supportive

X

Prevotella histicola

DSM 26979
Supportive

Proteocatella sphenisci

DSM 23131
Supportive

Providencia rettgeri

ATCC BAA-2525
Supportive

Roseburia intestinalis

DSM 14610
Supportive

Roseburia inulinivorans

DSM 16841
Supportive

X

X

Ruminococcaceae sp.
HM-79
Supportive

Ruminococcus albus

ATCC 27210
Supportive

Ruminococcus bromii

ATCC 27255
Supportive

Ruminococcus bromii

ATCC 51896
Supportive

Ruminococcus gauvreauii

DSM 19829
Supportive

X

X

Ruminococcus gnavus

ATCC 29149
Supportive

X

X

Ruminococcus gnavus

DSM 108212
Supportive

Ruminococcus gnavus

HM-1056
Supportive

Ruminococcus lactaris

ATCC 29176
Supportive

X

Ruminococcus lactaris

HM-1057
Supportive

Ruminococcus torques

ATCC 27756
Supportive

X

X

s_Parabacteroides distasonis
ATCC 8503
Supportive

X

X

Slackia exigua

DSM 15923
Supportive

X

Slackia heliotrinireducens

DSM 20476
Supportive

X

Solobacterium moorei

DSM 22971
Supportive

X

X

Streptococcus thermophilus

ATCC BAA-491
Supportive

X

X

Streptococcus thermophilus

ATCC 14485
Supportive

Subdoligranulum variabile

DSM 15176
Supportive

X

Turicibacter sanguinis

DSM 14220
Supportive

X

Veillonella dispar

ATCC 17748
Supportive

Veillonella parvula

HM-49
Supportive

Veillonella parvula

HM-64
Supportive

FIG. 5A and FIG. 5B show the % body weight gain and food consumption, respectively, of the uncolonized mice, mice gavaged with either O. formigenes alone, active microbes alone, supportive microbes alone, or a complete microbial consortium (active and supportives) as described above.

Table 9 shows the incidence of diarrhea in the uncolonized mice, mice gavaged with either O. formigenes alone, active microbes alone, supportive microbes alone, or a complete microbial consortium (active and supportives) as described above. Mice treated with a complete microbial consortium were observed to have normal stool pellets and a reduced incidence of diarrhea.

TABLE 9

Uncolonized

O. formigenes

Actives
Supportives
Full Community

Control
Oxalate
Control
Oxalate
Control
Oxalate
Control
Oxalate
Control
Oxalate

Diet
Diet
Diet
Diet
Diet
Diet
Diet
Diet
Diet
Diet

3/3
3/3
3/3
3/3
3/3
3/3
3/3
3/3
0/3
0/3

Runny stool
Soft stool
Normal stool

Table 10 shows the incidence of fatty liver in the uncolonized mice, mice gavaged with either O. formigenes alone, active microbes alone, supportive microbes alone, or a complete microbial consortium (active and supportives) as described above.

TABLE 10

Uncolonized

O. formigenes

Actives
Supportives
Full Community

Control
Oxalate
Control
Oxalate
Control
Oxalate
Control
Oxalate
Control
Oxalate

Diet
Diet
Diet
Diet
Diet
Diet
Diet
Diet
Diet
Diet

0/3
0/3
1/3
2/3
0/3
1/3
0/3
2/3
0/3
0/3

No Fatty Liver
Fatty Liver observed in 6/18 mice
No Fatty Liver

Urinary Oxalate Concentrations

To assess the effect of a microbial consortium described herein on steady-state levels of oxalate in urine, which correlates well with human urolithiasis, urine was terminally collected from all test groups. Each mouse was transferred to the bottom of a standard petri dish, placed into a CO₂chamber, and administered CO₂for 90 seconds according to the approved IACUC protocol until the mouse ceased moving and was lying prone on the chamber floor. The CO₂chamber lid was opened and the anaesthetized mouse was placed on its side on the petri dish. The CO₂chamber lid was then replaced and terminal urination collected in the petri dish and transferred to a sterile microcentrifuge tube. Urine samples were processed and prepared for solid phase extraction followed by LC/MS-based analysis as described in Example 4 above.

As shown in Table 11 and FIG. 6A-B, mice fed with control diet lacking supplemental oxalate predictably exhibited low levels of urinary oxalate (1.2 mM in uncolonized controls) compared with mice fed a diet containing excess oxalate (11.9 mM in uncolonized controls), showing that dietary supplementation with oxalate can induce hyperoxaluria in gnotobiotic mice.

Regardless of diet, the lowest levels of urinary oxalate were observed in mice colonized with the complete microbial consortium (active and supportives); average oxalate levels in consortium-colonized mice fed the oxalate-free (control) diet were approximately 50% lower than observed in uncolonized mice, and in animals fed the high oxalate diet, steady-state urinary oxalate levels were approximately 66% lower in consortium-colonized mice compared to uncolonized controls (4.5 mM vs. 11.9 mM).

Mice treated with a complete microbial consortium outperformed mice treated with the plurality of active microbes and supportive community of microbes alone, as well as mice treated with O. formigenes alone, with respect to urinary oxalate concentrations. Mice colonized with O. formigenes alone or the plurality of active microbes alone and fed the oxalate-supplemented diet exhibited urinary oxalate concentrations that were not significantly different from those observed in uncolonized mice. Furthermore, mice colonized with the supportive community of microbes alone exhibited significantly higher urinary oxalate levels than uncolonized controls (16.7 mM and 11.9 mM, respectively). Whereas colonization with either the plurality of active microbes alone or the supportive community alone did not reduce levels of urinary oxalate, colonization with the full consortium resulted in a synergistic drop in urinary oxalate concentration.

TABLE 11

Urinary Oxalate (mM)

n = 3 mice/group

Communities
Oxalate Diet
Control Diet

Control (gnotobiotic)
11.9 ± 1.8
1.2 ± 0.2

Supportive Community only
16.7 ± 3.0
0.6 ± 0.1

O. formigenes only
10.5 ± 2.2
1.2 ± 0.2

Plurality of Active Microbes only
9.5 ± 0.4
1.5 ± 0.2

Full Microbial Consortium
4.5 ± 0.1
0.6 ± 0.1

(Active ± Supportive)

Serum Liver Enzyme Assay

Mouse serum samples were analyzed for a standard panel of serum liver enzymes by the Charles River Laboratories. FIGS. 7A, 7B, 7C, 7D, 7E, 7F, 7G, and 7H show serum levels or function of alanine transaminase, aspartate transaminase, albumin, alanine phosphatase, albumin/globulin ratio, total bilirubin, gamma-glutamyl transferase, and prothrombin time, respectively, in gnotobiotic Balb/c mice on a normal (non-bold) or high oxalate diet (bold), treated by gavage with Oxalobacter formigenes only (O. formigenes), active strains only (Active), supportive strains only (Supportive), both active and supportive strains (Active and Supportive), or saline vehicle control (Saline) as described above.

Kidney Function Assay

Mouse serum samples were analyzed for a standard panel of serum kidney metabolites/electrolytes by the Charles River Laboratories. FIGS. 8A, 8B, 8C, 8D, 8E, 8F, 8G, and 8H show serum levels of urea, creatinine, phosphorus, calcium, chloride, sodium, potassium, and globulin, respectively, in gnotobiotic Balb/c mice on a normal (non-bold) or high oxalate diet (bold), treated by gavage with Oxalobacter formigenes only (O. formigenes), active strains only (Active), supportive strains only (Supportive), both active and supportive strains (Active+Supportive), or saline vehicle control (Saline) as described above.

Triglyceride, Cholesterol, Glucose and Creatine Kinase Assay

Mouse serum samples were analyzed for a standard triglyceride, cholesterol, glucose and creatine kinase panel by the Charles River Laboratories. FIGS. 9A, 9B, 9C, and 9D shows serum triglyceride, cholesterol, glucose, and creatine kinase levels, respectively, in gnotobiotic Balb/c mice on a normal (non-bold) or high oxalate diet (bold), treated by gavage with Oxalobacter formigenes only (O. formigenes), active strains only (Active), supportive strains only (Supportive), both active and supportive strains (Active+Supportive), or saline vehicle control as described above.

Example 6: In Vivo Oxalate Metabolization in C57/B6 Female Mice Treated with a Microbial Consortium Containing Commercial Strains of Microbes

This example describes a study testing the ability of a microbial consortium, containing commercially-sourced strains of microbes, to degrade oxalate in vivo in C57/B6 female mice.

To test whether the in vivo activity of a microbial consortium as presently described was observed in a different sex and strain of study mouse, female C57/B6 mice (n=3 per condition) were colonized by oral gavage with either a plurality of active microbes alone, a supportive community alone, a supportive community plus O. formigenes alone, a supportive community plus a plurality of active microbes lacking O. formigenes, a complete microbial consortium (active and supportive s), or a fecal sample from a human donor found to be positive for O. formigenes DNA. The plurality of active microbes and the supportive community contained the strains in Table 8 marked with an ‘X’ in the indicated columns. Colonized mice were fed either a defined, low-complexity diet supplemented with excess oxalate in order to induce hyperoxaluria (see Table 2 above) or a nutritionally equivalent control diet lacking oxalate (see Table 1 above). After a two-week period, mice were sacrificed and urine, stool, serum and tissue samples were collected for analysis.

Urinary Oxalate Concentrations

Urine was terminally collected from all groups and processed for solid phase extraction followed by LC-MS-based analysis of oxalate concentrations as described in Example 4. Absolute oxalate concentrations detected in individual urine samples were normalized based on the ratio of oxalate to creatinine.

As shown in Table 12, urinary oxalate levels were reduced in mice colonized with the complete microbial consortium. Partial reduction was also observed in mice colonized with the supportive community alone, the supportive community plus the plurality of active microbes lacking O. formigenes, and the plurality of active microbes alone.

TABLE 12

Normalized Urinary

Oxalate (mM)

n = 3 mice/group

% of Urinary

Oxalate:Cre-
Oxalate

atinine
(normalized) in

Communities
(μM)
Supportive Only

Control (gnotobiotic)
4.5 ± 0.73
120.4% ± 19.6

Supportive Community only
3.74 ± 1.27
100.0% ± 34.0

Plurality of Active Microbes
2.13 ± 1.81
57% ± 48.4

only

Supportive Community +
2.10 ± 0.90
56.1% ± 24.0

O. formigenes

Supportive Community +
2.82 ± 1.94
75.5% ± 52.0

Plurality of Active

Microbes (minus O. formigenes)

Full Microbial Consortium
0.91 ± 0.42
24.3% ± 11.3

(Active + Supportive)

Human donor fecal sample
1.64 ± 1.49
44.0% ± 40.0

(O. formigenes positive)

Example 7: In Vivo Oxalate Metabolization in C57/B6 Female Mice Treated with Frozen Stocks of Microbial Consortium

To test whether a microbial consortium as presently described maintains in vivo activity after freezing, individual live microbial cultures of commercially-sourced strains were pooled in approximately equal proportions to form a supportive community alone, a supportive community plus a plurality of active microbes lacking O. formigenes, and an O. formigenes community comprising two commercial strains of O. formigenes, and frozen as aliquots in 30% glycerol in the vapor phase of a liquid nitrogen dewar for one month prior to administration to mice. The plurality of active microbes and the supportive community contained the strains in Table 8 marked with an ‘X’ in the indicated column.

Gnotobiotic, female, C57/B6 mice (n=3 per condition) were colonized by oral gavage with either a plurality of active microbes alone (including O. formigenes), a supportive community alone, or a complete microbial consortium (active and supportives). Hyperoxaluria was induced in colonized mice by providing ad libitum drinking water sweetened with sucralose and containing 0.875% oxalate. Control mice were provided with sucralose-sweetened drinking water without oxalate. All mice were maintained on a standard Autoclavable Mouse Breeder Diet (LabDiet®, St. Louis, Mo.). After a two week period, mice were sacrificed and a variety of samples were collected including urine, stool, serum, and kidneys.

Urinary Oxalate Concentrations

As in Example 6, urine was terminally collected from all groups and processed for solid phase extraction followed by LC/MS-based analysis of oxalate concentrations. Absolute oxalate concentrations detected in individual urine samples were normalized based on the ratio of oxalate to creatinine.

As shown in Table 13, mice provided with drinking water containing 0.875% oxalate exhibited significantly elevated levels of urinary oxalate compared with mice given control water (e.g., an approximate 4-fold increase in both the mice administered with the plurality of active microbes alone and the mice administered with the supportive community alone). Consistent with Examples 5 and 6, mice colonized with the complete microbial consortium had significantly lower urinary oxalate levels compared with the mice administered with the plurality of active microbes alone or the mice administered with the supportive community alone. Furthermore, as compared to Examples 5 and 6, the complete microbial consortium still exhibited significant oxalate metabolizing activity in mice maintained on a markedly different standard dietary formulation

TABLE 13

Oxalate:Creatinine

Communities
(μM)
SD

No Oxalate Treatment

Supportive Community +
0.254
0.021

Plurality of Active Microbes

Supportive Community only
0.246
0.025

Plurality of Active Microbes only
0.279
0.019

0.875% Oxalate Treatment

Supportive Community +
0.618
0.085

Plurality of Active Microbes

Supportive Community only
0.937
0.111

Plurality of Active Microbes only
2.427
2.284

Example 8: In Vivo Engraftment of Oxalate-Metabolizing Microbial Strains

Stool samples from the treated mice described in Example 5 were analyzed for the presence of oxalate-metabolizing microbial strains by whole genome shotgun sequencing of microbial DNA extracted from fecal pellets. DNA extraction from fecal samples and whole genome shotgun sequencing were performed by methods as previously described in Example 1. Sequence reads were mapped against a comprehensive database of complete, sequenced genomes of all the defined microbial strains comprising the microbial consortium. The results of this experiment are summarized in FIGS. 10A-F.

Table 14 shows detection of engrafted oxalate-metabolizing active microbial strains in the treated mice described in Example 5. Microbial strains were counted as “detected” if their relative abundance was >0.1% of total sequence reads.

TABLE 14

Actives +
Actives +

Actives-
Actives-
Sup-
Sup-

only
only
portives
portives

Active community
(Control
(Oxalate
(Control
(Oxalate

component
Diet)
Diet)
Diet)
Diet)

Oxalobacter formigenes

0%
100%
0%
100%

Bifidobacterium dentium

100%
100%
0%
0%

Eggerthella lenta

100%
100%
0%
0%

Enterococcus faecalis

100%
100%
0%
0%

Lactobacillus rhamnosus

100%
100%
0%
0%

Dialister invisus

33.3%
66.6%
0%
0%

Lactobacillus helveticus

33.3%
0%
0%
0%

Lactobacillus acidophilus

0%
0%
0%
0%

Lactobacillus gasseri

0%
0%
0%
0%

Lactobacillus reuteri

0%
0%
0%
0%

Table 15 shows detection of engrafted supportive microbial strains in the treated mice described in Example 5. Microbial strains were counted as “detected” if their relative abundance was >0.1% of total sequence reads.

TABLE 15

Sup-
Sup-
Actives +
Actives +

portives-
portives-
Sup-
Sup-

only
only
portives
portives

Supportive Community
(Control
(Oxalate
(Control
(Oxalate

Component
Diet)
Diet)
Diet)
Diet)

13 species
100%
100%
100%
100%

Alistipes senegalensis

100%
0%
66.6%
100%

Catenibacterium

100%
0%
66.6%
100%

mitsuokai

Bacteroides coprocola

0%
0%
0%
100%

Clostridium scindens

0%
0%
66.6%
66.6%

Bacteroides

100%
0%
66.6%
0%

cellulosilyticus

Tyzzerella nexilis

100%
0%
66.6%
0%

17 species
0 to
0 to
0 to
0 to

100%
100%
100%
100%

33 species
0%
0%
0%
0%

Example 9: In Vitro Oxalate Metabolization by Donor-Derived Strains

In order to determine the in vitro oxalate-metabolizing activity of three donor-derived O. formigenes strains, strains were grown in YFCAC base medium at either pH 7.0, 6.0, or 5.0 in the presence of 80 mM oxalate. Strains were incubated at 37° C. for 72, and at the conclusion of the protocol the amount of oxalate in the medium was quantified by LC-MS as described in Example 4. For all three strains, the amount of oxalate remaining in the culture medium after 72 hours was below the limit of detection when assayed at pH 7.0 or 6.0. No oxalate degradation was detected for cultures of any of the three strains when incubated at pH 5.0.

To determine the oxalate-metabolizing activity of additional donor-derived microbial strains, strains were grown in anaerobic conditions in YCFAC base medium at either pH 7.0, 6.0, or 5.0 in the presence of 2 mM oxalate. Strains were incubated at 37° C. for 120 hours, and at the conclusion of the protocol the amount of oxalate in the medium was quantified by LC/MS as described in Example 4. A donor-derived strain of O. formigenes was included as a positive control. Results are reported as the percentage of oxalate remaining in the media at the conclusion of the assay relative to the starting concentration (FIG. 11). As expected, the amount of oxalate remaining in a culture of donor-derived O. formigenes was below the limit of detection when assayed at pH 6 or pH 7, although no oxalate degradation was detected at pH 5. By contrast, none of the other tested donor-derived isolates were found to reduce oxalate by more than 11% at any pH tested.

Example 10: Growth of Donor-Derived O. formigenes Strains at Different pHs and Oxalate Concentrations

Three O. formigenes strains isolated from donor fecal samples were assayed for their ability to grow at different pHs (5.0, 6.0, or 7.0) and at different oxalate concentrations (0 mM, 2 mM, 40 mM, 80 mM, 120 mM, 160 mM). Strains were grown under anaerobic conditions in the appropriate banking medium, and culture turbidity was recorded after 24, 48, 72, and 144 hours. The results of this assay are reported in FIGS. 12A-12C. One O. formigenes strain (FBI00067) was observed to grow better at a lower pH; another strain (FBI00133) was observed to be more tolerant of higher oxalate concentrations.

Example 11: Design of Supportive Communities Comprising Donor-Derived Strains

Supportive communities of microbes were designed using donor-derived strains. Five candidate communities were designed according to different design principles.

The supportive community of candidate consortium I was designed to incorporate all isolated species that were present in more than 50% of a set of healthy donor fecal samples. The community further included donor-derived strains whose identified species had been represented in the proof-of-concept consortium of commercial strains, or (if no matching species had been isolated) then a strain of the species that was the closest relative within the genus. The final consortium (actives and supportives) contained 152 strains and 70 species in total, listed in Table 16.

The supportive communities of candidate consortia II and III were designed to maximize consumption and/or production of a defined set of metabolites using a minimal number of strains. In both cases, metabolites of interest were identified by conducting a literature review, as well as by bioinformatic annotation of healthy microbiomes. Next, the genomes of donor-derived strains were bioinformatically analyzed to identify strains capable of producing or consuming said metabolites of interest. A literature review was also conducted to identify donor-derived strains belonging to species known to consume and/or produce each metabolite of interest. Donor-derived strains were scored for their ability to produce or consume said metabolite, and the community was designed to maximize the desired metabolic coverage with the fewest number of species. The supportive community of candidate consortium II was designed to enrich for consumption of 51 dietary carbon and energy sources. The supportive community of candidate consortia III was designed to enrich for the production or consumption of metabolites present in the host, including bile acids, sugars, amino acids, vitamins, SCFAs, and gasses. The strains included in candidate consortium II are listed in Table 17, and the strains included in candidate consortium III are listed in Table 18.

The supportive community of candidate consortium IV was constructed using strains isolated exclusively from fecal samples of two healthy donors. Sourcing many supportive strains from one or a small number of donors may have the benefit of enhancing co-culturability and/or ecological stability. The two specific donors selected both had stool that was found to be capable of reducing urinary oxalate in vivo, potentially enhancing the use of the community in embodiments of the invention designed to degrade oxalate. The strains included in candidate consortium IV are listed in Table 19.

The supportive community of candidate consortium V was designed to include all strains isolated from healthy donor fecal samples, with the exception of species known to be associated with pathogenesis. This diverse community incorporated species from all five major phyla that comprise normal gut commensals (Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, and Verrucomicrobia). The final consortium contained 103 species and 158 strains in total, which are listed in Table 20.

TABLE 16

NCBI

Strain

Taxonomy

% Match
SEQ ID

#
Species ID
Kingdom
Phylum
ID
Closest 16S Species
(16S)
NO: X

FBI00001

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.64
1

FBI00002

Bacteroides salyersiae

bacteria
bacteroidetes
291644

Bacteroides salyersiae

99.5
2

FBI00004

Neglecta timonensis

bacteria
firmicutes
1776382

Neglecta timonensis

99.14
4

FBI00008

Blautia luti

bacteria
firmicutes
89014

Blautia luti

97.02
8

FBI00010

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.12
10

FBI00011

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.28
11

FBI00012

Alistipes onderdonkii

bacteria
bacteroidetes
328813

Alistipes onderdonkii

99.71
12

FBI00013

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.5
13

FBI00015

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
15

FBI00016

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.64
16

pseudocatenulatum

pseudocatenulatum

FBI00017

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.34
17

FBI00018

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.71
18

FBI00019

Alistipes timonensis

bacteria
bacteroidetes
1465754

Alistipes timonensis

99.78
19

FBI00020

Bacteroides

bacteria
bacteroidetes
818

Bacteroides

99.57
20

thetaiotaomicron

thetaiotaomicron

FBI00022

Alistipes putredinis

bacteria
bacteroidetes
28117

Alistipes putredinis

99.93
22

FBI00025

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

99.21
25

FBI00029

Parabacteroides distasonis

bacteria
bacteroidetes
823

Parabacteroides distasonis

99.26
29

FBI00030

Eggerthella lenta

bacteria
firmicutes
84112

Eggerthella lenta

98.47
30

FBI00032

Anaerostipes hadrus

bacteria
firmicutes
649756

Anaerostipes hadrus

99.64
32

FBI00033

Lachnospiraceae sp. FBI00033
bacteria
firmicutes
186803

Clostridium amygdalinum

93.56
33

FBI00034

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.78
34

FBI00036

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.53
36

FBI00038

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

95.96
38

FBI00039

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.71
39

FBI00040

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio desulfuricans

91.38
40

FBI00042

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

99.71
42

FBI00043

Bifidobacterium dentium

bacteria
actinobacteria
1689

Bifidobacterium dentium

99.35
43

FBI00044

Blautia wexlerae

bacteria
firmicutes
418240

Blautia wexlerae

98.69
44

FBI00046

Bacteroides caccae

bacteria
bacteroidetes
47678

Bacteroides caccae

99.71
46

FBI00047

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.79
47

FBI00050

Bacteroides nordii

bacteria
bacteroidetes
291645

Bacteroides nordii

98.63
50

FBI00051

Dorea formicigenerans

bacteria
firmicutes
39486

Dorea formicigenerans

98.07
51

FBI00052

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

99.14
52

FBI00056

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.2
56

FBI00057

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.7
57

FBI00058

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.71
58

FBI00059

Bacteroides stercorirosoris

bacteria
bacteroidetes
871324

Bacteroides oleiciplenus

98.81
59

FBI00060

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.49
60

FBI00061

Alistipes shahii

bacteria
bacteroidetes
328814

Alistipes shahii

99.19
61

FBI00062

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.48
62

FBI00066

Parasutterella excrementihominis

bacteria
proteobacteria
487175

Parasutterella excrementihominis

99.13
66

FBI00067

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

98.84
67

FBI00068

Akkermansia muciniphila

bacteria
verrucomicrobia
239935

Akkermansia muciniphila

99.42
68

FBI00069

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.84
69

FBI00072

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

96.17
72

FBI00073

Parabacteroides distasonis

bacteria
bacteroidetes
823

Parabacteroides distasonis

98.99
73

FBI00074

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.03
74

FBI00075

Paraprevotella clara

bacteria
bacteroidetes
454154

Paraprevotella clara

98.85
75

FBI00076

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides thetaiotaomicron

99.78
76

FBI00078

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.34
78

FBI00085

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.62
85

FBI00086

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.77
86

FBI00087

Clostridium scindens

bacteria
firmicutes
29347

Clostridium scindens

98.28
87

FBI00090

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.71
90

FBI00091

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.86
91

FBI00093

Roseburia hominis

bacteria
firmicutes
301301

Roseburia hominis

99.71
93

FBI00096

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.76
96

FBI00099

Gordonibacter pamelaeae

bacteria
actinobacteria
471189

Gordonibacter pamelaeae

99.56
99

FBI00101

Faecalibacterium prausnitzii

bacteria
firmicutes
853

Faecalibacterium prausnitzii

97.97
101

FBI00102

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.31
102

FBI00104

Blautia wexlerae

bacteria
firmicutes
418240

Blautia luti

97.18
104

FBI00109

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

98.39
109

FBI00111

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.43
111

FBI00112

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
112

FBI00113

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.79
113

FBI00115

Dorea formicigenerans

bacteria
firmicutes
39486

Dorea formicigenerans

97.98
115

FBI00116

Ruminococcus faecis

bacteria
firmicutes
592978

Ruminococcus faecis

99.57
116

FBI00117

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.52
117

FBI00118

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.84
118

FBI00120

Hungatella effluvii

bacteria
firmicutes
154046

Hungatella hathewayi

98.78
120

FBI00122

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.57
122

FBI00123

Roseburia hominis

bacteria
firmicutes
301301

Roseburia hominis

100
123

FBI00124

Anaerostipes hadrus

bacteria
firmicutes
649756

Anaerostipes hadrus

99.86
124

FBI00125

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

99.64
125

FBI00126

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium adolescentis

98.98
126

FBI00127

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

98.81
127

FBI00130

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

99.35
130

FBI00132

Gordonibacter pamelaeae

bacteria
actinobacteria
471189

Gordonibacter pamelaeae

99.48
132

FBI00133

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
133

FBI00135

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.57
135

pseudocatenulatum

pseudocatenulatum

FBI00137

Bacteroides fragilis

bacteria
bacteroidetes
817

Bacteroides fragilis

99.71
137

FBI00138

Blautia massiliensis

bacteria
firmicutes
1737424

Blautia luti

97.94
138

FBI00139

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides thetaiotaomicron

99.5
139

FBI00142

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.07
142

FBI00143

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.07
143

FBI00145

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium adolescentis

99.14
145

FBI00147

Clostridium bolteae

bacteria
firmicutes
208479

Clostridium bolteae

99.28
147

FBI00151

Clostridium aldenense

bacteria
firmicutes
358742

Clostridium aldenense

98.55
151

FBI00152

Dialister invisus

bacteria
firmicutes
218538

Dialister invisus

99.58
152

FBI00155

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.7
155

FBI00162

Bifidobacterium catenulatum

bacteria
actinobacteria
1686

Bifidobacterium catenulatum

99.14
162

FBI00164

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

98.56
164

FBI00165

Bacteroides massiliensis

bacteria
bacteroidetes
204516

Bacteroides massiliensis

99.71
165

FBI00167

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.39
167

FBI00168

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.26
168

FBI00169

Parabacteroides distasonis

bacteria
bacteroidetes
823

Parabacteroides distasonis

98.7
169

FBI00170

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.61
170

FBI00171

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio desulfuricans

91.45
171

FBI00172

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.05
172

FBI00173

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

100
173

FBI00175

Holdemanella biformis

bacteria
firmicutes
1735

Holdemanella biformis

98.19
175

FBI00177

Parasutterella excrementihominis

bacteria
proteobacteria
487175

Parasutterella excrementihominis

99.71
177

FBI00180

Alistipes sp. FBI00180
bacteria
bacteroidetes
239759

Alistipes senegalensis

97.56
180

FBI00181

Blautia wexlerae

bacteria
firmicutes
418240

Blautia wexlerae

97.17
181

FBI00182

Bacteroides coprocola

bacteria
bacteroidetes
310298

Bacteroides coprocola

99.64
182

FBI00186

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

99.06
186

FBI00188

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.05
188

FBI00190

Bacteroides finegoldii

bacteria
bacteroidetes
338188

Bacteroides finegoldii

98.91
190

FBI00193

Alistipes onderdonkii

bacteria
bacteroidetes
328813

Alistipes onderdonkii

99.64
193

FBI00194

Ruminococcus faecis

bacteria
firmicutes
592978

Ruminococcus faecis

98.41
194

FBI00199

Clostridium bolteae

bacteria
firmicutes
208479

Clostridium bolteae

99.28
199

FBI00201

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.83
201

FBI00205

Blautia massiliensis

bacteria
firmicutes
1737424

Blautia luti

97.55
205

FBI00206

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

99.56
206

FBI00208

Anaerotruncus massiliensis

bacteria
firmicutes
1673720

Anaerotruncus colihominis

96.52
208

FBI00211

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.78
211

FBI00212

Clostridium aldenense

bacteria
firmicutes
358742

Clostridium aldenense

99.1
212

FBI00217

Alistipes shahii

bacteria
bacteroidetes
328814

Alistipes shahii

98.77
217

FBI00218

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.42
218

FBI00219

Roseburia hominis

bacteria
firmicutes
301301

Roseburia hominis

99.78
219

FBI00229

Alistipes senegalensis

bacteria
bacteroidetes
1288121

Alistipes senegalensis

99.19
229

FBI00232

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

98.84
232

FBI00235

Alistipes shahii

bacteria
bacteroidetes
328814

Alistipes shahii

99.86
235

FBI00238

Alistipes sp. FBI00238
bacteria
bacteroidetes
239759

Alistipes finegoldii

95.84
238

FBI00241

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.34
241

FBI00243

Eubacterium siraeum

bacteria
firmicutes
39492

Eubacterium siraeum

98.53
243

FBI00244

Faecalibacterium prausnitzii

bacteria
firmicutes
853

Faecalibacterium prausnitzii

98.69
244

FBI00245

Acidaminococcus intestini

bacteria
firmicutes
187327

Acidaminococcus intestini

99.72
245

FBI00246

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.7
246

FBI00251

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.85
251

pseudocatenulatum

pseudocatenulatum

FBI00253

Roseburia hominis

bacteria
firmicutes
301301

Roseburia hominis

99.71
253

FBI00254

Eubacterium hallii

bacteria
firmicutes
39488

Eubacterium hallii

99.08
254

FBI00255

Hungatella effluvii

bacteria
firmicutes
1096246

Hungatella hathewayi

98.56
255

FBI00257

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

99.28
257

FBI00258

Turicibacter sanguinis

bacteria
firmicutes
154288

Turicibacter sanguinis

99.93
258

FBI00259

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.7
259

FBI00260

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.64
260

FBI00262

Bacteroides massiliensis

bacteria
bacteroidetes
204516

Bacteroides massiliensis

99.71
262

FBI00263

Bacteroides caccae

bacteria
bacteroidetes
47678

Bacteroides caccae

99.56
263

FBI00265

Bacteroides cellulosilyticus

bacteria
bacteroidetes
246787

Bacteroides cellulosilyticus

99.21
265

FBI00266

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

99.2
266

FBI00267

Anaerofustis stercorihominis

bacteria
firmicutes
214853

Anaerofustis stercorihominis

97.29
267

FBI00269

Alistipes putredinis

bacteria
bacteroidetes
28117

Alistipes putredinis

100
269

FBI00271

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

98.42
271

FBI00274

Eubacterium xylanophilum

bacteria
firmicutes
39497

Eubacterium xylanophilum

93.5
274

FBI00275

Holdemanella biformis

bacteria
firmicutes
1735

Holdemanella biformis

98.99
275

FBI00276

Dorea formicigenerans

bacteria
firmicutes
39486

Dorea formicigenerans

98.19
276

FBI00277

Alistipes onderdonkii

bacteria
bacteroidetes
328813

Alistipes onderdonkii

99.63
277

FBI00278

Eubacterium ventriosum

bacteria
firmicutes
39496

Eubacterium ventriosum

94.14
278

FBI00283

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

96.02
283

FBI00288

Blautia hydrogenotrophica

bacteria
firmicutes
53443

Blautia hydrogenotrophica

99.57
288

FBI00289

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
289

TABLE 17

%

NCBI

Match
SEQ ID

Strain #
Species ID
Kingdom
Phylum
Taxonomy ID
Closest 16S Species
(16S)
NO: X

FBI00001

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.64
1

FBI00002

Bacteroides salyersiae

bacteria
bacteroidetes
291644

Bacteroides salyersiae

99.5
2

FBI00004

Neglecta timonensis

bacteria
firmicutes
1776382

Neglecta timonensis

99.14
4

FBI00011

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.28
11

FBI00013

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.5
13

FBI00015

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
15

FBI00016

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.64
16

pseudocatenulatum

pseudocatenulatum

FBI00018

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.71
18

FBI00020

Bacteroides

bacteria
bacteroidetes
818

Bacteroides

99.57
20

thetaiotaomicron

thetaiotaomicron

FBI00029

Parabacteroides

bacteria
bacteroidetes
823

Parabacteroides distasonis

99.26
29

distasonis

FBI00030

Eggerthella lenta

bacteria
firmicutes
84112

Eggerthella lenta

98.47
30

FBI00033

Lachnospiraceae sp.
bacteria
firmicutes
186803

Clostridium amygdalinum

93.56
33

FBI00033

FBI00039

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.71
39

FBI00040

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio

91.38
40

desulfuricans

FBI00043

Bifidobacterium dentium

bacteria
actinobacteria
1689

Bifidobacterium dentium

99.35
43

FBI00046

Bacteroides caccae

bacteria
bacteroidetes
47678

Bacteroides caccae

99.71
46

FBI00056

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.2
56

FBI00057

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.7
57

FBI00058

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.71
58

FBI00060

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.49
60

FBI00062

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.48
62

FBI00064

Dorea sp. FBI00064
bacteria
firmicutes
189330

Ruminococcus gnavus

95.58
64

FBI00067

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

98.84
67

FBI00068

Akkermansia muciniphila

bacteria
verrucomicrobia
239935

Akkermansia muciniphila

99.42
68

FBI00069

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.84
69

FBI00073

Parabacteroides

bacteria
bacteroidetes
823

Parabacteroides distasonis

98.99
73

distasonis

FBI00074

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.03
74

FBI00076

Bacteroides

bacteria
bacteroidetes
818

Bacteroides

99.78
76

thetaiotaomicron

thetaiotaomicron

FBI00077

Sutterella wadsworthensis

bacteria
proteobacteria
40545

Sutterella wadsworthensis

99.86
77

FBI00085

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.62
85

FBI00086

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.77
86

FBI00087

Clostridium scindens

bacteria
firmicutes
29347

Clostridium scindens

98.28
87

FBI00091

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.86
91

FBI00096

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.76
96

FBI00099

Gordonibacter pamelaeae

bacteria
actinobacteria
471189

Gordonibacter pamelaeae

99.56
99

FBI00101

Faecalibacterium

bacteria
firmicutes
853

Faecalibacterium

97.97
101

prausnitzii

prausnitzii

FBI00102

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.31
102

FBI00109

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

98.39
109

FBI00111

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.43
111

FBI00112

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
112

FBI00113

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.79
113

FBI00122

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.57
122

FBI00125

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

99.64
125

FBI00126

Bifidobacterium

bacteria
actinobacteria
1680

Bifidobacterium

98.98
126

adolescentis

adolescentis

FBI00127

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

98.81
127

FBI00130

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

99.35
130

FBI00132

Gordonibacter pamelaeae

bacteria
actinobacteria
471189

Gordonibacter pamelaeae

99.48
132

FBI00133

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
133

FBI00135

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.57
135

pseudocatenulatum

pseudocatenulatum

FBI00137

Bacteroides fragilis

bacteria
bacteroidetes
817

Bacteroides fragilis

99.71
137

FBI00139

Bacteroides

bacteria
bacteroidetes
818

Bacteroides

99.5
139

thetaiotaomicron

thetaiotaomicron

FBI00142

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.07
142

FBI00143

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.07
143

FBI00145

Bifidobacterium

bacteria
actinobacteria
1680

Bifidobacterium

99.14
145

adolescentis

adolescentis

FBI00162

Bifidobacterium

bacteria
actinobacteria
1686

Bifidobacterium

99.14
162

catenulatum

catenulatum

FBI00164

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

98.56
164

FBI00165

Bacteroides massiliensis

bacteria
bacteroidetes
204516

Bacteroides massiliensis

99.71
165

FBI00167

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.39
167

FBI00168

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.26
168

FBI00169

Parabacteroides

bacteria
bacteroidetes
823

Parabacteroides distasonis

98.7
169

distasonis

FBI00170

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.61
170

FBI00171

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio

91.45
171

desulfuricans

FBI00172

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.05
172

FBI00173

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

100
173

FBI00186

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

99.06
186

FBI00192

Sutterella wadsworthensis

bacteria
proteobacteria
40545

Sutterella wadsworthensis

99.71
192

FBI00197

Bifidobacterium bifidum

bacteria
actinobacteria
1681

Bifidobacterium bifidum

99.85
197

FBI00201

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.83
201

FBI00208

Anaerotruncus

bacteria
firmicutes
1673720

Anaerotruncus colihominis

96.52
208

massiliensis

FBI00210

Bifidobacterium bifidum

bacteria
actinobacteria
1681

Bifidobacterium bifidum

99.93
210

FBI00211

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.78
211

FBI00218

Bacteroides uniforms

bacteria
bacteroidetes
820

Bacteroides uniformis

99.42
218

FBI00224

Sutterella wadsworthensis

bacteria
proteobacteria
40545

Sutterella wadsworthensis

99.71
224

FBI00232

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

98.84
232

FBI00233

Ruminococcaceae sp.
bacteria
firmicutes
474960

Anaerotruncus colihominis

91.63
233

FBI00233

FBI00239

Lactonifactor

bacteria
firmicutes
341220

Lactonifactor

98.99
239

longoviformis

longoviformis

FBI00241

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.34
241

FBI00243

Eubacterium siraeum

bacteria
firmicutes
39492

Eubacterium siraeum

98.53
243

FBI00246

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.7
246

FBI00249

Citrobacter portucalensis

bacteria
proteobacteria
1639133

Citrobacter freundii

99.79
249

FBI00251

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.85
251

pseudocatenulatum

pseudocatenulatum

FBI00259

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.7
259

FBI00260

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.64
260

FBI00262

Bacteroides massiliensis

bacteria
bacteroidetes
204516

Bacteroides massiliensis

99.71
262

FBI00263

Bacteroides caccae

bacteria
bacteroidetes
47678

Bacteroides caccae

99.56
263

FBI00265

Bacteroides

bacteria
bacteroidetes
246787

Bacteroides

99.21
265

cellulosilyticus

cellulosilyticus

FBI00283

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

96.02
283

FBI00289

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
289

TABLE 18

%

NCBI

Match
SEQ ID

Strain #
Species ID
Kingdom
Phylum
Taxonomy ID
Closest 16S Species
(16S)
NO: X

FBI00001

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.64
1

FBI00002

Bacteroides salyersiae

bacteria
bacteroidetes
291644

Bacteroides salyersiae

99.5
2

FBI00004

Neglecta timonensis

bacteria
firmicutes
1776382

Neglecta timonensis

99.14
4

FBI00010

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.12
10

FBI00011

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.28
11

FBI00013

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.5
13

FBI00016

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.64
16

pseudocatenulatum

pseudocatenulatum

FBI00017

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.34
17

FBI00020

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides thetaiotaomicron

99.57
20

FBI00022

Alistipes putredinis

bacteria
bacteroidetes
28117

Alistipes putredinis

99.93
22

FBI00030

Eggerthella lenta

bacteria
firmicutes
84112

Eggerthella lenta

98.47
30

FBI00033

Lachnospiraceae sp.
bacteria
firmicutes
186803

Clostridium amygdalinum

93.56
33

FBI00033

FBI00034

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.78
34

FBI00038

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

95.96
38

FBI00039

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.71
39

FBI00040

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio desulfuricans

91.38
40

FBI00042

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

99.71
42

FBI00043

Bifidobacterium dentium

bacteria
actinobacteria
1689

Bifidobacterium dentium

99.35
43

FBI00046

Bacteroides caccae

bacteria
bacteroidetes
47678

Bacteroides caccae

99.71
46

FBI00047

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.79
47

FBI00052

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

99.14
52

FBI00056

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.2
56

FBI00057

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.7
57

FBI00060

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.49
60

FBI00062

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.48
62

FBI00067

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

98.84
67

FBI00069

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.84
69

FBI00072

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

96.17
72

FBI00074

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.03
74

FBI00076

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides thetaiotaomicron

99.78
76

FBI00077

Sutterella wadsworthensis

bacteria
proteobacteria
40545

Sutterella wadsworthensis

99.86
77

FBI00085

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.62
85

FBI00086

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.77
86

FBI00087

Clostridium scindens

bacteria
firmicutes
29347

Clostridium scindens

98.28
87

FBI00090

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.71
90

FBI00096

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.76
96

FBI00101

Faecalibacterium prausnitzii

bacteria
firmicutes
853

Faecalibacterium prausnitzii

97.97
101

FBI00102

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.31
102

FBI00109

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

98.39
109

FBI00111

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.43
111

FBI00112

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
112

FBI00113

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.79
113

FBI00115

Dorea formicigenerans

bacteria
firmicutes
39486

Dorea formicigenerans

97.98
115

FBI00120

Hungatella effluvii

bacteria
firmicutes
154046

Hungatella hathewayi

98.78
120

FBI00122

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.57
122

FBI00125

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

99.64
125

FBI00127

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

98.81
127

FBI00133

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
133

FBI00135

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.57
135

pseudocatenulatum

pseudocatenulatum

FBI00137

Bacteroides fragilis

bacteria
bacteroidetes
817

Bacteroides fragilis

99.71
137

FBI00139

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides thetaiotaomicron

99.5
139

FBI00142

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.07
142

FBI00143

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.07
143

FBI00147

Clostridium bolteae

bacteria
firmicutes
208479

Clostridium bolteae

99.28
147

FBI00162

Bifidobacterium catenulatum

bacteria
actinobacteria
1686

Bifidobacterium catenulatum

99.14
162

FBI00164

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

98.56
164

FBI00167

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.39
167

FBI00168

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.26
168

FBI00170

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.61
170

FBI00171

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio desulfuricans

91.45
171

FBI00172

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.05
172

FBI00173

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

100
173

FBI00182

Bacteroides coprocola

bacteria
bacteroidetes
310298

Bacteroides coprocola

99.64
182

FBI00197

Bifidobacterium bifidum

bacteria
actinobacteria
1681

Bifidobacterium bifidum

99.85
197

FBI00199

Clostridium bolteae

bacteria
firmicutes
208479

Clostridium bolteae

99.28
199

FBI00201

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.83
201

FBI00206

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

99.56
206

FBI00208

Anaerotruncus massiliensis

bacteria
firmicutes
1673720

Anaerotruncus colihominis

96.52
208

FBI00210

Bifidobacterium bifidum

bacteria
actinobacteria
1681

Bifidobacterium bifidum

99.93
210

FBI00211

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.78
211

FBI00232

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

98.84
232

FBI00238

Alistipes sp. FBI00238
bacteria
bacteroidetes
239759

Alistipes finegoldii

95.84
238

FBI00241

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.34
241

FBI00243

Eubacterium siraeum

bacteria
firmicutes
39492

Eubacterium siraeum

98.53
243

FBI00244

Faecalibacterium prausnitzii

bacteria
firmicutes
853

Faecalibacterium prausnitzii

98.69
244

FBI00246

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.7
246

FBI00251

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.85
251

pseudocatenulatum

pseudocatenulatum

FBI00254

Eubacterium hallii

bacteria
firmicutes
39488

Eubacterium hallii

99.08
254

FBI00255

Hungatella effluvii

bacteria
firmicutes
1096246

Hungatella hathewayi

98.56
255

FBI00257

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

99.28
257

FBI00260

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.64
260

FBI00265

Bacteroides cellulosilyticus

bacteria
bacteroidetes
246787

Bacteroides cellulosilyticus

99.21
265

FBI00266

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

99.2
266

FBI00269

Alistipes putredinis

bacteria
bacteroidetes
28117

Alistipes putredinis

100
269

FBI00271

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

98.42
271

FBI00278

Eubacterium ventriosum

bacteria
firmicutes
39496

Eubacterium ventriosum

94.14
278

FBI00283

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

96.02
283

FBI00288

Blautia hydrogenotrophica

bacteria
firmicutes
53443

Blautia hydrogenotrophica

99.57
288

FBI00289

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
289

TABLE 19

%

NCBI

Match
SEQ ID

Strain #
Species ID
Kingdom
Phylum
Taxonomy ID
Closest 16S Species
(16S)
NO: X

FBI00001

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.64
1

FBI00002

Bacteroides salyersiae

bacteria
bacteroidetes
291644

Bacteroides salyersiae

99.5
2

FBI00003

Enterococcus faecalis

bacteria
firmicutes
1351

Enterococcus faecalis

99.93
3

FBI00004

Neglecta timonensis

bacteria
firmicutes
1776382

Neglecta timonensis

99.14
4

FBI00005

Enterococcus casseliflavus

bacteria
firmicutes
37734

Enterococcus gallinarum

99.65
5

FBI00006

Enterobacter himalayensis

bacteria
proteobacteria
547

Enterobacter

99
6

hormaechei

FBI00009

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium faecale

98.6
9

FBI00010

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.12
10

FBI00011

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.28
11

FBI00012

Alistipes onderdonkii

bacteria
bacteroidetes
328813

Alistipes onderdonkii

99.71
12

FBI00013

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.5
13

FBI00015

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
15

FBI00016

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.64
16

pseudocatenulatum

pseudocatenulatum

FBI00017

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.34
17

FBI00018

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.71
18

FBI00019

Alistipes timonensis

bacteria
bacteroidetes
1465754

Alistipes timonensis

99.78
19

FBI00020

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides

99.57
20

thetaiotaomicron

FBI00021

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides kribbi

99.07
21

Bacteroides koreensis

species cluster

FBI00022

Alistipes putredinis

bacteria
bacteroidetes
28117

Alistipes putredinis

99.93
22

FBI00025

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

99.21
25

FBI00027

Fusicatenibacter saccharivorans

bacteria
firmicutes
1150298

Fusicatenibacter

97.6
27

saccharivorans

FBI00029

Parabacteroides distasonis

bacteria
bacteroidetes
823

Parabacteroides

99.26
29

distasonis

FBI00030

Eggerthella lenta

bacteria
firmicutes
84112

Eggerthella lenta

98.47
30

FBI00031

Enterobacter hormaechei

bacteria
proteobacteria
158836

Enterobacter

99.43
31

hormaechei

FBI00033

Lachnospiraceae sp. FBI00033
bacteria
firmicutes
186803

Clostridium

93.56
33

amygdalinum

FBI00034

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.78
34

FBI00036

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.53
36

FBI00038

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

95.96
38

FBI00040

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio

91.38
40

desulfuricans

FBI00041

Phascolarctobacterium faecium

bacteria
firmicutes
33025

Phascolarctobacterium

99.23
41

faecium

FBI00043

Bifidobacterium dentium

bacteria
actinobacteria
1689

Bifidobacterium

99.35
43

dentium

FBI00044

Blautia wexlerae

bacteria
firmicutes
418240

Blautia wexlerae

98.69
44

FBI00046

Bacteroides caccae

bacteria
bacteroidetes
47678

Bacteroides caccae

99.71
46

FBI00047

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.79
47

FBI00048

Fusicatenibacter saccharivorans

bacteria
firmicutes
1150298

Fusicatenibacter

97.95
48

saccharivorans

FBI00049

Dialister succinatiphilus

bacteria
firmicutes
487173

Dialister succinatiphilus

95.74
49

FBI00050

Bacteroides nordii

bacteria
bacteroidetes
291645

Bacteroides nordii

98.63
50

FBI00051

Dorea formicigenerans

bacteria
firmicutes
39486

Dorea formicigenerans

98.07
51

FBI00052

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides

99.14
52

xylanisolvens

FBI00053

Lactobacillus rogosae

bacteria
firmicutes
706562

Lachnospira

97.36
53

pectinoschiza

FBI00055

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides kribbi

99.64
55

Bacteroides koreensis

species cluster

FBI00056

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.2
56

FBI00057

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.7
57

FBI00058

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.71
58

FBI00060

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.49
60

FBI00061

Alistipes shahii

bacteria
bacteroidetes
328814

Alistipes shahii

99.19
61

FBI00062

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.48
62

FBI00066

Parasutterella excrementihominis

bacteria
proteobacteria
487175

Parasutterella

99.13
66

excrementihominis

FBI00067

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

98.84
67

FBI00068

Akkermansia muciniphila

bacteria
verrucomicrobia
239935

Akkermansia

99.42
68

muciniphila

FBI00069

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.84
69

FBI00070

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides koreensis

99.71
70

Bacteroides koreensis

species cluster

FBI00073

Parabacteroides distasonis

bacteria
bacteroidetes
823

Parabacteroides

98.99
73

distasonis

FBI00075

Paraprevotella clara

bacteria
bacteroidetes
454154

Paraprevotella clara

98.85
75

FBI00076

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides

99.78
76

thetaiotaomicron

FBI00077

Sutterella wadsworthensis

bacteria
proteobacteria
40545

Sutterella

99.86
77

wadsworthensis

FBI00080

Sutterella massiliensis

bacteria
proteobacteria
1816689

Sutterella massiliensis

99.78
80

FBI00085

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.62
85

FBI00087

Clostridium scindens

bacteria
firmicutes
29347

Clostridium scindens

98.28
87

FBI00092

Monoglobus pectinilyticus

bacteria
firmicutes
1981510

Monoglobus

99.5
92

pectinilyticus

FBI00093

Roseburia hominis

bacteria
firmicutes
301301

Roseburia hominis

99.71
93

FBI00098

Bacteroides dorei

bacteria
bacteroidetes
357276

Bacteroides dorei

99.93
98

FBI00101

Faecalibacterium prausnitzii

bacteria
firmicutes
853

Faecalibacterium

97.97
101

prausnitzii

FBI00102

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.31
102

FBI00104

Blautia wexlerae

bacteria
firmicutes
418240

Blautia luti

97.18
104

FBI00110

Lachnoclostridium pacaense

bacteria
firmicutes
1917870

Lachnoclostridium

98.92
110

pacaense

FBI00111

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.43
111

FBI00116

Ruminococcus faecis

bacteria
firmicutes
592978

Ruminococcus faecis

99.57
116

FBI00117

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.52
117

FBI00132

Gordonibacter pamelaeae

bacteria
actinobacteria
471189

Gordonibacter

99.48
132

pamelaeae

FBI00133

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
133

FBI00140

Phascolarctobacterium faecium

bacteria
firmicutes
33025

Phascolarctobacterium

99.58
140

faecium

FBI00141

Phascolarctobacterium faecium

bacteria
firmicutes
33025

Phascolarctobacterium

99.15
141

faecium

FBI00155

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.7
155

FBI00289

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
289

TABLE 20

%

NCBI

Match
SEQ ID

Strain #
Species ID
Kingdom
Phylum
Taxonomy ID
Closest 16S Species
(16S)
NO: X

FBI00001

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.64
1

FBI00002

Bacteroides salyersiae

bacteria
bacteroidetes
291644

Bacteroides salyersiae

99.5
2

FBI00004

Neglecta timonensis

bacteria
firmicutes
1776382

Neglecta timonensis

99.14
4

FBI00009

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium faecale

98.6
9

FBI00010

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.12
10

FBI00011

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.28
11

FBI00012

Alistipes onderdonkii

bacteria
bacteroidetes
328813

Alistipes onderdonkii

99.71
12

FBI00013

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.5
13

FBI00015

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
15

FBI00016

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.64
16

pseudocatenulatum

pseudocatenulatum

FBI00018

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.71
18

FBI00019

Alistipes timonensis

bacteria
bacteroidetes
1465754

Alistipes timonensis

99.78
19

FBI00020

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides

99.57
20

thetaiotaomicron

FBI00021

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides kribbi

99.07
21

Bacteroides koreensis

species cluster

FBI00022

Alistipes putredinis

bacteria
bacteroidetes
28117

Alistipes putredinis

99.93
22

FBI00025

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

99.21
25

FBI00027

Fusicatenibacter saccharivorans

bacteria
firmicutes
1150298

Fusicatenibacter

97.6
27

saccharivorans

FBI00029

Parabacteroides distasonis

bacteria
bacteroidetes
823

Parabacteroides

99.26
29

distasonis

FBI00030

Eggerthella lenta

bacteria
firmicutes
84112

Eggerthella lenta

98.47
30

FBI00032

Anaerostipes hadrus

bacteria
firmicutes
649756

Anaerostipes hadrus

99.64
32

FBI00033

Lachnospiraceae sp. FBI00033
bacteria
firmicutes
186803

Clostridium

93.56
33

amygdalinum

FBI00034

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.78
34

FBI00036

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.53
36

FBI00038

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

95.96
38

FBI00040

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio

91.38
40

desulfuricans

FBI00043

Bifidobacterium dentium

bacteria
actinobacteria
1689

Bifidobacterium dentium

99.35
43

FBI00044

Blautia wexlerae

bacteria
firmicutes
418240

Blautia wexlerae

98.69
44

FBI00046

Bacteroides caccae

bacteria
bacteroidetes
47678

Bacteroides caccae

99.71
46

FBI00047

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.79
47

FBI00048

Fusicatenibacter saccharivorans

bacteria
firmicutes
1150298

Fusicatenibacter

97.95
48

saccharivorans

FBI00049

Dialister succinatiphilus

bacteria
firmicutes
487173

Dialister succinatiphilus

95.74
49

FBI00050

Bacteroides nordii

bacteria
bacteroidetes
291645

Bacteroides nordii

98.63
50

FBI00051

Dorea formicigenerans

bacteria
firmicutes
39486

Dorea formicigenerans

98.07
51

FBI00052

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides

99.14
52

xylanisolvens

FBI00053

Lactobacillus rogosae

bacteria
firmicutes
706562

Lachnospira

97.36
53

pectinoschiza

FBI00055

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides kribbi

99.64
55

Bacteroides koreensis

species cluster

FBI00056

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.2
56

FBI00057

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.7
57

FBI00059

Bacteroides stercorirosoris

bacteria
bacteroidetes
871324

Bacteroides oleiciplenus

98.81
59

FBI00060

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.49
60

FBI00061

Alistipes shahii

bacteria
bacteroidetes
328814

Alistipes shahii

99.19
61

FBI00062

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.48
62

FBI00066

Parasutterella excrementihominis

bacteria
proteobacteria
487175

Parasutterella

99.13
66

excrementihominis

FBI00067

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

98.84
67

FBI00068

Akkemiansia muciniphila

bacteria
verrucomicrobia
239935

Akkermansia

99.42
68

muciniphila

FBI00069

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.84
69

FBI00070

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides koreensis

99.71
70

Bacteroides koreensis

species cluster

FBI00071

Lachnospiraceae sp. FBI00071
bacteria
firmicutes
186803

Roseburia faecis

94.92
71

FBI00072

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

96.17
72

FBI00074

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.03
74

FBI00075

Paraprevotella clara

bacteria
bacteroidetes
454154

Paraprevotella clara

98.85
75

FBI00076

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides

99.78
76

thetaiotaomicron

FBI00077

Sutterella wadsworthensis

bacteria
proteobacteria
40545

Sutterella

99.86
77

wadsworthensis

FBI00078

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.34
78

FBI00079

Clostridium clostridioforme

bacteria
firmicutes
1531

Clostridium

99.14
79

clostridioforme

FBI00080

Sutterella massiliensis

bacteria
proteobacteria
1816689

Sutterella massiliensis

99.78
80

FBI00081

Porphyromonas asaccharolytica

bacteria
bacteroidetes
28123

Porphyromonas

99.35
81

asaccharolytica

FBI00082

Ruminococcaceae sp. FBI00082
bacteria
firmicutes
541000

Phocea massiliensis

93.08
82

FBI00097

FBI00085

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.62
85

FBI00087

Clostridium scindens

bacteria
firmicutes
29347

Clostridium scindens

98.28
87

FBI00092

Monoglobus pectinilyticus

bacteria
firmicutes
1981510

Monoglobus

99.5
92

pectinilyticus

FBI00093

Roseburia hominis

bacteria
firmicutes
301301

Roseburia hominis

99.71
93

FBI00096

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.76
96

FBI00097

Ruminococcaceae sp. FBI00082
bacteria
firmicutes
541000

Phocea massiliensis

93.07
97

FBI00097

FBI00099

Gordonibacter pamelaeae

bacteria
actinobacteria
471189

Gordonibacter

99.56
99

pamelaeae

FBI00101

Faecalibacterium prausnitzii

bacteria
firmicutes
853

Faecalibacterium

97.97
101

prausnitzii

FBI00102

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.31
102

FBI00104

Blautia wexlerae

bacteria
firmicutes
418240

Blautia luti

97.18
104

FBI00109

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

98.39
109

FBI00110

Lachnoclostridium pacacnse

bacteria
firmicutes
1917870

Lachnoclostridium

98.92
110

pacaense

FBI00111

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.43
111

FBI00112

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
112

FBI00113

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.79
113

FBI00115

Dorea formicigenerans

bacteria
firmicutes
39486

Dorea formicigenerans

97.98
115

FBI00116

Ruminococcus faecis

bacteria
firmicutes
592978

Ruminococcus faecis

99.57
116

FBI00117

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.52
117

FBI00120

Hungatella effluvii

bacteria
firmicutes
154046

Hungatella hathewayi

98.78
120

FBI00123

Roseburia hominis

bacteria
firmicutes
301301

Roseburia hominis

100
123

FBI00124

Anaerostipes hadrus

bacteria
firmicutes
649756

Anaerostipes hadrus

99.86
124

FBI00125

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

99.64
125

FBI00126

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium

98.98
126

adolescentis

FBI00127

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

98.81
127

FBI00128

Hungatella effluvii

bacteria
firmicutes
1096246

Hungatella effluvii

98.71
128

FBI00132

Gordonibacter pamelaeae

bacteria
actinobacteria
471189

Gordonibacter

99.48
132

pamelaeae

FBI00133

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
133

FBI00135

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.57
135

pseudocatenulatum

pseudocatenulatum

FBI00137

Bacteroides fragilis

bacteria
bacteroidetes
817

Bacteroides fragilis

99.71
137

FBI00140

Phascolarctobacterium faecium

bacteria
firmicutes
33025

Phascolarctobacterium

99.58
140

faecium

FBI00141

Phascolarctobacterium faecium

bacteria
firmicutes
33025

Phascolarctobacterium

99.15
141

faecium

FBI00145

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium

99.14
145

adolescentis

FBI00147

Clostridium bolteae

bacteria
firmicutes
208479

Clostridium bolteae

99.28
147

FBI00149

Monoglobus pectinilyticus

bacteria
firmicutes
1981510

Monoglobus

99.5
149

pectinilyticus

FBI00151

Clostridium aldenense

bacteria
firmicutes
358742

Clostridium aldenense

98.55
151

FBI00152

Dialister invisus

bacteria
firmicutes
218538

Dialister invisus

99.58
152

FBI00159

Eisenbergiella tayi

bacteria
firmicutes
1432052

Eisenbergiella tayi

99.03
159

FBI00162

Bifidobacterium catenulatum

bacteria
actinobacteria
1686

Bifidobacterium

99.14
162

catenulatum

FBI00165

Bacteroides massiliensis

bacteria
bacteroidetes
204516

Bacteroides massiliensis

99.71
165

FBI00167

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.39
167

FBI00170

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.61
170

FBI00171

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio

91.45
171

desulfuricans

FBI00174

Lactobacillus rogosae

bacteria
firmicutes
706562

Lachnospira

97.92
174

pectinoschiza

FBI00175

Holdemanella biformis

bacteria
firmicutes
1735

Holdemanella biformis

98.19
175

FBI00176

Ruthenibacterium lactatiformans

bacteria
firmicutes
1550024

Ruthenibacterium

99.71
176

lactatiformans

FBI00177

Parasutterella excrementihominis

bacteria
proteobacteria
487175

Parasutterella

99.71
177

excrementihominis

FBI00180

Alistipes sp. FBI00180
bacteria
bacteroidetes
239759

Alistipes senegalensis

97.56
180

FBI00182

Bacteroides coprocola

bacteria
bacteroidetes
310298

Bacteroides coprocola

99.64
182

FBI00184

Bacteroides faecis

bacteria
bacteroidetes
674529

Bacteroides faecis

99.78
184

FBI00189

Bacteroides ovatus

bacteria
bacteroidetes
28116

Bacteroides koreensis

99.93
189

FBI00190

Bacteroides finegoldii

bacteria
bacteroidetes
338188

Bacteroides finegoldii

98.91
190

FBI00191

Clostridiaceae sp. FBI00191
bacteria
firmicutes
31979

Clostridium

96.24
191

swellfunianum

FBI00194

Ruminococcus faecis

bacteria
firmicutes
592978

Ruminococcus faecis

98.41
194

FBI00197

Bifidobacterium bifidum

bacteria
actinobacteria
1681

Bifidobacterium bifidum

99.85
197

FBI00198

Lachnoclostridium pacaense

bacteria
firmicutes
1917870

Lachnoclostridium

99.71
198

pacaense

FBI00199

Clostridium bolteae

bacteria
firmicutes
208479

Clostridium bolteae

99.28
199

FBI00200

Longicatena caecimuris

bacteria
firmicutes
1796635

Longicatena caecimuris

99.71
200

FBI00201

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.83
201

FBI00205

Blautia massiliensis

bacteria
firmicutes
1737424

Blautia luti

97.55
205

FBI00206

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

99.56
206

FBI00208

Anaerotruncus massiliensis

bacteria
firmicutes
1673720

Anaerotruncus colihominis

96.52
208

FBI00210

Bifidobacterium bifidum

bacteria
actinobacteria
1681

Bifidobacterium bifidum

99.93
210

FBI00211

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.78
211

FBI00212

Clostridium aldenense

bacteria
firmicutes
358742

Clostridium aldenense

99.1
212

FBI00220

Megasphaera massiliensis

bacteria
firmicutes
1232428

Megasphaera massiliensis

98.8
220

FBI00221

Butyricimonas faecihominis

bacteria
bacteroidetes
1472416

Butyricimonas faecihominis

98.61
221

FBI00224

Sutterella wadsworthensis

bacteria
proteobacteria
40545

Sutterella wadsworthensis

99.71
224

FBI00226

Catabacter hongkongensis

bacteria
firmicutes
270498

Catabacter hongkongensis

99.71
226

FBI00229

Alistipes senegalensis

bacteria
bacteroidetes
1288121

Alistipes senegalensis

99.19
229

FBI00232

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

98.84
232

FBI00233

Ruminococcaceae sp. FBI00233
bacteria
firmicutes
474960

Anaerotruncus

91.63
233

colihominis

FBI00234

Faecalicatena contorta

bacteria
firmicutes
39482

Faecalicatena contorta

99.21
234

FBI00236

Eisenbergiella tayi

bacteria
firmicutes
1432052

Eisenbergiella tayi

99.41
236

FBI00237

Dielma fastidiosa

bacteria
firmicutes
1034346

Dielma fastidiosa

99.78
237

FBI00238

Alistipes sp. FBI00238
bacteria
bacteroidetes
239759

Alistipes finegoldii

95.84
238

FBI00239

Lactonifactor longoviformis

bacteria
firmicutes
341220

Lactonifactor

98.99
239

longoviformis

FBI00243

Eubacterium siraeum

bacteria
firmicutes
39492

Eubacterium siraeum

98.53
243

FBI00244

Faecalibacterium prausnitzii

bacteria
firmicutes
853

Faecalibacterium

98.69
244

prausnitzii

FBI00245

Acidaminococcus intestini

bacteria
firmicutes
187327

Acidaminococcus

99.72
245

intestini

FBI00248

Neglecta timonensis

bacteria
firmicutes
1776382

Emergencia timonensis

99.64
248

FBI00249

Citrobacter portucalensis

bacteria
proteobacteria
1639133

Citrobacter freundii

99.79
249

FBI00251

Bifidobacterium

bacteria
actinobacteria
28026

Bifidobacterium

99.85
251

pseudocatenulatum

pseudocatenulatum

FBI00254

Eubacterium hallii

bacteria
firmicutes
39488

Eubacterium hallii

99.08
254

FBI00255

Hungatella effluvii

bacteria
firmicutes
1096246

Hungatella hathewayi

98.56
255

FBI00258

Turicibacter sanguinis

bacteria
firmicutes
154288

Turicibacter sanguinis

99.93
258

FBI00260

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.64
260

FBI00263

Bacteroides caccae

bacteria
bacteroidetes
47678

Bacteroides caccae

99.56
263

FBI00267

Anaerofustis stercorihominis

bacteria
firmicutes
214853

Anaerofustis

97.29
267

stercorihominis

FBI00269

Alistipes putredinis

bacteria
bacteroidetes
28117

Alistipes putredinis

100
269

FBI00271

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides

98.42
271

xylanisolvens

FBI00273

Barnesiella intestinihominis

bacteria
bacteroidetes
487174

Barnesiella

99.43
273

intestinihominis

FBI00274

Eubacterium xylanophilum

bacteria
firmicutes
39497

Eubacterium

93.5
274

xylanophilum

FBI00275

Holdemanella biformis

bacteria
firmicutes
1735

Holdemanella biformis

98.99
275

FBI00277

Alistipes onderdonkii

bacteria
bacteroidetes
328813

Alistipes onderdonkii

99.63
277

FBI00278

Eubacterium ventriosum

bacteria
firmicutes
39496

Eubacterium ventriosum

94.14
278

FBI00281

Senegalimassilia anaerobia

bacteria
actinobacteria
1473216

Senegalimassilia anaerobia

99.45
281

FBI00282

Porphyromonas asaccharolytica

bacteria
bacteroidetes
28123

Porphyromonas

99.35
282

asaccharolytica

FBI00288

Blautia hydrogenotrophica

bacteria
firmicutes
53443

Blautia hydrogenotrophica

99.57
288

FBI00289

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
289

FBI00290

Lachnospiraceae sp. FBI00290
bacteria
firmicutes
186803

Eubacterium

94.81
290

ruminantium

Example 12: In Vivo Oxalate Reduction by Candidate Consortia in a Germ-Free Mouse Model Fed a Low-Complexity Diet

A set of five candidate oxalate-eliminating microbial consortia, comprising active and supportive microbes isolated from human fecal samples as described in Example 1, were tested for the ability to control oxalate levels in vivo in germ-free mice fed a limited ingredient, low-complexity diet supplemented with oxalate (see Table 1).

One week prior to colonization, germ-free C57Bl/6NTac mice (n=4 per condition) were fed a refined diet rich in casein and simple sugars supplemented with oxalate to induce hyperoxaluria (see Table 2). One week later, the candidate consortia described in Example 11 (I to V) were introduced to the mice via oral gavage. One group of mice was mock-colonized with PBS alone as a negative control. Another group of mice was colonized with a previously-characterized microbial consortium as a positive control, which contains microbial strains sourced from depositories and was previously shown to reduce oxalate levels in vivo (see Examples 6 and 7; Table 8). Urine and fecal samples were collected each week for two weeks thereafter, with an endpoint at 14 days following colonization. Terminal urine (collected immediately following euthanasia) was processed by solid-phase extraction and oxalate levels were quantified by LC/MS as described in Example 4.

Average urinary oxalate concentrations for each study group at study endpoint are reported in FIG. 13. Mice colonized with the positive control proof-of-concept community containing commercially sourced strains of O. formigenes (+) exhibited a 53% average reduction in urinary oxalate relative to the uncolonized negative control (−). The five proprietary candidate communities (I-V), each of which comprised three internally isolated strains of O. formigenes, were found to reduce urinary oxalate by 32-70%, demonstrating efficacy on par with the positive control community. The reduction in urinary oxalate for all tested communities was statistically significant relative to the negative control.

Example 13: In Vivo Oxalate Reduction by Candidate Consortia in a Germ Free Mouse Fed a High-Complexity Diet

The set of five candidate oxalate-eliminating microbial consortia described in Example 10 were further tested for the ability to control oxalate levels in vivo in germ free mice fed a complex, nutritionally complete diet.

One week prior to colonization, germ-free C57Bl/6NTac mice (n=4 per condition) were fed a complex, grain-based diet and given ad libitum drinking water supplemented with 0.875% oxalate to induce hyperoxaluria. One week later, the mice were colonized with the therapeutic communities via oral gavage. One group of mice was mock-colonized with PBS alone as a negative control. Another group of mice was colonized with a previously-characterized microbial consortium as a positive control, which contained microbial strains sourced from depositories and was previously shown to reduce oxalate levels in vivo (see Examples 6 and 7; Table 8). Urine and fecal samples were collected each week for two weeks thereafter, with a study endpoint at 8 days following colonization. Terminal urine (collected immediately following euthanasia) was processed by solid-phase extraction and oxalate levels were quantified using LC-MS as described in Example 4.

Average urinary oxalate concentrations for each study group at study endpoint are presented in FIG. 14. Mice colonized with the positive control community containing commercially sourced strains of O. formigenes (+) exhibited a 54% average reduction in urinary oxalate relative to the uncolonized negative control (−). The five proprietary candidate communities (I-V), each of which comprised three internally isolated strains of O. formigenes, were found to reduce urinary oxalate by 49-75%, demonstrating efficacy on par with the positive control community. The reduction in urinary oxalate for all tested communities was statistically significant relative to the negative control.

Example 14: In Vivo Oxalate Reduction by Candidate Consortia in a Humanized Gnotobiotic Mouse

The set of five candidate oxalate-eliminating microbial consortia described in Example 11 were further tested for the ability to control oxalate levels in vivo in humanized, recolonized mice fed a complex, nutritionally complete diet.

Germ-free C57B1/6NTac mice (n=4 per condition) were humanized by introducing a previously characterized human donor fecal sample that lacks O. formigenes and does not appreciably degrade urinary oxalate. One week following colonization, the humanized mice were fed a complex, grain-based diet supplemented with oxalate to induce hyperoxaluria. One week later, the mice were given an antibiotic cocktail containing ampicillin (1 mg/ml) and enrofloxacin (0.575 mg/ml) ad libidum in drinking water for seven days, after which the antibiotic treatment was ended and the therapeutic communities (I-V) were introduced via oral gavage. One group of mice was mock-colonized with PBS alone as a negative control. Another group of mice was colonized with a previously-characterized microbial consortium as a positive control, which contained microbial strains sourced from depositories and was previously shown to reduce oxalate levels in vivo (see Examples 6 and 7; Table 8). A final group of mice was colonized with a set of strains (“Putative Oxalate Degraders”) that included three donor-derived strains of O. formigenes in addition to other donor-derived strains predicted to have oxalate-degrading activity. This set of strains is listed in Table 21.

TABLE 21

SEQ ID

Strain #
Species ID
NO: X

FBI00001

Clostridium citroniae

1

FBI00002

Bacteroides salyersiae

2

FBI00004

Neglecta timonensis

4

FBI00008

Blautia luti

8

FBI00009

Bifidobacterium adolescentis

9

FBI00011

Bifidobacterium longum

11

FBI00016

Bifidobacterium pseudocatenulatum

16

FBI00017

Blautia obeum

17

FBI00020

Bacteroides thetaiotaomicron

20

FBI00021

Bacteroides kribbi/Bacteroides koreensis
21

species cluster

FBI00028

Oscillibacter sp. FBI00028
28

FBI00030

Eggerthella lenta

30

FBI00033
Lachnospiraceae sp. FBI00033
33

FBI00041

Phascolarctobacterium faecium

41

FBI00043

Bifidobacterium dentium

43

FBI00045

Bifidobacterium adolescentis

45

FBI00050

Bacteroides nordii

50

FBI00052

Bacteroides xylanisolvens

52

FBI00053

Lactobacillus rogosae

53

FBI00056

Clostridium citroniae

56

FBI00060

Bifidobacterium longum

60

FBI00063

Lachnospira sp. FBI00063 FBI00285 FBI00364
63

FBI00064

Dorea sp. FBI00064
64

FBI00067

Oxalobacter formigenes

67

FBI00069

Ruminococcus bromii

69

FBI00070

Bacteroides kribbi/Bacteroides koreensis
70

species cluster

FBI00133

Oxalobacter formigenes

133

FBI00289

Oxalobacter formigenes

289

Mice were sampled each week for two weeks following recolonization to determine microbiome composition and urinary oxalate levels, with a study endpoint at 14 days following colonization with the experimental communities. Average urinary oxalate concentrations for each study group at study endpoint are presented in FIG. 15. Re-colonization with the positive control proof-of-concept community containing commercially sourced strains of O. formigenes (+) yielded a 52% average reduction in urinary oxalate relevant to the mock-treated negative control (−). The five proprietary candidate communities (I-V), each of which comprises three donor-derived strains of O. formigenes, were found to reduce urinary oxalate by 22-65%, demonstrating efficacy on par with the positive control community. The reduction in urinary oxalate for all tested communities was statistically significant for all but one community (IV), with no significant differences observed between the remaining colonized groups. Notably, recolonization with the set of putative oxalate-degrading microbes alone did not result in a reduction in urinary oxalate, demonstrating the enhanced effect of combining a plurality of active oxalate-degrading microbes with a rationally designed supportive community.

Mouse fecal samples were analyzed by metagenomic sequencing in order to determine the composition of the microbiome. Briefly, genomic DNA was extracted from mouse fecal pellets and sequenced using short-read (Illumina) sequencing. Individual reads were classified against a comprehensive reference database, containing genomes from species throughout the tree of life. The total reads classified to a species were summed and normalized by genome size to obtain estimates of relative abundance. The results of this analysis are summarized in FIG. 16. Re-colonization with one of the candidate microbial consortia (I-V) resulted in enhanced microbiome species diversity relative to both the proof-of-concept consortium and the collection of Putative Oxalate Degraders.

Example 15: Effect of Candidate Supportive Communities on In Vivo Engraftment of O. Formigenes

The set of five candidate oxalate-eliminating microbial consortia described in Example 10 were further tested for the ability to support engraftment of the active oxalate-degrading microbe O. formigenes into germ-free mice.

Germ-free C57Bl/6NTac mice (n=4 per condition) were colonized with candidate microbial consortia (I to V) via oral gavage. One group of mice was colonized with only a supportive community of microbes as a negative control. At the conclusion of the experiment, fecal samples were analyzed via metagenomic sequencing to measure the relative and absolute abundance of O. formigenes in the microbiome. Briefly, genomic DNA was extracted from mouse fecal pellets and sequenced using short-read (Illumina) sequencing. Individual reads were classified against a comprehensive reference database, containing genomes from species throughout the tree of life. The total reads classified to a species were summed and normalized by genome size to obtain estimates of relative abundance. Absolute abundance estimates were obtained by injecting a known quantity of heterologous cells into the fecal sample prior to DNA extraction and sequencing.

The results of this study are reported in FIG. 17. O. formigenes was detected in all mice colonized with one of the five candidate consortia, and treatment with candidate V resulted in the largest quantity of O. formigenes in the fecal sample.

Example 16: Production of an Exemplary Therapeutic Oxalate-Degrading Consortium

This example describes the production of an exemplary microbial consortium intended for use in human subjects. In one embodiment of the invention, said exemplary consortium consists of the strains listed in Table 22, including three active oxalate-degrader strains of donor-derived O. formigenes. In another embodiment of the invention, said exemplary consortium consists of the strains listed in in Table 23. In another embodiment of the invention, said exemplary consortium consists of the strains listed in Table 24. All strains included in the exemplary consortium meet at least one of five criteria:

- a. Has an experimentally confirmed ability to eliminate oxalate in vitro
- b. Belongs to a species that is known to metabolize formate, a primary byproduct and potential inhibitor of oxalate metabolism in the gut
- c. Belongs to a species known to contribute to metabolism of one or more nutrients typically found in the human diet
- d. Belongs to species known to fulfill unique and potentially beneficial biological functions in the GI tract (e.g., bile salt hydrolase activity or butyrate production)
- e. Belongs to a species found in the GI tract of one or more healthy human adults.

The final drug product consists of up to 7 drug substances, each comprising at least one characterized bacterial strain. Some drug substances are pure cultures, whereas others are from mixed-culture fermentation of anaerobic and facultative aerobic bacteria. The drug substance culture conditions are determined by one skilled in the art.

Cells are harvested and concentrated by a combination of microfiltration using 0.2-0.45 μm pore size membranes made of nonreactive polymers such as Polyvinylidene fluoride, Polysulfones, and/or nitrocellulose; and centrifugation (10,000-20,000 g force) to a final CFU concentration of 1×10⁶to 1×10¹²CFU/ml. The concentrated biomass is mixed with sterilized cryoprotectant agent (CPA) at a volumetric ratio between 10:1 to 1:10.

The CPA is composed of a cryoprotectant/carbohydrate/bulking agent/nutrient such as glycerol (0 to 250 g/l), maltodextrin (0 to 100 g/l), sucrose (0 to 100 g/l), inulin (0 to 40 g/l), trehalose (0 to 50 g/l) and/or alginate (0 to 10 g/l). Additionally, antioxidants such as cysteine (0.25 to 0.50 g/l), ascorbic acid (0 to 5 g/l) and/or riboflavin (0 to 0.01 g/l) are added to CPA. The specific concentrations are determined by a person skilled in the art.

Finally, additional nutrients such as oxalate (0-100 mM) or formate (0-100 mM) are added to support robust revival of specific strains from the capsule, the specific concentrations being determined by one skilled in the art.

The cells are either stored frozen in a CPA or combination of CPAs, or are lyophilized to prepare various solid oral dosage forms (e.g., enteric coated capsules or enteric coated tablets). The formulated cells are lyophilized to yield a stable product. Primary drying is conducted below collapse temperature of the chosen formulation (typically below −20° C.), followed by secondary drying at higher temperature (5° C. or higher). Lyophilized powder is filled in “0” to “000” size capsules to accommodate various strengths. To prepare tablets, lyophilized powder is added to a binding agent (e.g. sucrose or starch) and pressed into tablets. The tablets are enteric coated to protect the drug product from the low pH gastric environment.

Composition of the drug product is defined by the Relative Abundance of the various intended strains. The relative abundance of microbial strains in the drug substance or drug product is determined as follows: total bacterial genomic DNA is extracted from a pelleted aliquot (e.g. 1 ml) of the drug substance/product and quantified, normalized by concentration, and prepared into an indexed library for whole-genome shotgun sequencing on an Illumina sequencer (e.g. NovaSeq). Following quality trimming, short paired-end Illumina reads (PE-150) are classified using a custom bioinformatics pipeline and taxonomically-structured database built from the genome sequences of strains in the drug product. The taxonomically-structured database links genome nucleotide sequences of a fixed length (k-mers) to a least common ancestor(s) (strain, species . . . phylum) that contain the same k-mer in the database. 150 base-pair sequencing reads are classified by retrieving the taxa for all k-mers in the read and assigning a classification based on the least common ancestor. Sequences that have no k-mers in the database are discarded. Reads that do not get classified to the strain level are distributed to the strain level using Bayes theorem to estimate true strain-level abundance. The relative abundance of a strain is calculated as the percentage of reads that are classified as that strain, divided by genome size. Absolute abundance is calculated by dividing the total bacterial cell number in the drug product (quantified by Beckman Coulter Counter) by the percent relative abundance.

A person of ordinary skill in the art shall be able to determine useful ratios of active and supportive microbes that constitute the exemplary consortium, and shall ensure that the relative abundance of supportive microbial strains is at least sufficient to enable function and stable engraftment of the plurality of active microbes.

TABLE 22

NCBI

%
SEQ

Taxonomy

Match
ID NO:

Strain #
Species ID
Kingdom
Phylum
ID
Closest 16S Species
(16S)
X

FBI00001

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.64
1

FBI00002

Bacteroides salyersiae

bacteria
bacteroidetes
291644

Bacteroides salyersiae

99.5
2

FBI00004

Neglecta timonensis

bacteria
firmicutes
1776382

Neglecta timonensis

99.14
4

FBI00009

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium faecale

98.6
9

FBI00010

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.12
10

FBI00011

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.28
11

FBI00012

Alistipes onderdonkii

bacteria
bacteroidetes
328813

Alistipes onderdonkii

99.71
12

FBI00013

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.5
13

FBI00015

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
15

FBI00016

Bifidobacterium pseudocatenulatum

bacteria
actinobacteria
28026

Bifidobacterium pseudocatenulatum

99.64
16

FBI00018

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.71
18

FBI00019

Alistipes timonensis

bacteria
bacteroidetes
1465754

Alistipes timonensis

99.78
19

FBI00020

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides thetaiotaomicron

99.57
20

FBI00021

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides kribbi

99.07
21

Bacteroides koreensis species

cluster

FBI00022

Alistipes putredinis

bacteria
bacteroidetes
28117

Alistipes putredinis

99.93
22

FBI00025

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

99.21
25

FBI00027

Fusicatenibacter saccharivorans

bacteria
firmicutes
1150298

Fusicatenibacter saccharivorans

97.6
27

FBI00029

Parabacteroides distasonis

bacteria
bacteroidetes
823

Parabacteroides distasonis

99.26
29

FBI00030

Eggerthella lenta

bacteria
firmicutes
84112

Eggerthella lenta

98.47
30

FBI00032

Anaerostipes hadrus

bacteria
firmicutes
649756

Anaerostipes hadrus

99.64
32

FBI00033

Lachnospiraceae sp. FBI00033
bacteria
firmicutes
186803

Clostridium amygdalinum

93.56
33

FBI00034

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.78
34

FBI00036

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.53
36

FBI00038

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

95.96
38

FBI00040

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio desulfuricans

91.38
40

FBI00043

Bifidobacterium dentium

bacteria
actinobacteria
1689

Bifidobacterium dentium

99.35
43

FBI00044

Blautia wexlerae

bacteria
firmicutes
418240

Blautia wexlerae

98.69
44

FBI00046

Bacteroides caccae

bacteria
bacteroidetes
47678

Bacteroides caccae

99.71
46

FBI00047

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.79
47

FBI00048

Fusicatenibacter saccharivorans

bacteria
firmicutes
1150298

Fusicatenibacter saccharivorans

97.95
48

FBI00049

Dialister succinatiphilus

bacteria
firmicutes
487173

Dialister succinatiphilus

95.74
49

FBI00050

Bacteroides nordii

bacteria
bacteroidetes
291645

Bacteroides nordii

98.63
50

FBI00051

Dorea formicigenerans

bacteria
firmicutes
39486

Dorea formicigenerans

98.07
51

FBI00052

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

99.14
52

FBI00053

Lactobacillus rogosae

bacteria
firmicutes
706562

Lachnospira pectinoschiza

97.36
53

FBI00055

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides kribbi

99.64
55

Bacteroides koreensis species

cluster

FBI00056

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.2
56

FBI00057

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.7
57

FBI00059

Bacteroides stercorirosoris

bacteria
bacteroidetes
871324

Bacteroides oleiciplenus

98.81
59

FBI00060

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.49
60

FBI00061

Alistipes shahii

bacteria
bacteroidetes
328814

Alistipes shahii

99.19
61

FBI00062

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.48
62

FBI00066

Parasutterella excrementihominis

bacteria
proteobacteria
487175

Parasutterella excrementihominis

99.13
66

FBI00067

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

98.84
67

FBI00068

Akkermansia muciniphila

bacteria
verruco-
239935

Akkermansia muciniphila

99.42
68

microbia

FBI00069

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.84
69

FBI00070

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides koreensis

99.71
70

Bacteroides koreensis species

cluster

FBI00071

Lachnospiraceae sp. FBI00071
bacteria
firmicutes
186803

Roseburia faecis

94.92
71

FBI00072

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

96.17
72

FBI00074

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.03
74

FBI00075

Paraprevotella clara

bacteria
bacteroidetes
454154

Paraprevotella clara

98.85
75

FBI00076

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides thetaiotaomicron

99.78
76

FBI00077

Sutterella wadsworthensis

bacteria
proteobacteria
40545

Sutterella wadsworthensis

99.86
77

FBI00078

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.34
78

FBI00079

Clostridium clostridioforme

bacteria
firmicutes
1531

Clostridium clostridioforme

99.14
79

FBI00080

Sutterella massiliensis

bacteria
proteobacteria
1816689

Sutterella massiliensis

99.78
80

FBI00081

Porphyromonas asaccharolytica

bacteria
bacteroidetes
28123

Porphyromonas asaccharolytica

99.35
81

FBI00082

Ruminococcaceae sp. FBI00082
bacteria
firmicutes
541000

Phocea massiliensis

93.08
82

FBI00097

FBI00085

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.62
85

FBI00087

Clostridium scindens

bacteria
firmicutes
29347

Clostridium scindens

98.28
87

FBI00092

Monoglobus pectinilyticus

bacteria
firmicutes
1981510

Monoglobus pectinilyticus

99.5
92

FBI00093

Roseburia hominis

bacteria
firmicutes
301301

Roseburia hominis

99.71
93

FBI00096

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.76
96

FBI00097

Ruminococcaceae sp. FBI00082
bacteria
firmicutes
541000

Phocea massiliensis

93.07
97

FBI00097

FBI00099

Gordonibacter pamelaeae

bacteria
actinobacteria
471189

Gordonibacter pamelaeae

99.56
99

FBI00101

Faecalibacterium prausnitzii

bacteria
firmicutes
853

Faecalibacterium prausnitzii

97.97
101

FBI00102

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.31
102

FBI00104

Blautia wexlerae

bacteria
firmicutes
418240

Blautia luti

97.18
104

FBI00109

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

98.39
109

FBI00110

Lachnoclostridium pacaense

bacteria
firmicutes
1917870

Lachnoclostridium pacaense

98.92
110

FBI00111

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.43
111

FBI00112

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
112

FBI00113

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.79
113

FBI00115

Dorea formicigenerans

bacteria
firmicutes
39486

Dorea formicigenerans

97.98
115

FBI00116

Ruminococcus faecis

bacteria
firmicutes
592978

Ruminococcus faecis

99.57
116

FBI00117

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.52
117

FBI00120

Hungatella effluvii

bacteria
firmicutes
154046

Hungatella hathewayi

98.78
120

FBI00123

Roseburia hominis

bacteria
firmicutes
301301

Roseburia hominis

100
123

FBI00124

Anaerostipes hadrus

bacteria
firmicutes
649756

Anaerostipes hadrus

99.86
124

FBI00125

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

99.64
125

FBI00126

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium adolescentis

98.98
126

FBI00127

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

98.81
127

FBI00128

Hungatella effluvii

bacteria
firmicutes
1096246

Hungatella effluvii

98.71
128

FBI00132

Gordonibacter pamelaeae

bacteria
actinobacteria
471189

Gordonibacter pamelaeae

99.48
132

FBIOO133

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
133

FBI00135

Bifidobacterium pseudocatenulatum

bacteria
actinobacteria
28026

Bifidobacterium pseudocatenulatum

99.57
135

FBI00137

Bacteroides fragilis

bacteria
bacteroidetes
817

Bacteroides fragilis

99.71
137

FBI00140

Phascolarctobacterium faecium

bacteria
firmicutes
33025

Phascolarctobacterium faecium

99.58
140

FBI00141

Phascolarctobacterium faecium

bacteria
firmicutes
33025

Phascolarctobacterium faecium

99.15
141

FBI00145

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium adolescentis

99.14
145

FBI00147

Clostridium bolteae

bacteria
firmicutes
208479

Clostridium bolteae

99.28
147

FBI00149

Monoglobus pectinilyticus

bacteria
firmicutes
1981510

Monoglobus pectinilyticus

99.5
149

FBI00151

Clostridium aldenense

bacteria
firmicutes
358742

Clostridium aldenense

98.55
151

FBI00152

Dialister invisus

bacteria
firmicutes
218538

Dialister invisus

99.58
152

FBI00159

Eisenbergiella tayi

bacteria
firmicutes
1432052

Eisenbergiella tayi

99.03
159

FBI00162

Bifidobacterium catenulatum

bacteria
actinobacteria
1686

Bifidobacterium catenulatum

99.14
162

FBI00165

Bacteroides massiliensis

bacteria
bacteroidetes
204516

Bacteroides massiliensis

99.71
165

FBI00167

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.39
167

FBI00170

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.61
170

FBI00171

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio desulfuricans

91.45
171

FBI00174

Lactobacillus rogosae

bacteria
firmicutes
706562

Lachnospira pectinoschiza

97.92
174

FBI00175

Holdemanella biformis

bacteria
firmicutes
1735

Holdemanella biformis

98.19
175

FBI00176

Ruthenibacterium lactatiformans

bacteria
firmicutes
1550024

Ruthenibacterium lactatiformans

99.71
176

FBI00177

Parasutterella excrementihominis

bacteria
proteobacteria
487175

Parasutterella excrementihominis

99.71
177

FBI00180

Alistipes sp. FBI00180
bacteria
bacteroidetes
239759

Alistipes senegalensis

97.56
180

FBI00182

Bacteroides coprocola

bacteria
bacteroidetes
310298

Bacteroides coprocola

99.64
182

FBI00184

Bacteroides faecis

bacteria
bacteroidetes
674529

Bacteroides faecis

99.78
184

FBI00189

Bacteroides ovatus

bacteria
bacteroidetes
28116

Bacteroides koreensis

99.93
189

FBI00190

Bacteroides finegoldii

bacteria
bacteroidetes
338188

Bacteroides finegoldii

98.91
190

FBI00191

Clostridiaceae sp. FBI00191
bacteria
firmicutes
31979

Clostridium swellfunianum

96.24
191

FBI00194

Ruminococcus faecis

bacteria
firmicutes
592978

Ruminococcus faecis

98.41
194

FBI00197

Bifidobacterium bifidum

bacteria
actinobacteria
1681

Bifidobacterium bifidum

99.85
197

FBI00198

Lachnoclostridium pacaense

bacteria
firmicutes
1917870

Lachnoclostridium pacaense

99.71
198

FBI00199

Clostridium bolteae

bacteria
firmicutes
208479

Clostridium bolteae

99.28
199

FBI00200

Longicatena caecimuris

bacteria
firmicutes
1796635

Longicatena caecimuris

99.71
200

FBI00201

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.83
201

FBI00205

Blautia massiliensis

bacteria
firmicutes
1737424

Blautia luti

97.55
205

FBI00206

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

99.56
206

FBI00208

Anaerotruncus massiliensis

bacteria
firmicutes
1673720

Anaerotruncus colihominis

96.52
208

FBI00210

Bifidobacterium bifidum

bacteria
actinobacteria
1681

Bifidobacterium bifidum

99.93
210

FBI00211

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.78
211

FBI00212

Clostridium aldenense

bacteria
firmicutes
358742

Clostridium aldenense

99.1
212

FBI00220

Megasphaera massiliensis

bacteria
firmicutes
1232428

Megasphaera massiliensis

98.8
220

FBI00221

Butyricimonas faecihominis

bacteria
bacteroidetes
1472416

Butyricimonas faecihominis

98.61
221

FBI00224

Sutterella wadsworthensis

bacteria
proteobacteria
40545

Sutterella wadsworthensis

99.71
224

FBI00226

Catabacter hongkongensis

bacteria
firmicutes
270498

Catabacter hongkongensis

99.71
226

FBI00229

Alistipes senegalensis

bacteria
bacteroidetes
1288121

Alistipes senegalensis

99.19
229

FBI00231

Parabacteroides distasonis

bacteria
bacteroidetes
823

Parabacteroides distasonis

99.11
231

FBI00232

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

98.84
232

FBI00233

Ruminococcaceae sp. FBI00233
bacteria
firmicutes
474960

Anaerotruncus colihominis

91.63
233

FBI00235

Alistipes shaliii

bacteria
bacteroidetes
328814

Alistipes shahii

99.86
235

FBI00236

Eisenbergiella tayi

bacteria
firmicutes
1432052

Eisenbergiella tayi

99.41
236

FBI00237

Dielma fastidiosa

bacteria
firmicutes
1034346

Dielma fastidiosa

99.78
237

FBI00238

Alistipes sp. FBI00238
bacteria
bacteroidetes
239759

Alistipes finegoldii

95.84
238

FBI00243

Eubacterium siraeum

bacteria
firmicutes
39492

Eubacterium siraeum

98.53
243

FBI00244

Faecalibacterium prausnitzii

bacteria
firmicutes
853

Faecalibacterium prausnitzii

98.69
244

FBI00245

Acidaminococcus intestini

bacteria
firmicutes
187327

Acidaminococcus intestini

99.72
245

FBI00248

Neglecta timonensis

bacteria
firmicutes
1776382

Emergencia timonensis

99.64
248

FBI00251

Bifidobacterium pseudocatenulatum

bacteria
actinobacteria
28026

Bifidobacterium pseudocatenulatum

99.85
251

FBI00254

Eubacterium hallii

bacteria
firmicutes
39488

Eubacterium hallii

99.08
254

FBI00255

Hungatella effluvii

bacteria
firmicutes
1096246

Hungatella hathewayi

98.56
255

FBI00258

Turicibacter sanguinis

bacteria
firmicutes
154288

Turicibacter sanguinis

99.93
258

FBI00260

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.64
260

FBI00263

Bacteroides caccae

bacteria
bacteroidetes
47678

Bacteroides caccae

99.56
263

FBI00267

Anaerofustis stercorihominis

bacteria
firmicutes
214853

Anaerofustis stercorihominis

97.29
267

FBI00269

Alistipes putredinis

bacteria
bacteroidetes
28117

Alistipes putredinis

100
269

FBI00270

Methanobrevibacter smithii

archaea
euryarchaeota
2173

Methanobrevibacter smithii

99.69
270

FBI00271

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

98.42
271

FBI00273

Bamesiella intestinihominis

bacteria
bacteroidetes
487174

Bamesiella intestinihominis

99.43
273

FBI00274

Eubacterium xylanophilum

bacteria
firmicutes
39497

Eubacterium xylanophilum

93.5
274

FBI00275

Holdemanella biformis

bacteria
firmicutes
1735

Holdemanella biformis

98.99
275

FBI00277

Alistipes onderdonkii

bacteria
bacteroidetes
328813

Alistipes onderdonkii

99.63
277

FBI00278

Eubacterium ventriosum

bacteria
firmicutes
39496

Eubacterium ventriosum

94.14
278

FBI00281

Senegalimassilia anaerobia

bacteria
actinobacteria
1473216

Senegalimassilia anaerobia

99.45
281

FBI00282

Porphyromonas asaccharolytica

bacteria
bacteroidetes
28123

Porphyromonas asaccharolytica

99.35
282

FBI00288

Blautia hydrogenotrophica

bacteria
firmicutes
53443

Blautia hydrogenotrophica

99.57
288

FBI00289

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
289

FBI00290

Lachnospiraceae sp. FBI00290
bacteria
firmicutes
186803

Eubacterium ruminantium

94.81
290

FBI00292

Methanobrevibacter smithii

archaea
euryarchaeota
2173

Methanobrevibacter smithii

99.44
292

FBI00377

Clostridiales sp. FBI00377
bacteria
firmicutes
186802

Christensenella massiliensis

88.69
377

TABLE 23

NCBI

%
SEQ

Taxonomy

Match
ID NO:

Strain #
Species ID
Kingdom
Phylum
ID
Closest 16S Species
(16S)
X

FBI00001

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.64
1

FBI00002

Bacteroides salyersiae

bacteria
bacteroidetes
291644

Bacteroides salyersiae

99.5
2

FBI00004

Neglecta timonensis

bacteria
firmicutes
1776382

Neglecta timonensis

99.14
4

FBI00009

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium faecale

98.6
9

FBI00010

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.12
10

FBI00011

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.28
11

FBI00012

Alistipes onderdonkii

bacteria
bacteroidetes
328813

Alistipes onderdonkii

99.71
12

FBI00013

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.5
13

FBI00015

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
15

FBI00016

Bifidobacterium pseudocatenulatum

bacteria
actinobacteria
28026

Bifidobacterium pseudocatenulatum

99.64
16

FBI00018

Eubacterium rectale

bacteria
firmicutes
39491

Eubacterium rectale

99.71
18

FBI00019

Alistipes timonensis

bacteria
bacteroidetes
1465754

Alistipes timonensis

99.78
19

FBI00020

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides thetaiotaomicron

99.57
20

FBI00021

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides kribbi

99.07
21

Bacteroides koreensis species

cluster

FBI00022

Alistipes putredinis

bacteria
bacteroidetes
28117

Alistipes putredinis

99.93
22

FBI00025

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

99.21
25

FBI00027

Fusicatenibacter saccharivorans

bacteria
firmicutes
1150298

Fusicatenibacter saccharivorans

97.6
27

FBI00029

Parabacteroides distasonis

bacteria
bacteroidetes
823

Parabacteroides distasonis

99.26
29

FBI00030

Eggerthella lenta

bacteria
firmicutes
84112

Eggerthella lenta

98.47
30

FBI00032

Anaerostipes hadrus

bacteria
firmicutes
649756

Anaerostipes hadrus

99.64
32

FBI00033

Lachnospiraceae sp. FBI00033
bacteria
firmicutes
186803

Clostridium amygdalinum

93.56
33

FBI00034

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.78
34

FBI00036

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.53
36

FBI00038

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

95.96
38

FBI00040

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio desulfuricans

91.38
40

FBI00043

Bifidobacterium dentium

bacteria
actinobacteria
1689

Bifidobacterium dentium

99.35
43

FBI00044

Blautia wexlerae

bacteria
firmicutes
418240

Blautia wexlerae

98.69
44

FBI00046

Bacteroides caccae

bacteria
bacteroidetes
47678

Bacteroides caccae

99.71
46

FBI00047

Eubacterium eligens

bacteria
firmicutes
39485

Eubacterium eligens

98.79
47

FBI00048

Fusicatenibacter saccharivorans

bacteria
firmicutes
1150298

Fusicatenibacter saccharivorans

97.95
48

FBI00049

Dialister succinatiphilus

bacteria
firmicutes
487173

Dialister succinatiphilus

95.74
49

FBI00050

Bacteroides nordii

bacteria
bacteroidetes
291645

Bacteroides nordii

98.63
50

FBI00051

Dorea formicigenerans

bacteria
firmicutes
39486

Dorea formicigenerans

98.07
51

FBI00052

Bacteroides xylanisolvens

bacteria
bacteroidetes
371601

Bacteroides xylanisolvens

99.14
52

FBI00053

Lactobacillus rogosae

bacteria
firmicutes
706562

Lachnospira pectinoschiza

97.36
53

FBI00055

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides kribbi

99.64
55

Bacteroides koreensis species

cluster

FBI00056

Clostridium citroniae

bacteria
firmicutes
358743

Clostridium citroniae

99.2
56

FBI00057

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.7
57

FBI00059

Bacteroides stercorirosoris

bacteria
bacteroidetes
871324

Bacteroides oleiciplenus

98.81
59

FBI00060

Bifidobacterium longum

bacteria
actinobacteria
216816

Bifidobacterium longum

99.49
60

FBI00061

Alistipes shahii

bacteria
bacteroidetes
328814

Alistipes shahii

99.19
61

FBI00062

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

99.48
62

FBI00066

Parasutterella excrementihominis

bacteria
proteobacteria
487175

Parasutterella excrementihominis

99.13
66

FBI00067

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

98.84
67

FBI00068

Akkermansia muciniphila

bacteria
verrucomicrobi a
239935

Akkermansia muciniphila

99.42
68

FBI00069

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.84
69

FBI00070

Bacteroides kribbi/
bacteria
bacteroidetes
816

Bacteroides koreensis

99.71
70

Bacteroides koreensis species

cluster

FBI00071

Lachnospiraceae sp. FBI00071
bacteria
firmicutes
186803

Roseburia faecis

94.92
71

FBI00072

Coprococcus eutactus

bacteria
firmicutes
33043

Coprococcus eutactus

96.17
72

FBI00074

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.03
74

FBI00075

Paraprevotella clara

bacteria
bacteroidetes
454154

Paraprevotella clara

98.85
75

FBI00076

Bacteroides thetaiotaomicron

bacteria
bacteroidetes
818

Bacteroides thetaiotaomicron

99.78
76

FBI00077

Sutterella wadsworthensis

bacteria
proteobacteria
40545

Sutterella wadsworthensis

99.86
77

FBI00078

Blautia obeum

bacteria
firmicutes
40520

Blautia obeum

98.34
78

FBI00079

Clostridium clostridioforme

bacteria
firmicutes
1531

Clostridium clostridioforme

99.14
79

FBI00080

Sutterella massiliensis

bacteria
proteobacteria
1816689

Sutterella massiliensis

99.78
80

FBI00081

Porphyromonas asaccharolytica

bacteria
bacteroidetes
28123

Porphyromonas asaccharolytica

99.35
81

FBI00082

Ruminococcaceae sp. FBI00082
bacteria
firmicutes
541000

Phocea massiliensis

93.08
82

FBI00097

FBI00085

Ruminococcus bromii

bacteria
firmicutes
40518

Ruminococcus bromii

98.62
85

FBI00087

Clostridium scindens

bacteria
firmicutes
29347

Clostridium scindens

98.28
87

FBI00092

Monoglobus pectinilyticus

bacteria
firmicutes
1981510

Monoglobus pectinilyticus

99.5
92

FBI00093

Roseburia hominis

bacteria
firmicutes
301301

Roseburia hominis

99.71
93

FBI00096

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.76
96

FBI00097

Ruminococcaceae sp. FBI00082
bacteria
firmicutes
541000

Phocea massiliensis

93.07
97

FBI00097

FBI00099

Gordonibacter pamelaeae

bacteria
actinobacteria
471189

Gordonibacter pamelaeae

99.56
99

FBI00101

Faecalibacterium prausnitzii

bacteria
firmicutes
853

Faecalibacterium prausnitzii

97.97
101

FBI00102

Clostridium fessum

bacteria
firmicutes
2126740

Clostridium symbiosum

94.31
102

FBI00104

Blautia wexlerae

bacteria
firmicutes
418240

Blautia luti

97.18
104

FBI00109

Coprococcus comes

bacteria
firmicutes
410072

Coprococcus comes

98.39
109

FBI00110

Lachnoclostridium pacaense

bacteria
firmicutes
1917870

Lachnoclostridium pacaense

98.92
110

FBI00111

Bacteroides vulgatus

bacteria
bacteroidetes
821

Bacteroides vulgatus

99.43
111

FBI00112

Bacteroides uniformis

bacteria
bacteroidetes
820

Bacteroides uniformis

99.78
112

FBI00113

Parabacteroides merdae

bacteria
bacteroidetes
46503

Parabacteroides merdae

99.79
113

FBI00115

Dorea formicigenerans

bacteria
firmicutes
39486

Dorea formicigenerans

97.98
115

FBI00116

Ruminococcus faecis

bacteria
firmicutes
592978

Ruminococcus faecis

99.57
116

FBI00117

Blautia faecis

bacteria
firmicutes
871665

Blautia faecis

99.52
117

FBI00120

Hungatella effluvii

bacteria
firmicutes
154046

Hungatella hathewayi

98.78
120

FBI00123

Roseburia hominis

bacteria
firmicutes
301301

Roseburia hominis

100
123

FBI00124

Anaerostipes hadrus

bacteria
firmicutes
649756

Anaerostipes hadrus

99.86
124

FBI00125

Bacteroides stercoris

bacteria
bacteroidetes
46506

Bacteroides stercoris

99.64
125

FBI00126

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium adolescentis

98.98
126

FBI00127

Collinsella aerofaciens

bacteria
actinobacteria
74426

Collinsella aerofaciens

98.81
127

FBI00128

Hungatella effluvii

bacteria
firmicutes
1096246

Hungatella effluvii

98.71
128

FBI00132

Gordonibacter pamelaeae

bacteria
actinobacteria
471189

Gordonibacter pamelaeae

99.48
132

FBI00133

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
133

FBI00135

Bifidobacterium pseudocatenulatum

bacteria
actinobacteria
28026

Bifidobacterium pseudocatenulatum

99.57
135

FBI00137

Bacteroides fragilis

bacteria
bacteroidetes
817

Bacteroides fragilis

99.71
137

FBI00140

Phascolarctobacterium faecium

bacteria
firmicutes
33025

Phascolarctobacterium faecium

99.58
140

FBI00141

Phascolarctobacterium faecium

bacteria
firmicutes
33025

Phascolarctobacterium faecium

99.15
141

FBI00145

Bifidobacterium adolescentis

bacteria
actinobacteria
1680

Bifidobacterium adolescentis

99.14
145

FBI00147

Clostridium bolteae

bacteria
firmicutes
208479

Clostridium bolteae

99.28
147

FBI00149

Monoglobus pectinilyticus

bacteria
firmicutes
1981510

Monoglobus pectinilyticus

99.5
149

FBI00151

Clostridium aldenense

bacteria
firmicutes
358742

Clostridium aldenense

98.55
151

FBI00152

Dialister invisus

bacteria
firmicutes
218538

Dialister invisus

99.58
152

FBI00159

Eisenbergiella tayi

bacteria
firmicutes
1432052

Eisenbergiella tayi

99.03
159

FBI00162

Bifidobacterium catenulatum

bacteria
actinobacteria
1686

Bifidobacterium catenulatum

99.14
162

FBI00165

Bacteroides massiliensis

bacteria
bacteroidetes
204516

Bacteroides massiliensis

99.71
165

FBI00167

Dorea longicatena

bacteria
firmicutes
88431

Dorea longicatena

99.39
167

FBI00170

Eggerthella lenta

bacteria
actinobacteria
84112

Eggerthella lenta

98.61
170

FBI00171

Bilophila wadsworthia

bacteria
proteobacteria
35833

Desulfovibrio desulfuricans

91.45
171

FBI00174

Lactobacillus rogosae

bacteria
firmicutes
706562

Lachnospira pectinoschiza

97.92
174

FBI00175

Holdemanella biformis

bacteria
firmicutes
1735

Holdemanella biformis

98.19
175

FBI00176

Ruthenibacterium lactatiformans

bacteria
firmicutes
1550024

Ruthenibacterium lactatiformans

99.71
176

FBI00289

Oxalobacter formigenes

bacteria
proteobacteria
847

Oxalobacter formigenes

99.21
289

TABLE 24

NCBI

% Match

Taxonomy
SEQ ID

Strain #
Species: 16S Best-BLAST
(16S)
Kingdom
Phylum
ID
NO: X

FBI00002

Bacteroides salyersiae

99.5
bacteria
bacteroidetes
291644
2

FBI00004

Neglecta timonensis

99.14
bacteria
firmicutes
1776382
4

FBI00009

Bifidobacterium faecale

98.6
bacteria
actinobacteria
1454229
9

FBI00010

Blautia obeum

98.12
bacteria
firmicutes
40520
10

FBI00012

Alistipes onderdonkii

99.71
bacteria
bacteroidetes
328813
12

FBI00013

Parabacteroides merdae

99.5
bacteria
bacteroidetes
46503
13

FBI00015

Bacteroides uniformis

99.78
bacteria
bacteroidetes
820
15

FBI00016

Bifidobacterium pseudocatenulatum

99.64
bacteria
actinobacteria
28026
16

FBI00018

Eubacterium rectale

99.71
bacteria
firmicutes
39491
18

FBI00019

Alistipes timonensis

99.78
bacteria
bacteroidetes
1465754
19

FBI00021

Bacteroides kribbi

99.07
bacteria
bacteroidetes
1912894
21

FBI00022

Alistipes putredinis

99.93
bacteria
bacteroidetes
28117
22

FBI00029

Parabacteroides distasonis

99.26
bacteria
bacteroidetes
823
29

FBI00032

Anaerostipes hadrus

99.64
bacteria
firmicutes
649756
32

FBI00033

Clostridium amygdalinum

93.56
bacteria
firmicutes
31979
33

FBI00034

Eubacterium eligens

98.78
bacteria
firmicutes
39485
34

FBI00038

Coprococcus eutactus

95.96
bacteria
firmicutes
33043
38

FBI00043

Bifidobacterium dentium

99.35
bacteria
actinobacteria
1689
43

FBI00044

Blautia wexlerae

98.69
bacteria
firmicutes
418240
44

FBI00046

Bacteroides caccae

99.71
bacteria
bacteroidetes
47678
46

FBI00048

Fusicatenibacter saccharivorans

97.95
bacteria
firmicutes
1150298
48

FBI00049

Dialister succinatiphilus

95.74
bacteria
firmicutes
487173
49

FBI00050

Bacteroides nordii

98.63
bacteria
bacteroidetes
291645
50

FBI00051

Dorea formicigenerans

98.07
bacteria
firmicutes
39486
51

FBI00052

Bacteroides xylanisolvens

99.14
bacteria
bacteroidetes
28116
52

FBI00056

Clostridium citroniae

99.2
bacteria
firmicutes
358743
56

FBI00057

Dorea longicatena

99.7
bacteria
firmicutes
88431
57

FBI00059

Bacteroides oleiciplenus

98.81
bacteria
bacteroidetes
626931
59

FBI00060

Bifidobacterium longum

99.49
bacteria
actinobacteria
216816
60

FBI00061

Alistipes shahii

99.19
bacteria
bacteroidetes
328814
61

FBI00067

Oxalobacter formigenes

98.84
bacteria
proteobacteria
847
67

FBI00068

Akkermansia muciniphila

99.42
bacteria
verrucomicrobia
239935
68

FBI00069

Ruminococcus bromii

98.84
bacteria
firmicutes
40518
69

FBI00070

Bacteroides koreensis

99.71
bacteria
bacteroidetes
1912896
70

FBI00071

Roseburia faecis

94.92
bacteria
firmicutes
1732
71

FBI00075

Paraprevotella clara

98.85
bacteria
bacteroidetes
454154
75

FBI00076

Bacteroides thetaiotaomicron

99.78
bacteria
bacteroidetes
818
76

FBI00079

Clostridium clostridioforme

99.14
bacteria
firmicutes
1531
79

FBI00080

Sutterella massiliensis

99.78
bacteria
proteobacteria
1816689
80

FBI00087

Clostridium scindens

98.28
bacteria
firmicutes
29347
87

FBI00093

Roseburia hominis

99.71
bacteria
firmicutes
301301
93

FBI00097

Phocea massiliensis

93.07
bacteria
firmicutes
1841867
97

FBI00101

Faecalibacterium prausnitzii

97.97
bacteria
firmicutes
853
101

FBI00102

Clostridium symbiosum

94.31
bacteria
firmicutes
1512
102

FBI00104

Blautia luti

97.18
bacteria
firmicutes
418240
104

FBI00109

Coprococcus comes

98.39
bacteria
firmicutes
410072
109

FBI00117

Blautia faecis

99.52
bacteria
firmicutes
871665
117

FBI00120

Hungatella hathewayi

98.78
bacteria
firmicutes
154046
120

FBI00125

Bacteroides stercoris

99.64
bacteria
bacteroidetes
46506
125

FBI00127

Collinsella aerofaciens

98.81
bacteria
actinobacteria
74426
127

FBI00128

Hungatella effluvii

98.71
bacteria
firmicutes
1096246
128

FBI00132

Gordonibacter pamelaeae

99.48
bacteria
actinobacteria
471189
132

FBI00133

Oxalobacter formigenes

99.21
bacteria
proteobacteria
847
133

FBI00137

Bacteroides fragilis

99.71
bacteria
bacteroidetes
817
137

FBI00141

Phascolarctobacterium faecium

99.15
bacteria
firmicutes
33025
141

FBI00145

Bifidobacterium adolescentis

99.14
bacteria
actinobacteria
1680
145

FBI00149

Monoglobus pectinilyticus

99.5
bacteria
firmicutes
1981510
149

FBI00151

Clostridium aldenense

98.55
bacteria
firmicutes
358742
151

FBI00152

Dialister invisus

99.58
bacteria
firmicutes
218538
152

FBI00162

Bifidobacterium catenulatum

99.14
bacteria
actinobacteria
1686
162

FBI00165

Bacteroides massiliensis

99.71
bacteria
bacteroidetes
204516
165

FBI00171

Desulfovibrio desulfuricans

91.45
bacteria
proteobacteria
876
171

FBI00174

Lachnospira pectinoschiza

97.92
bacteria
firmicutes
28052
174

FBI00176

Ruthenibacterium lactatiformans

99.71
bacteria
firmicutes
1550024
176

FBI00177

Parasutterella excrementihominis

99.71
bacteria
proteobacteria
487175
177

FBI00180

Alistipes senegalensis

97.56
bacteria
bacteroidetes
1288121
180

FBI00182

Bacteroides coprocola

99.64
bacteria
bacteroidetes
310298
182

FBI00184

Bacteroides faecis

99.78
bacteria
bacteroidetes
674529
184

FBI00190

Bacteroides finegoldii

98.91
bacteria
bacteroidetes
338188
190

FBI00191

Clostridium swellfunianum

96.24
bacteria
firmicutes
1367462
191

FBI00194

Ruminococcus faecis

98.41
bacteria
firmicutes
592978
194

FBI00197

Bifidobacterium bifidum

99.85
bacteria
actinobacteria
1681
197

FBI00198

Lachnoclostridium pacaense

99.71
bacteria
firmicutes
1917870
198

FBI00199

Clostridium bolteae

99.28
bacteria
firmicutes
208479
199

FBI00200

Longicatena caecimuris

99.71
bacteria
firmicutes
1796635
200

FBI00201

Eggerthella lenta

98.83
bacteria
actinobacteria
84112
201

FBI00205

Blautia luti

97.55
bacteria
firmicutes
89014
205

FBI00208

Anaerotruncus colihominis

96.52
bacteria
firmicutes
169435
208

FBI00211

Bacteroides vulgatus

99.78
bacteria
bacteroidetes
821
211

FBI00220

Megasphaera massiliensis

98.8
bacteria
firmicutes
1232428
220

FBI00221

Butyricimonas faecihominis

98.61
bacteria
bacteroidetes
1472416
221

FBI00224

Sutterella wadsworthensis

99.71
bacteria
proteobacteria
40545
224

FBI00226

Catabacter hongkongensis

99.71
bacteria
firmicutes
270498
226

FBI00233

Anaerotruncus colihominis

91.63
bacteria
firmicutes
474960
233

FBI00236

Eisenbergiella tayi

99.41
bacteria
firmicutes
1432052
236

FBI00237

Dielma fastidiosa

99.78
bacteria
firmicutes
1034346
237

FBI00238

Alistipes finegoldii

95.84
bacteria
bacteroidetes
214856
238

FBI00243

Eubacterium siraeum

98.53
bacteria
firmicutes
39492
243

FBI00245

Acidaminococcus intestini

99.72
bacteria
firmicutes
187327
245

FBI00248

Emergencia timonensis

99.64
bacteria
firmicutes
1776384
248

FBI00254

Eubacterium hallii

99.08
bacteria
firmicutes
39488
254

FBI00258

Turicibacter sanguinis

99.93
bacteria
firmicutes
154288
258

FBI00267

Anaerofustis stercorihominis

97.29
bacteria
firmicutes
214853
267

FBI00273

Bamesiella intestinihominis

99.43
bacteria
bacteroidetes
487174
273

FBI00274

Eubacterium xylanophilum

93.5
bacteria
firmicutes
39497
274

FBI00275

Holdemanella biformis

98.99
bacteria
firmicutes
1735
275

FBI00278

Eubacterium ventriosum

94.14
bacteria
firmicutes
39496
278

FBI00281

Senegalimassilia anaerobia

99.45
bacteria
actinobacteria
1473216
281

FBI00282

Porphyromonas asaccharolytica

99.35
bacteria
bacteroidetes
28123
282

FBI00288

Blautia hydrogenotrophica

99.57
bacteria
firmicutes
53443
288

FBI00289

Oxalobacter formigenes

99.21
bacteria
proteobacteria
847
289

FBI00290

Eubacterium ruminantium

94.81
bacteria
firmicutes
42322
290

FBI00292

Methanobrevibacter smithii

99.44
archaea
euryarchaeota
2173
292

FBI00377

Christensenella massiliensis

88.69
bacteria
firmicutes
186802
377

Example 17: In Vivo Oxalate Reduction by a Therapeutic Microbial Consortium in Healthy Humans Treated with a High Oxalate/Low Calcium Diet

This study evaluates the ability of a rationally designed oxalate-degrading microbial consortium to reduce urinary oxalate levels in vivo in human subjects.

Approximately 64 healthy subjects are enrolled for the study. Six days prior to administration of the consortium, subjects are placed on a high oxalate/low calcium (HOLC) diet in order to create a temporary hyperoxaluric state akin to what is seen in enteric hyperoxaluria (Langman et al., 2016, “A double-blind, placebo controlled, randomized phase 1 cross-over study with ALLN-177, an orally administered oxalate degrading enzyme,” Am J Nephrol. 44(2):150-8). When administered to healthy subjects over 7 days, this diet has been previously shown to increase urinary oxalate from 27.2±9.5 mg/day during screening to 80.8±24.1 mg/day. This is well above the generally accepted upper limit of normal (40 mg/day) and clearly within the range seen in enteric hyperoxaluria.

Some subjects are additionally pre-treated with a course of broad spectrum antibiotics (a combination of metronidazole and clarithromycin) in order to pre-clear bacteria from the gut and facilitate subsequent engraftment of the heterologous community. This combination is selected based on the complementary coverage of gram-positive as well as gram-negative bacteria, broad coverage of obligate anaerobes (which dominate the microbial population in the GI tract) as well as facultative anaerobes, including enteric pathobionts (i.e. human commensals with pathogenic potential), and the relatively favorable safety and tolerability profiles of the constituent drugs. The goal of antibiotic pretreatment is to reduce pre-existing gastrointestinal bacterial load in an attempt to suppress colonization resistance, a microbially-mediated phenomenon that could limit the engraftment of strains in the consortium.

On Day 6 of administration of the HOLC diet and (optionally) the antibiotic pretreatment, some subjects are additionally given a polyethylene glycol (PEG) bowel preparation treatment, an approach commonly used in fecal matter transplant administration and that will be familiar to one skilled in the art. This treatment is designed to clear remaining antibiotics from the gastrointestinal tract and further reduce remaining bacterial load from the host.

Six days following administration of the HOLC diet, subjects are administered the therapeutic microbial consortium. The duration of treatment with the consortium or the placebo is 10 days. Urine oxalate excretion is used as a biomarker for treatment efficacy, and is monitored by LC-MS as described in Example 4. Stool samples are collected at all stages of the trial (including 1 month post-treatment) and used to monitor the composition of the microbiome by metagenomic sequencing. This facilitates monitoring the level and duration of engraftment of consortium strains.

Approximately 64 healthy human subjects are randomly assigned to one of the following five regimens in a 1:1:1:1 ratio:

- a. Antibiotic pretreatment followed by bowel preparation with PEG followed by the treatment with the consortium.
- b. Antibiotic pretreatment followed by treatment with the consortium.
- c. Antibiotic placebo treatment followed by bowel preparation with PEG followed by treatment with the consortium.
- d. Antibiotic pretreatment followed by treatment with a placebo.

Subjects are kept in confinement for two periods, separated by an approximately 20 day washout. The first confinement period is approximately 18 days, which includes antibiotic/antibiotic placebo pretreatment, followed by either a bowel preparation with PEG or no bowel preparation, followed by 10-day course of a therapeutic consortium or a placebo. The second confinement period is approximately 6 days. The sample size of this study was chosen to distinguish an approximately 20% change in in urinary oxalate levels between cohorts. This study enables evaluation of the ability of a therapeutic consortium to reduce levels of urine oxalate in a human subject. This study further evaluates the efficacy of the described pretreatment methods (antibiotic pretreatment and PEG preparation).

Example 18: In Vivo Oxalate Reduction by a Therapeutic Microbial Consortium in Humans Patients with Enteric Hyperoxaluria

Enteric hyperoxaluria is characterized by excess absorption or consumption of dietary oxalate leading to increased renal oxalate excretion (>40 mg/day), recurrent kidney stones, renal calcium deposition (nephrocalcinosis) and, in severe cases, progressive renal impairment and end-stage renal failure (Liu and Nazzal, 2019, “Enteric hyperoxaluria: role of microbiota and antibiotics,” Curr Opin Nephrol Hypertens. 28(4):352-359; Ermer et al., 2016, “Oxalate, inflammasome, and progression of kidney disease,” Curr Opin Nephrol Hypertens. 25(4):363-71). Roux-en-Y Gastric Bypass (RYGB) surgery is a common comorbidity associated with enteric hyperoxaluria (˜60% of RYGB patients). This study evaluates the ability of an oxalate-degrading microbial consortium to reduce urinary oxalate levels in vivo in a cohort of up to approximately 16 Roux-en-Y Gastric Bypass (RYGB) patients with enteric hyperoxaluria.

A cohort of up to approximately 16 subjects is given an antibiotic pretreatment, a PEG bowel preparation treatment, and a 10-day treatment with a therapeutic microbial consortium as described in Example 17. Urine and stool samples are collected at different stages of the treatment to monitor urine oxalate levels and engraftment of consortium strains as described in Example 17. Stool samples are further collected after 30, 60, and 90 days to evaluate long-term engraftment of consortium strains by metagenomic sequencing. This study will demonstrate the ability of the consortium to reduce urinary oxalate levels in the RYGB patients.

Example 19: Screening Strains for In Vitro Bile Acid Compound Metabolic Activity

in vitro metabolic screening is necessary to definitively characterize the ability of a microbial strain to degrade bile acid compounds. Strains are screened against a panel of bile acid compounds and structural conversion of the bile acids are evaluated as described. Briefly, overnight microbial monocultures are harvested by anaerobic centrifugation and resuspended in fresh pre-reduced growth medium (e.g. Mega Medium) spiked with 100 μM of bile acid (e.g. TCA, TCDCA, GCA, GCDCA, CA, CDCA, 3oxoCA, 7oxoCA, 12oxoCA, UDCA, DCA, LCA, 3oxoLCA) and allowed to incubate at 37° C. for 24 h. Cultures are sampled for bile acid analysis at 0, 6 and 24 h post-bile acid spike. For bile acid analysis, 2 ml of culture are sampled and immediately acidified with 50 μl of 6 N HCl to stop all metabolic activity and protonate bile acids to make them more soluble in organic solvent. Acidified cultures are extracted for bile acids and analyzed by LCMS (UPLC-QTOF or UPLC-QQQ).

Preliminary screening of commercial strains using TCA as the feeder molecule were obtained using this protocol, and the results are illustrated in FIG. 18.

Example 20: Screening Strains for Resistance to Bile Acids

To determine the effect of the presence of bile acid on microbial strain growth, microbial cultures are grown in their respective banking medium (e.g. Mega Media or Chopped Meat Media) to saturation and back-diluted into the same respective banking medium containing a variable concentration of bile acids. % growth inhibition is calculated by determining the ratio of background-subtracted optical density (O.D.) of a microbial strain grown in the presence of bile acid to the O.D. of the same microbial strain grown in the absence of bile acid.

Example 21: Murine Model of Chemically-Induced Primary Sclerosing Cholangitis and Microbiome-Induced Shift in Bile Acid Composition

This example describes the establishment of a chemically-induced murine model of primary sclerosing cholangitis (PSC) and demonstrates that alterations to a microbiome can alter the composition of the bile acid pool and affect disease severity.

On Day 0 of the experiment, germ-free 7-9 week-old germ-free C57B/6N female mice are weighed and colonized by oral gavage with one of two rationally-designed microbial consortia. One cohort of mice is colonized with a full microbial consortium that comprises a plurality of microbes including species having 7α-dehydroxylation activity and species having bile salt hydrolase (BSH) activity. A second cohort of mice is colonized with a partial microbial consortium which is identical in composition to the full consortium except that it lacks species having 7α-dehydroxylation activity. A control cohort of mice is treated with sterile saline.

The mice are fed for two weeks on a standard laboratory diet while the microbiome stabilizes. Beginning on Day 14 and for the following 14 days, the standard diet is supplemented either with 1% (w/w) hepatotoxic secondary bile acid LCA to induce PSC, or with an equimolar concentration of the conjugated bile acid GCDCA or the primary bile acid CDCA. GCDCA can be metabolized into CDCA by a population of microbes having BSH activity, and CDCA can be metabolized into LCA by a population of microbes having 7α-dehydroxylation activity.

On Days 0, 7, 14, 21, and 28, mice are monitored for indicators of chemically-induced PSC (e.g. reduced body weight, reduced food consumption, elevated liver enzyme levels) and fecal samples are collected. Fecal samples are analyzed by both LC/MS to determine the composition of the bile acid pool and by metagenomic sequencing to monitor microbial strain engraftment. Mice are euthanized on or before Day 28 and terminal samples are collected to enable screening for additional PSC indicators (e.g. changes to GI physiology, cecum bile acid composition).

Mice fed a diet supplemented with hepatotoxic LCA are expected to have elevated levels of fecal LCA and are expected to exhibit signs of PSC, thereby establishing a murine model of the disease. Mice colonized with the full set of microbes and fed a diet supplemented with GCDCA or CDCA are likewise expected to have elevated LCA content, as the upstream substrates can be metabolized into LCA by the engrafted set of microbes. Mice implanted with the partial set of microbes and fed a diet supplemented with conjugated bile acid are expected to not have LCA in their bile acid pool because the implanted microbial population lacks the activity necessary to metabolize the upstream substrates into LCA; these mice are accordingly expected to exhibit less severe signs of PSC. Taken together, these results will demonstrate that alterations to the microbiome can drive shifts in the bile acid pool in an animal and affect disease severity.

Example 22: In Vivo Reduction of Hepatotoxic Bile Acids in a Mouse Model of PSC by Treatment with a Microbial Consortium

This example evaluates the ability of a bile-acid-metabolizing microbial consortium, comprising a plurality of active microbes and a supportive community of microbes, to alter the bile acid pool of an animal and affect disease severity. Said microbial consortium comprises a plurality of active microbes and a supportive community of microbes, wherein said plurality of active microbes comprises strains experimentally verified to have 3α-HSDH and/or 3β-HSDH activity, and said supportive community of microbes comprises strains experimentally verified to have 7α-HSDH activity, 7β-HSDH activity, and/or bile salt hydrolase activity.

To test the in vivo activity of a bile-acid-metabolizing microbial consortium described herein, germ-free C57B/6N female mice are weighed on Day 0 and colonized by oral gavage with either a plurality of active microbes alone, a supportive community alone, or a complete microbial consortium (actives and supportives). The mice are fed for two weeks on a standard laboratory diet while the microbiome stabilizes. Beginning on Day 14 and for the following 14 days, the standard diet is supplemented with the hepatotoxic secondary bile acid LCA (1% w/w) to induce PSC. Body weight, food weight, and fecal bile acid composition are monitored over the course of two weeks. After the two-week period, mice are sacrificed and a variety of terminal samples are collected including the cecum, feces, and serum.

Mice treated with the complete microbial consortium (actives and supportives) are expected to have reduced levels of hepatotoxic LCA and are expected to exhibit less severe signs of PSC relative to an untreated control (no microbial implantation). The mice treated with the active microbes alone are also expected to have lowered LCA levels relative to the untreated mice, but less so than the mice treated with the full consortium. The mice implanted with the supportive community only are not expected to have substantially lower LCA levels than the untreated mice. Taken together, these results will demonstrate the ability of a bile-acid-metabolizing microbial consortium to alter the pool of bile acids in an animal and consequently alleviate PSC symptoms.

MICROBIAL CONSORTIA FOR THE TREATMENT OF DISEASE

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