Patent Grant
12011467
Aspects of the present disclosure relate to bacterial isolates, methods of isolating and culturing said bacterial isolates, and methods of using these bacterial isolates to prevent, treat, or inhibit a disease. More specifically, certain features of the present disclosure concern beneficial bacterial strains, which can be provided to subjects to prevent, treat, or inhibit a disease or an adverse health condition associated with subjects that lack or have diminished amounts of said beneficial bacterial strains.
The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled ReplacementSeqListing_JCVEN007A.TXT, which was created and last modified on Aug. 15, 2022 and is 10,983 bytes in size. The information in the electronic Sequence Listing is hereby incorporated by reference in its entirety.
The microbiome is a genomic collection of the entire repertoire of microbiota of a subject. This microbiome includes beneficial and benign microbes, as well as harmful microbes. The human intestinal microbiota consists of trillions of microorganisms including 150-200 prevalent and 1000 less common bacterial species, harboring over 100-fold more genes than those present in the human genome. The gastrointestinal tract is the largest habitat of microbiota and is composed of predominantly bacteria, yet also contains archaea, protozoa, and viruses. The microbiota performs vital functions essential to health maintenance, including food processing, digestion of complex indigestible polysaccharides, synthesis of vitamins, and immune system functions. The microbiome also secretes bioactive metabolites with diverse functions, ranging from inhibition of pathogens, metabolism of toxic compounds, and the modulation of the metabolism of the host.
Dysbiosis is a state of imbalance in the composition or function of microbial taxa in a subject, which can lead to many diseases and adverse health conditions such as gastrointestinal and urogenital infections and the adverse health conditions associated therewith. The restoration of microbiotic homeostasis can be an effective therapeutic approach to attenuating dysbiosis-induced disease and several in the field have sought to address such dysbiosis-induced disease by administration of probiotics or fecal microbiota transplantation or both. Although the understanding of how the gut microbiota contributes to host health has progressed greatly, there remains a need for more approaches to address imbalances in the composition or function of microbial taxa of a subject.
Some aspects of the present disclosure relate to a composition comprising an isolate of Bacteroides designated LJ00115, wherein said isolate of Bacteroides comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of the rDNA sequence of SEQ ID NO: 1 or the complement thereof. This selected isolate of Bacteroides designated LJ00115 is deposited under the Budapest Treaty with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149345. Accordingly, aspects of the invention concern compositions comprising the aforementioned Bacteroides isolate designated LJ00115 deposited under reference number CBS 149345, wherein said composition further comprises a prebiotic, stabilizer, antibacterial agent, antifungal agent, preservative, or media component, optionally wherein said composition or isolate is lyophilized, spray dried, or freeze-dried, optionally, wherein said isolate is inactivated, such as by heat inactivation and, optionally, wherein said composition or isolate is formulated in a powder, liquid, capsule, caplet, spray, or food, such as for oral delivery.
Some aspects of the present disclosure relate to a composition comprising an isolate of Odoribacter designated LJ00541, wherein said isolate of Odoribacter comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of the rDNA sequence of SEQ ID NO: 2 or the complement thereof. This selected isolate of Odoribacter designated LJ00541 is deposited under the Budapest Treaty with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149346. Accordingly, aspects of the invention concern compositions comprising the aforementioned Odoribacter isolate designated LJ00541 deposited under reference number CBS 149346, wherein said composition further comprises a prebiotic, stabilizer, antibacterial agent, antifungal agent, preservative, or media component, optionally wherein said composition or isolate is lyophilized, spray dried, or freeze-dried, optionally, wherein said isolate is inactivated, such as by heat inactivation and, optionally, wherein said composition or isolate is formulated in a powder, liquid, capsule, caplet, spray, or food, such as for oral delivery.
Some aspects of the present disclosure relate to a composition comprising an isolate of Bacteroides designated PRB03A2_ANA_TSB_B11, wherein said isolate of Bacteroides comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of the rDNA sequence of SEQ ID NO: 3 or the complement thereof. This selected isolate of Bacteroides designated PRB03A2_ANA_TSB_B11 is deposited under the Budapest Treaty with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149347. Accordingly, aspects of the invention concern compositions comprising the aforementioned Bacteroides isolate designated PRB03A2_ANA_TSB_B11 deposited under reference number CBS 149347, wherein said composition further comprises a prebiotic, stabilizer, antibacterial agent, antifungal agent, preservative, or media component, optionally wherein said composition or isolate is lyophilized, spray dried, or freeze-dried, optionally, wherein said isolate is inactivated, such as by heat inactivation and, optionally, wherein said composition or isolate is formulated in a powder, liquid, capsule, caplet, spray, or food, such as for oral delivery.
Some aspects of the present disclosure relate to a composition comprising an isolate of Parabacteroides designated PRB02A2_ANA_TSB_F6, wherein said isolate of Parabacteroides comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of the rDNA sequence of SEQ ID NO: 4 or the complement thereof. This selected isolate of Parabacteroides designated PRB02A2_ANA_TSB_F6 is deposited under the Budapest Treaty with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149348. Accordingly, aspects of the invention concern compositions comprising the aforementioned Parabacteroides isolate designated PRB02A2_ANA_TSB_F6 deposited under reference number CBS 149348, wherein said composition further comprises a prebiotic, stabilizer, antibacterial agent, antifungal agent, preservative, or media component, optionally wherein said composition or isolate is lyophilized, spray dried, or freeze-dried, optionally, wherein said isolate is inactivated, such as by heat inactivation and, optionally, wherein said composition or isolate is formulated in a powder, liquid, capsule, caplet, spray, or food, such as for oral delivery
Some aspects of the present disclosure relate to a composition comprising an isolate of Bacteroides designated PRB01A2_ANA_MRS_C7, wherein said isolate of Bacteroides comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of the rDNA sequence of SEQ ID NO: 5 or the complement thereof. This selected isolate of Bacteroides designated PRB01A2_ANA_MRS_C7 is deposited under the Budapest Treaty with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149340. Accordingly, aspects of the invention concern compositions comprising the aforementioned Bacteroides isolate designated PRB01A2_ANA_MRS_C7 deposited under reference number CBS 149340, wherein said composition further comprises a prebiotic, stabilizer, antibacterial agent, antifungal agent, preservative, or media component, optionally wherein said composition or isolate is lyophilized, spray dried, or freeze-dried, optionally, wherein said isolate is inactivated, such as by heat inactivation and, optionally, wherein said composition or isolate is formulated in a powder, liquid, capsule, caplet, spray, or food, such as for oral delivery.
Some aspects of the present disclosure relate to a composition comprising an isolate of Paraprevotella designated LJ00262, wherein said isolate of Paraprevotella comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of the rDNA sequence of SEQ ID NO: 6 or the complement thereof. This selected isolate of Paraprevotella designated LJ00262 is deposited under the Budapest Treaty with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149341. Accordingly, aspects of the invention concern compositions comprising the aforementioned Paraprevotella isolate designated LJ00262 deposited under reference number CBS 149341, wherein said composition further comprises a prebiotic, stabilizer, antibacterial agent, antifungal agent, preservative, or media component, optionally wherein said composition or isolate is lyophilized, spray dried, or freeze-dried, optionally, wherein said isolate is inactivated, such as by heat inactivation and, optionally, wherein said composition or isolate is formulated in a powder, liquid, capsule, caplet, spray, or food, such as for oral delivery.
Some aspects of the present disclosure relate to a composition comprising an isolate of Coprococcus designated LJ00622, wherein said isolate of Coprococcus comprises a 16S rRNA gene sequence encoding or corresponding to at least 99% or 100% sequence identity of the rDNA sequence of SEQ ID NO: 7 or the complement thereof. This selected isolate of Coprococcus designated LJ00622 is deposited under the Budapest Treaty with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149349. Accordingly, aspects of the invention concern compositions comprising the aforementioned Coprococcus isolate designated LJ00622 deposited under reference number CBS 149349, wherein said composition further comprises a prebiotic, stabilizer, antibacterial agent, antifungal agent, preservative, or media component, optionally wherein said composition or isolate is lyophilized, spray dried, or freeze-dried, optionally, wherein said isolate is inactivated, such as by heat inactivation and, optionally, wherein said composition or isolate is formulated in a powder, liquid, capsule, caplet, spray, or food, such as for oral delivery.
Some aspects of the present disclosure relate to a composition comprising an isolate of Acidaminococcus designated PRB01A2_ANA_GAM_C8, wherein said isolate of Acidaminococcus comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of the rDNA sequence of SEQ ID NO: 8 or the complement thereof. This selected isolate of Acidaminococcus designated PRB01A2_ANA_GAM_C8 is deposited under the Budapest Treaty with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149342. Accordingly, aspects of the invention concern compositions comprising the aforementioned Acidaminococcus isolate designated PRB01A2_ANA_GAM_C8 deposited under reference number CBS 149342, wherein said composition further comprises a prebiotic, stabilizer, antibacterial agent, antifungal agent, preservative, or media component, optionally wherein said composition or isolate is lyophilized, spray dried, or freeze-dried, optionally, wherein said isolate is inactivated, such as by heat inactivation and, optionally, wherein said composition or isolate is formulated in a powder, liquid, capsule, caplet, spray, or food, such as for oral delivery.
Some aspects of the present disclosure relate to a composition comprising an isolate of Bifidobacterium designated PRB02A2_ANA_TSB_A11, wherein said isolate of Bifidobacterium comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of the rDNA sequence of SEQ ID NO: 9 or the complement thereof. This selected isolate of Bifidobacterium designated PRB02A2_ANA_TSB_A11 is deposited under the Budapest Treaty with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149343. Accordingly, aspects of the invention concern compositions comprising the aforementioned Bifidobacterium isolate designated PRB02A2_ANA_TSB_A11 deposited under reference number CBS 149343, wherein said composition further comprises a prebiotic, stabilizer, antibacterial agent, antifungal agent, preservative, or media component, optionally wherein said composition or isolate is lyophilized, spray dried, or freeze-dried, optionally, wherein said isolate is inactivated, such as by heat inactivation and, optionally, wherein said composition or isolate is formulated in a powder, liquid, capsule, caplet, spray, or food, such as for oral delivery.
Some aspects of the present disclosure relate to a composition comprising an isolate of Bifidobacterium designated PRB03A2_ANA_GAM.Ab_B11, wherein said isolate of Bifidobacterium comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of the rDNA sequence of SEQ ID NO: 10 or the complement thereof. This selected isolate of Bifidobacterium designated PRB03A2_ANA_GAM.Ab_B11 is deposited under the Budapest Treaty with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149344. Accordingly, aspects of the invention concern compositions comprising the aforementioned Bifidobacterium isolate designated PRB03A2_ANA_GAM.Ab_B11 deposited under reference number CBS 149344, wherein said composition further comprises a prebiotic, stabilizer, antibacterial agent, antifungal agent, preservative, or media component, optionally wherein said composition or isolate is lyophilized, spray dried, or freeze-dried, optionally, wherein said isolate is inactivated, such as by heat inactivation and, optionally, wherein said composition or isolate is formulated in a powder, liquid, capsule, caplet, spray, or food, such as for oral delivery.
Additional embodiments concern compositions comprising at least one bacterial isolate comprising a 16S rRNA gene sequence encoding or corresponding to a sequence selected from any one or more of the aforementioned sequences or the complement thereof e.g., a 16S rRNA encoding or corresponding to any one or more of the rDNA sequences of SEQ ID NOS: 1-10 or the complement thereof or a sequence having at least 95%, 96%, 97%, 98%, or 99% sequence identity to any one or more of SEQ ID NOS: 1-10 or the complement thereof, such as anyone or more of the deposited strains above and, optionally, further comprising a prebiotic, stabilizer, antibacterial agent, antifungal agent, or media component. In some embodiments, the prebiotic is inulin, fructooligosaccharide, galactooligosaccharide, xylooligosaccharide, or lactulose. In some embodiments, the stabilizer comprises a sugar, a sugar alcohol, an amino acid, a lipid, or a fatty acid, or any combination thereof (e.g., raffinose, soybean oligosaccharides, fructooligosaccharides, galactooligosaccharides, galactosyl lactose, palatinose, lactulose, lactitol, xylitol, sorbitol, mannitol, trehalose, glucose, sucrose, fructose, maltose, milk, milk powders, whey, whey protein concentrates, casein, casein hydrolysates, lactoferrin, lactoperoxidase, lactoglobulins, glycomacropeptides, lacto-saccharides, lacto-lipids, or short chain fatty acids including acetic, propionic, butyric, isobutyric, valeric, isovaleric, or caproic acids). In some embodiments, the stabilizer is glucose, sucrose, trehalose, lactose, maltodextrin, polydextrose, dextran, fructose, oligofructose, cellulose, glycerol, adonitol, inositol, mannitol, sorbitol, gums, hydrolyzed protein, skim milk powder, milk powder, or gel beads, or any combination thereof. In some embodiments, the antibacterial agent is bacteriocin, amoxicillin, ampicillin, azithromycin, cefaclor, cefdinir, cefotaxime, ceftazidime, ceftriaxone, cefuroxime, cephalexin, cephalosporin, ciprofloxacin, clarithromycin, clavulanate, clindamycin, clotrimazole, dalbavancin, demeclocycline, dicloxacillin, doxycycline, eravacycline, erythromycin, fluconazole, furazolidone, lansoprazole, levofloxacin, lincomycin, metronidazole, minocycline, moxifloxacin, nitroimidazole, omadacycline, oritavancin, oxacillin, penem, penicillin, penicillin V potassium, rifabutin, sulfamethoxazole, sulfasalazine, telavancin, tetracycline, tinidazole, trimethoprim, an antimicrobial peptide, or vancomycin, or any combination thereof. In some embodiments, the antifungal agent is amphotericin B, clotrimazole, econazole, fluconazole, itraconazole, ketoconazole, miconazole, natamycin, nystatin, posaconazole, terconazole, terbinafine, or voriconazole, or any combination thereof. In some embodiments, the media component is selected from any one or more of the media components set forth in TABLE 2. In some embodiments, the media component further comprises agar. In some embodiments, the isolate or composition or both are lyophilized, spray dried, or freeze-dried. In some embodiments, the composition further comprises at least one additional bacterial population, wherein said at least one additional bacterial population comprises a 16S rRNA gene encoding or corresponding to an rDNA sequence selected from any one or more SEQ ID NOS: 1-10 or the complement thereof or any one or more of a sequence having at least 95%, 96%, 97%, 98%, or 99% sequence identity to any one or more of SEQ ID NOS: 1-10 or the complement thereof, such as anyone or more of the deposited strains above. In some embodiments, the composition comprises at least nine additional bacterial populations, wherein each of the at least nine additional bacterial populations comprises a 16S rRNA gene encoding or corresponding to a unique sequence selected from any one or more of rDNA sequence of SEQ ID NOS: 1-10 or the complement thereof or any one or more of a sequence having at least 95%, 96%, 97%, 98%, or 99% sequence identity to any one or more of SEQ ID NOS: 1-10 or the complement thereof such as anyone or more of the deposited strains above. In some embodiments, the composition further comprises at least one additional bacterial population selected from the bacteria set forth in TABLE 3. Each of these compositions may also contain any one or more of the aforementioned prebiotics, stabilizers, antibacterial agents, antifungal agents, or media components.
Further embodiments relate to methods of treating, ameliorating, preventing, or inhibiting a disease or a condition associated with a disease such as e.g., allergies, infection risk in the critically ill, sexually transmitted infections, acne, acute infectious diarrhea, acute respiratory tract infections, allergic rhinitis, Alzheimer's disease, antibiotic-associated diarrhea, atopic dermatitis, asthma, autism, bladder cancer, Candidal vaginitis, chronic kidney disease, Crohn's disease, Clostridium difficile infection, the common cold, constipation, dementia, dental caries (tooth decay), diabetes mellitus, diverticulosis, eczema, chronic obstructive pulmonary disease (COPD), Escherichia coli infection, gastrointestinal tract infections, gastrointestinal inflammation, gum disease, halitosis, Helicobacter pylori infection, hepatic encephalopathy, high cholesterol, Huntington's disease, infant colic, infectious childhood diarrhea, infectious diarrhea, inflammatory bowel diseases, irritable bowel syndrome, kidney disease, lactose intolerance, Listeria monocytogenes infection, lower respiratory infection, metabolic disorder, multidrug-resistant bacterial infection, necrotizing enterocolitis, neurodegeneration, pancreatitis, pneumonia, obesity, oral disease, Parkinson's disease, pouchitis, radiation-associated diarrhea, respiratory infection, Salmonella thymurium infection, sepsis, small intestinal bacteria overgrowth, surgical site infections, traveler's diarrhea, ulcerative colitis, upper respiratory infection, urinary tract infection, vaginal infection, ventilator associated pneumonia, vulvo vaginitis, vulvovaginal candidiasis, yeast infection, or any combination thereof, or conditions associated therewith comprising providing any of the aforementioned compositions such as anyone or more of the deposited strains above to a subject that has been preferably selected or identified as one that would benefit from an adjustment of the gut microbiome and, optionally evaluating or measuring the treatment, amelioration, or inhibition of allergies, infection risk in the critically ill, sexually transmitted infections, acne, acute infectious diarrhea, acute respiratory tract infections, allergic rhinitis, Alzheimer's disease, antibiotic-associated diarrhea, atopic dermatitis, asthma, autism, bladder cancer, Candidal vaginitis, chronic kidney disease, Crohn's disease, Clostridium difficile infection, the common cold, constipation, dementia, dental caries (tooth decay), diabetes mellitus, diverticulosis, eczema, Escherichia coli infection, gastrointestinal tract infections, gastrointestinal inflammation, gum disease, halitosis, Helicobacter pylori infection, hepatic encephalopathy, high cholesterol, Huntington's disease, infant colic, infectious childhood diarrhea, infectious diarrhea, inflammatory bowel diseases, irritable bowel syndrome, kidney disease, lactose intolerance, Listeria monocytogenes infection, lower respiratory infection, metabolic disorder, multidrug-resistant bacterial infection, necrotizing enterocolitis, neurodegeneration, pancreatitis, pneumonia, obesity, oral disease, Parkinson's disease, pouchitis, radiation-associated diarrhea, respiratory infection, Salmonella thymurium infection, sepsis, small intestinal bacteria overgrowth, surgical site infections, traveler's diarrhea, ulcerative colitis, upper respiratory infection, urinary tract infection, vaginal infection, ventilator associated pneumonia, vulvo vaginitis, vulvovaginal candidiasis, or yeast infection, or any combination thereof, or conditions associated therewith.
Accordingly, it is contemplated that one or more of the compositions disclosed herein are useful as a medicament. In some embodiments, one or more of the compositions disclosed herein such as anyone or more of the deposited strains above are for use in treating acne, acute infectious diarrhea, acute respiratory tract infections, allergic rhinitis, Alzheimer's disease, antibiotic-associated diarrhea, atopic dermatitis, asthma, autism, bladder cancer, Candidal vaginitis, chronic kidney disease, Crohn's disease, Clostridium difficile infection, the common cold, constipation, dementia, dental caries (tooth decay), diabetes mellitus, diverticulosis, eczema, chronic obstructive pulmonary disease (COPD), Escherichia coli infection, gastrointestinal tract infections, gastrointestinal inflammation, gum disease, halitosis, Helicobacter pylori infection, hepatic encephalopathy, high cholesterol, Huntington's disease, infant colic, infectious childhood diarrhea, infectious diarrhea, inflammatory bowel diseases, irritable bowel syndrome, kidney disease, lactose intolerance, Listeria monocytogenes infection, lower respiratory infection, metabolic disorder, multidrug-resistant bacterial infection, necrotizing enterocolitis, neurodegeneration, pancreatitis, pneumonia, obesity, oral disease, Parkinson's disease, pouchitis, radiation-associated diarrhea, respiratory infection, Salmonella thymurium infection, sepsis, small intestinal bacteria overgrowth, surgical site infections, traveler's diarrhea, ulcerative colitis, upper respiratory infection, urinary tract infection, vaginal infection, ventilator associated pneumonia, vulvo vaginitis, vulvovaginal candidiasis, or yeast infection, or any combination thereof. In some embodiments, the composition is formulated for oral delivery, such as a powder (e.g., a lyophilized powder), a liquid (such as a beverage, which may contain a flavoring), a capsule or a caplet (e.g., a capsule or caplet, which may contain a preservative, antifungal agent, or antibacterial agent), a spray (e.g., an emulsion, microemulsion, or nanoemulsion comprising a fatty acid), or a food.
Embodiments of the present disclosure provided herein are described by way of the following exemplary numbered alternatives:
1. A composition comprising an isolate of Bacteroides designated LJ00115, wherein said isolate of Bacteroides comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of the rDNA sequence of SEQ ID NO: 1 or the complement thereof, such as the selected isolate of Bacteroides designated LJ00115 deposited with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149345.
2. A composition comprising an isolate of Odoribacter designated LJ00541, wherein said isolate of Odoribacter comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99% or 100% sequence identity of the rDNA sequence of SEQ ID NO: 2 or the complement thereof, such as the selected isolate of Odoribacter designated LJ00541 deposited with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149346.
3. A composition comprising an isolate of Bacteroides designated PRB03A2_ANA_TSB_B11, wherein said isolate of Bacteroides comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99% or 100% sequence identity of the rDNA sequence of SEQ ID NO: 3 or the complement thereof, such as the selected isolate of Bacteroides designated PRB03A2_ANA_TSB_B11 deposited with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149347.
4. A composition comprising an isolate of Parabacteroides designated PRB02A2_ANA_TSB_F6, wherein said isolate of Parabacteroides comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99% or 100% sequence identity of the rDNA sequence of SEQ ID NO: 4 or the complement thereof, such as the selected isolate of Parabacteroides designated PRB02A2_ANA_TSB_F6 deposited with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149348.
5. A composition comprising an isolate of Bacteroides designated PRB01A2_ANA_MRS_C7, wherein said isolate of Bacteroides comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99% or 100% sequence identity of the rDNA sequence of SEQ ID NO: 5 or the complement thereof, such as the selected isolate of Bacteroides designated PRB01A2_ANA_MRS_C7 deposited with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149340.
6. A composition comprising an isolate of Paraprevotella designated LJ00262, wherein said isolate of Paraprevotella comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99% or 100% sequence identity of the rDNA sequence of SEQ ID NO: 6 or the complement thereof, such as the selected isolate of Paraprevotella designated LJ00262 deposited with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149341.
7. A composition comprising an isolate of Coprococcus designated LJ00622, wherein said isolate of Coprococcus comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity of the rDNA sequence of SEQ ID NO: 7 or the complement thereof, such as the selected isolate of Coprococcus designated LJ00622 deposited with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149349.
8. A composition comprising an isolate of Acidaminococcus designated PRB01A2_ANA_GAM_C8, wherein said isolate of Acidaminococcus comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99% or 100% sequence identity of the rDNA sequence of SEQ ID NO: 8 or the complement thereof, such as the selected isolate of Acidaminococcus designated PRB01A2_ANA_GAM_C8 deposited with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149342.
9. A composition comprising an isolate of Bifidobacterium designated PRB02A2_ANA_TSB_A11, wherein said isolate of Bifidobacterium comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99% or 100% sequence identity of the rDNA sequence of SEQ ID NO: 9 or the complement thereof, such as the selected isolate of Bifidobacterium designated PRB02A2_ANA_TSB_A11 deposited with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149343.
10. A composition comprising an isolate of Bifidobacterium designated PRB03A2_ANA_GAM_.Ab_B11 wherein said isolate of Bifidobacterium comprises a 16S rRNA gene sequence encoding or corresponding to at least 95%, 96%, 97%, 98%, 99% or 100% sequence identity of the rDNA sequence of SEQ ID NO: 10 or the complement thereof, such as the selected isolate of Bifidobacterium designated PRB03A2_ANA_GAM.Ab_B11 is deposited with the Westerdijk Fungal Biodiversity Institute, CBS collection, at Uppsalalaan 8, 3508 AD UTRECHT, The Netherlands under reference number CBS 149344.
11. The composition of any one of alternatives 1-10, further comprising a prebiotic, stabilizer, antibacterial agent, antifungal agent, or media component.
12. The composition of alternative 11, wherein the prebiotic is inulin, fructooligosaccharide, galactooligosaccharide, xylooligosaccharide, or lactulose.
13. The composition of alternative 11, wherein the stabilizer comprises a sugar, a sugar alcohol, an amino acid, a lipid, or any combination thereof.
14. The composition of alternative 13, wherein the stabilizer is glucose, sucrose, trehalose, lactose, maltodextrin, polydextrose, dextran, fructose, oligofructose, cellulose, glycerol, adonitol, inositol, mannitol, sorbitol, gums, hydrolyzed protein, skim milk powder, milk powder, gel beads, raffinose, soybean oligosaccharides, fructooligosaccharides, galactooligosaccharides, galactosyl lactose, palatinose, lactitol, xylitol, sorbitol, mannitol, trehalose, maltose, milk, whey, whey protein concentrates, casein, casein hydrolysates, lactoferrin, lactoperoxidase, lactoglobulins, glycomacropeptides, lacto-saccharides, lacto-lipids, or short chain fatty acids including acetic, propionic, butyric, isobutyric, valeric, isovaleric, or caproic acids or any combination thereof.
15. The composition of alternative 11, wherein the antibacterial agent is bacteriocin, amoxicillin, ampicillin, azithromycin, cefaclor, cefdinir, cefotaxime, ceftazidime, ceftriaxone, cefuroxime, cephalexin, cephalosporin, ciprofloxacin, clarithromycin, clavulanate, clindamycin, clotrimazole, dalbavancin, demeclocycline, dicloxacillin, doxycycline, eravacycline, erythromycin, fluconazole, furazolidone, lansoprazole, levofloxacin, lincomycin, metronidazole, minocycline, moxifloxacin, nitroimidazole, omadacycline, oritavancin, oxacillin, penem, penicillin, penicillin V potassium, rifabutin, sulfamethoxazole, sulfasalazine, telavancin, tetracycline, tinidazole, trimethoprim, or vancomycin, or any combination thereof.
16. The composition of alternative 11, wherein the antifungal agent is amphotericin B, clotrimazole, econazole, fluconazole, itraconazole, ketoconazole, miconazole, natamycin, nystatin, posaconazole, terconazole, terbinafine, or voriconazole, or any combination thereof.
17. The composition of alternative 11, wherein the media component is selected from any one or more of the components set forth in TABLE 2.
18. The composition of alternative 17, wherein the media component further comprises agar.
19. The composition of any one of alternatives 1-18, wherein the isolate or composition or both are lyophilized, spray dried, or freeze-dried.
20. The composition of any one of alternatives 1-19, further comprising at least one additional bacterial population, wherein said at least one additional bacterial population comprises a 16S rRNA gene encoding or corresponding to a sequence selected from any one or more of the rDNA sequences of SEQ ID NOS: 1-10 or the complement thereof or any one or more of a sequence having at least 95%, 96%, 97%, 98%, or 99% sequence identity to any one or more of SEQ ID NOS: 1-10 or the complement thereof.
21. The composition of any one of alternatives 1-20, wherein said composition comprises at least nine additional bacterial populations, wherein each of the at least nine additional bacterial populations comprises a 16S rRNA gene encoding or corresponding to a unique sequence selected from any one or more of the rDNA sequences of SEQ ID NOS: 1-10 or the complement thereof or any one or more of a sequence having at least 95%, 96%, 97%, 98%, or 99% sequence identity to any one or more of SEQ ID NOS: 1-10 or the complement thereof.
22. The composition of any one of alternatives 1-21, further comprising at least one additional bacterial population selected from the bacteria set forth in TABLE 3.
23. A method of treating, ameliorating, preventing, or inhibiting an allergy, infection, sexually transmitted infection, acne, acute infectious diarrhea, acute respiratory tract infections, allergic rhinitis, Alzheimer's disease, antibiotic-associated diarrhea, atopic dermatitis, asthma, autism, bladder cancer, Candidal vaginitis, chronic kidney disease, Crohn's disease, Clostridium difficile infection, the common cold, constipation, dementia, dental caries (tooth decay), diabetes mellitus, diverticulosis, eczema, chronic obstructive pulmonary disease (COPD), Escherichia coli infection, gastrointestinal tract infections, gastrointestinal inflammation, gum disease, halitosis, Helicobacter pylori infection, hepatic encephalopathy, high cholesterol, Huntington's disease, infant colic, infectious childhood diarrhea, infectious diarrhea, inflammatory bowel diseases, irritable bowel syndrome, kidney disease, lactose intolerance, Listeria monocytogenes infection, lower respiratory infection, metabolic disorder, multidrug-resistant bacterial infection, necrotizing enterocolitis, neurodegeneration, pancreatitis, pneumonia, obesity, oral disease, Parkinson's disease, pouchitis, radiation-associated diarrhea, respiratory infection, Salmonella thymurium infection, sepsis, small intestinal bacteria overgrowth, surgical site infections, traveler's diarrhea, ulcerative colitis, upper respiratory infection, urinary tract infection, vaginal infection, ventilator associated pneumonia, vulvo vaginitis, vulvovaginal candidiasis, yeast infection, or any combination thereof, or conditions associated therewith comprising providing any of the aforementioned compositions of alternatives 1-22 to a subject that has been preferably selected as one that would benefit from an adjustment of the microbiome and, optionally evaluating the treatment, amelioration, or inhibition of said allergy, infection, sexually transmitted infection, acne, acute infectious diarrhea, acute respiratory tract infections, allergic rhinitis, Alzheimer's disease, antibiotic-associated diarrhea, atopic dermatitis, asthma, autism, bladder cancer, Candidal vaginitis, chronic kidney disease, Crohn's disease, Clostridium difficile infection, the common cold, constipation, dementia, dental caries (tooth decay), diabetes mellitus, diverticulosis, eczema, Escherichia coli infection, gastrointestinal tract infections, gastrointestinal inflammation, gum disease, halitosis, Helicobacter pylori infection, hepatic encephalopathy, high cholesterol, Huntington's disease, infant colic, infectious childhood diarrhea, infectious diarrhea, inflammatory bowel diseases, irritable bowel syndrome, kidney disease, lactose intolerance, Listeria monocytogenes infection, lower respiratory infection, metabolic disorder, multidrug-resistant bacterial infection, necrotizing enterocolitis, neurodegeneration, pancreatitis, pneumonia, obesity, oral disease, Parkinson's disease, pouchitis, radiation-associated diarrhea, respiratory infection, Salmonella thymurium infection, sepsis, small intestinal bacteria overgrowth, surgical site infections, traveler's diarrhea, ulcerative colitis, upper respiratory infection, urinary tract infection, vaginal infection, ventilator associated pneumonia, vulvo vaginitis, vulvovaginal candidiasis, or yeast infection, or any combination thereof, or conditions associated therewith.
24. The composition of any one of alternatives 1-22, for use as a medicament.
25. The composition of any one of alternatives 1-22, for use in treating acne, acute infectious diarrhea, acute respiratory tract infections, allergic rhinitis, Alzheimer's disease, antibiotic-associated diarrhea, atopic dermatitis, asthma, autism, bladder cancer, Candidal vaginitis, chronic kidney disease, Crohn's disease, Clostridium difficile infection, the common cold, constipation, dementia, dental caries (tooth decay), diabetes mellitus, diverticulosis, eczema, chronic obstructive pulmonary disease (COPD), Escherichia coli infection, gastrointestinal tract infections, gastrointestinal inflammation, gum disease, halitosis, Helicobacter pylori infection, hepatic encephalopathy, high cholesterol, Huntington's disease, infant colic, infectious childhood diarrhea, infectious diarrhea, inflammatory bowel diseases, irritable bowel syndrome, kidney disease, lactose intolerance, Listeria monocytogenes infection, lower respiratory infection, metabolic disorder, multidrug-resistant bacterial infection, necrotizing enterocolitis, neurodegeneration, pancreatitis, pneumonia, obesity, oral disease, Parkinson's disease, pouchitis, radiation-associated diarrhea, respiratory infection, Salmonella thymurium infection, sepsis, small intestinal bacteria overgrowth, surgical site infections, traveler's diarrhea, ulcerative colitis, upper respiratory infection, urinary tract infection, vaginal infection, ventilator associated pneumonia, vulvo vaginitis, vulvovaginal candidiasis, yeast infection, or any combination thereof.
26. The composition of any one of alternatives 1-22, wherein said composition is formulated for oral delivery, such as powder, liquid, capsule, caplet, spray, or food.
The compositions and methods described herein are beneficial for reducing the use of antimicrobial and/or antipathogenic compounds in subjects, while at the same time allowing those subjects to be impervious to or capable of remaining healthy when confronted with harmful microbes such as pathogenic bacteria. These benefits may be accomplished by administering to a subject an effective amount of a beneficial, non-pathogenic microorganism or a composition comprising said microorganism as described herein, which will then reduce, inhibit, ameliorate, or mitigate the pathogenic microbial infection. In some embodiments, it is preferred that the formulation administered to the subject comprising the beneficial, non-pathogenic microorganism as described herein also comprises or is administered with (e.g., co-administration) with an effective amount of one or more prebiotics, stabilizers, antibacterial agents, antifungal agents, or media components. Administration of such beneficial, non-pathogenic microorganism as described herein and said prebiotics, stabilizers, antibacterial agents, antifungal agents, and/or media components can be accomplished together or as part of a planned system or method, and administration of both can provide a benefit that may not be available or experienced by the subject that received administration of either alone.
The term “anti-pathogenic,” is used herein, in accordance with its ordinary and plain meaning as understood by a person of ordinary skill in the art, which may include an anti-pathogenic compound or composition, which helps to kill, eliminate, or remove an agent of disease such as infectious organisms including bacteria, viruses, and fungi. Antipathogenic compounds or compositions may also include compounds, which help to remove a noninfectious agent of disease such as a chemical or a toxin.
As used herein, treatment of a disease or condition refers to reducing the severity or frequency of at least one symptom of that disease or condition, compared to a similar but untreated patient. Treatment can also refer to halting, slowing, or reversing the progression of a disease or condition, compared to a similar but untreated patient. Treatment may further comprise addressing the root cause of the disease and/or one or more symptoms. Non-limiting examples of diseases or conditions in a subject that may be treated or inhibited by administration of a composition disclosed herein include allergies, infection risk in the critically ill, sexually transmitted infections, acne, acute infectious diarrhea, acute respiratory tract infections, allergic rhinitis, Alzheimer's disease, antibiotic-associated diarrhea, atopic dermatitis, asthma, autism, bladder cancer, Candidal vaginitis, chronic kidney disease, Crohn's disease, Clostridium difficile infection, the common cold, constipation, dementia, dental caries (tooth decay), diabetes mellitus, diverticulosis, eczema, chronic obstructive pulmonary disease (COPD), Escherichia coli infection, gastrointestinal tract infections, gastrointestinal inflammation, gum disease, halitosis, Helicobacter pylori infection, hepatic encephalopathy, high cholesterol, Huntington's disease, infant colic, infectious childhood diarrhea, infectious diarrhea, inflammatory bowel diseases, irritable bowel syndrome, kidney disease, lactose intolerance, Listeria monocytogenes infection, lower respiratory infection, metabolic disorder, multidrug-resistant bacterial infection, necrotizing enterocolitis, neurodegeneration, pancreatitis, pneumonia, obesity, oral disease, Parkinson's disease, pouchitis, radiation-associated diarrhea, respiratory infection, Salmonella thymurium infection, sepsis, small intestinal bacteria overgrowth, surgical site infections, traveler's diarrhea, ulcerative colitis, upper respiratory infection, urinary tract infection, vaginal infection, ventilator associated pneumonia, vulvo vaginitis, vulvovaginal candidiasis, or yeast infection.
In some embodiments, the composition comprising the beneficial, non-pathogenic microorganism as isolated as described herein provides conditions that support nonpathogenic bacterium viability. For instance, the composition may promote growth and metabolism or may promote a dormant state (e.g., freezing, lyophilization, or freeze drying) from which viable nonpathogenic bacteria can be recovered. When the composition promotes growth or metabolism, it may contain water and/or nutrients that nonpathogenic bacteria consume, e.g., as ammonium, ammonia, urea, oxygen, carbon dioxide, or trace minerals. In some embodiments, the composition comprising nonpathogenic bacteria provides conditions that support beneficial bacteria viability. For instance, the composition may promote growth and metabolism or may promote a dormant state (e.g., freezing, lyophilization, or freeze drying) or storage state as described herein, from which viable beneficial bacteria can be recovered. When the composition promotes growth or metabolism, it may contain water and/or nutrients that beneficial bacteria consume, e.g., as ammonium ions, ammonia, urea, oxygen, carbon dioxide, or trace minerals.
Although described herein primarily with respect to humans, aspects of this disclosure can, in some embodiments, be applied to benefit a subject, which should be interpreted herein to include a livestock animal, a domestic animal, a wild animal, fish, birds, mammals, or humans.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art. All patents, applications, published applications and other publications referenced herein are incorporated by reference in their entirety unless stated otherwise.
As used herein, “a” or “an” may mean one or more than one.
As used herein, the term “about” or “approximately” has its usual meaning as understood by those skilled in the art and thus indicates that a value includes the inherent variation of error for the method being employed to determine a value, or the variation that exists among multiple determinations.
Throughout this specification, unless the context requires otherwise, the words “comprise,” “comprises,” and “comprising” will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements. By “consisting of” is meant including, and limited to, whatever follows the phrase “consisting of.” Thus, the phrase “consisting of” indicates that the listed elements are required or mandatory, and that no other elements may be present. By “consisting essentially of” is meant including any elements listed after the phrase and limited to other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase “consisting essentially of” indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they materially affect the activity or action of the listed elements.
The terms “function” and “functional” as used herein have their plain and ordinary meaning as understood in light of the specification, and refer to a biological, enzymatic, or therapeutic function.
As used herein, the terms “isolated” or “isolate” have their plain and ordinary meaning as understood in light of the specification, and refer to a substance and/or entity that has been (1) separated from at least some of the components with which it was associated when initially produced (whether in nature and/or in an experimental setting), and/or (2) produced, prepared, and/or manufactured by a human. Isolated substances and/or entities may be separated from equal to, about, at least, at least about, not more than, or not more than about, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 100% of the other components with which they were initially associated (or ranges including and/or spanning the aforementioned values). In some embodiments, isolated agents are, are about, are at least, are at least about, are not more than, or are not more than 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% pure (or within a range of purity defined by any two of the aforementioned values). As used herein, an organism that is “isolated” may be “pure” (e.g., substantially free of other components). As used herein, the term “isolated cell” may refer to a cell not contained in a multi-cellular organism or tissue.
As used herein, “in vivo” is given its plain and ordinary meaning as understood in light of the specification and refers to the performance of a method inside living organisms, usually animals, mammals, including humans, and plants, or living cells which make up these living organisms, as opposed to a tissue extract or dead organism.
As used herein, “ex vivo” is given its plain and ordinary meaning as understood in light of the specification and refers to the performance of a method outside a living organism with little alteration of natural conditions.
As used herein, “in vitro” is given its plain and ordinary meaning as understood in light of the specification and refers to the performance of a method outside of biological conditions, e.g., in a petri dish or test tube.
The terms “nucleic acid” or “nucleic acid molecule” as used herein have their plain and ordinary meaning as understood in light of the specification, and refer to polynucleotides, such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), oligonucleotides, those that appear in a cell naturally, fragments generated by the polymerase chain reaction (PCR), or fragments generated by any of ligation, scission, endonuclease action, or exonuclease action. Nucleic acid molecules can be composed of monomers that are naturally-occurring nucleotides (such as DNA and RNA), or analogs of naturally-occurring nucleotides (e.g., enantiomeric forms of naturally-occurring nucleotides), or a combination of both. The term “nucleic acid molecule” also includes so-called “peptide nucleic acids,” which comprise naturally-occurring or modified nucleic acid bases attached to a polyamide backbone. Nucleic acids can be either single stranded or double stranded. “Oligonucleotide” can be used interchangeable with nucleic acid and can refer to either double stranded or single stranded DNA or RNA. A nucleic acid or nucleic acids can be contained in a nucleic acid vector or nucleic acid construct (e.g. plasmid, virus, retrovirus, lentivirus, bacteriophage, cosmid, fosmid, phagemid, bacterial artificial chromosome (BAC), yeast artificial chromosome (YAC), or human artificial chromosome (HAC)) that can be used for amplification and/or expression of the nucleic acid or nucleic acids in various biological systems. Typically, the vector or construct will also contain elements including but not limited to promoters, enhancers, terminators, inducers, ribosome binding sites, translation initiation sites, start codons, stop codons, polyadenylation signals, origins of replication, cloning sites, multiple cloning sites, restriction enzyme sites, epitopes, reporter genes, selection markers, antibiotic selection markers, targeting sequences, peptide purification tags, or accessory genes, or any combination thereof.
The terms “peptide”, “polypeptide”, and “protein” as used herein have their plain and ordinary meaning as understood in light of the specification and refer to macromolecules comprised of amino acids linked by peptide bonds. The numerous functions of peptides, polypeptides, and proteins are known in the art, and include but are not limited to enzymes, structure, transport, defense, hormones, or signaling. Peptides, polypeptides, and proteins are often, but not always, produced biologically by a ribosomal complex using a nucleic acid template, although chemical syntheses are also available.
The term “gene” as used herein have their plain and ordinary meaning as understood in light of the specification, and generally refers to a portion of a nucleic acid that encodes a protein or functional RNA; however, the term may optionally encompass regulatory sequences. It will be appreciated by those of ordinary skill in the art that the term “gene” may include gene regulatory sequences (e.g., promoters, enhancers, etc.) and/or intron sequences. It will further be appreciated that definitions of gene include references to nucleic acids that do not encode proteins but rather encode functional RNA molecules such as rRNAs, tRNAs and miRNAs. In some cases, the gene includes regulatory sequences involved in transcription, or message production or composition. In other embodiments, the gene comprises transcribed sequences that encode for a protein, polypeptide or peptide. In keeping with the terminology described herein, an “isolated gene” may comprise transcribed nucleic acid(s), regulatory sequences, coding sequences, or the like, isolated substantially away from other such sequences, such as other naturally occurring genes, regulatory sequences, polypeptide or peptide encoding sequences, etc. In this respect, the term “gene” is used for simplicity to refer to a nucleic acid comprising a nucleotide sequence that is transcribed, and the complement thereof. As will be understood by those in the art, this functional term “gene” includes both genomic sequences, RNA or cDNA sequences, or smaller engineered nucleic acid segments, including nucleic acid segments of a non-transcribed part of a gene, including but not limited to the non-transcribed promoter or enhancer regions of a gene. Smaller engineered gene nucleic acid segments may express or may be adapted to express using nucleic acid manipulation technology, proteins, polypeptides, domains, peptides, fusion proteins, mutants and/or such like.
Some embodiments described herein relate to pharmaceutical compositions or dietary supplements that comprise, consist essentially of, or consist of an effective amount of any one or more of the cell compositions described herein. Such pharmaceutical compositions and dietary supplements are suitable for human and/or veterinary applications.
The terms “individual”, “subject”, “host,” or “patient” as used herein have their usual meaning as understood by those skilled in the art and thus includes a human or a non-human mammal. The term “mammal” is used in its usual biological sense. Thus, it specifically includes, but is not limited to, primates, including simians (chimpanzees, apes, monkeys), humans, cattle, horses, sheep, goats, swine, rabbits, dogs, cats, rodents, rats, mice, or guinea pigs.
The terms “effective amount” or “effective dose” as used herein have their usual meaning as understood by those skilled in the art and refer to that amount of a recited composition or compound that results in an observable biological effect. Actual dosage levels of active ingredients in an active composition of the presently disclosed subject matter can be varied so as to administer an amount of the active composition or compound that is effective to achieve the desired response for a particular subject and/or application. The selected dosage level will depend upon a variety of factors including, but not limited to, the activity of the composition, formulation, route of administration, combination with other drugs or treatments, severity of the condition being treated, and the physical condition and prior medical history of the subject being treated. In some embodiments, a minimal dose is administered, and dose is escalated in the absence of dose-limiting toxicity to a minimally effective amount. Determination and adjustment of an effective dose, as well as evaluation of when and how to make such adjustments, are contemplated herein.
As used herein, “pharmaceutically acceptable” has its plain and ordinary meaning as understood in light of the specification and refers to carriers, excipients, and/or stabilizers that are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed or that have an acceptable level of toxicity. A “pharmaceutically acceptable” “diluent,” “excipient,” and/or “carrier” as used herein have their plain and ordinary meaning as understood in light of the specification and are intended to include any and all solvents, dispersion media, coatings, antibacterial or antifungal agents, isotonic or absorption delaying agents, compatible with administration to humans, cats, dogs, or other vertebrate hosts. Typically, a pharmaceutically acceptable diluent, excipient, and/or carrier is a diluent, excipient, and/or carrier approved by a regulatory agency of a Federal, a state government, or other regulatory agency, or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, including humans as well as non-human mammals, such as cats and dogs. The term diluent, excipient, and/or “carrier” can refer to a diluent, adjuvant, excipient, or vehicle with which the pharmaceutical composition is administered. Such pharmaceutical diluent, excipient, and/or carriers, which can be incorporated in any one or more of the compositions described herein, include sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin. Water, saline solutions or aqueous dextrose and glycerol solutions can be employed as liquid diluents, excipients, and/or carriers. Suitable pharmaceutical diluents and/or excipients, which can be incorporated in any one or more of the compositions described herein, also include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, or ethanol. The physiologically acceptable carrier may also comprise one or more of the following: antioxidants, such as ascorbic acid, low molecular weight (less than about 10 residues) polypeptides, proteins, such as serum albumin, gelatin, immunoglobulins, hydrophilic polymers such as polyvinylpyrrolidone, amino acids, carbohydrates such as glucose, mannose, or dextrins, chelating agents such as EDTA, sugar alcohols such as mannitol or sorbitol, salt-forming counterions such as sodium, and nonionic surfactants such as TWEEN®, polyethylene glycol (PEG), PLURONICS® or preservatives such as an essential oil, methyl paraben, propyl paraben, or sodium salt of parabens. Preferably, the preservative is bronidiol. The composition, if desired, can also contain minor amounts of wetting, bulking, emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsion, sustained release formulations and the like. The formulation should suit the mode of administration.
In some embodiments, the bacterial cells isolated as described herein are frozen or cryopreserved and then thawed or lyophilized or freeze-dried. Freezing or cryopreserving can be done in any conventional matter as a means of prolonging the shelf life of cells. This includes but is not limited to dry ice, liquid nitrogen, or refrigeration. In some embodiments, cryoprotectants are added to the cells prior to freezing.
Cryoprotectants are cell composition additives to improve efficiency and yield of low temperature cryopreservation by preventing formation of large ice crystals. Cryoprotectants include but are not limited to dimethyl sulfoxide (DMSO), ethylene glycol, glycerol, propylene glycol, trehalose, formamide, methyl-formamide, dimethyl-formamide, glycerol 3-phosphate, proline, sorbitol, diethyl glycol, sucrose, triethylene glycol, polyvinyl alcohol, polyethylene glycol, or hydroxyethyl starch. Cryoprotectants can be used as part of a cryopreservation medium, which include other components such as nutrients (e.g. albumin, serum, bovine serum, fetal calf serum [FCS]) to enhance post-thawing survivability of the cells. In these cryopreservation media, at least one cryoprotectant may be found at a concentration that is, is about, is at least, is at least about, is not more than, or is not more than about, 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or any percentage within a range defined by any two of the aforementioned numbers.
Additional excipients with desirable properties include but are not limited to preservatives, adjuvants, stabilizers, solvents, buffers, diluents, solubilizing agents, detergents, surfactants, chelating agents, antioxidants, alcohols, ketones, aldehydes, ethylenediaminetetraacetic acid (EDTA), citric acid, salts, sodium chloride, sodium bicarbonate, sodium phosphate, sodium borate, sodium citrate, potassium chloride, potassium phosphate, magnesium sulfate sugars, dextrose, fructose, mannose, lactose, galactose, sucrose, sorbitol, cellulose, serum, amino acids, polysorbate 20, polysorbate 80, sodium deoxycholate, sodium taurodeoxycholate, magnesium stearate, octylphenol ethoxylate, benzethonium chloride, thimerosal, gelatin, esters, ethers, 2-phenoxyethanol, urea, or vitamins, or any combination thereof. Some excipients may be in residual amounts or contaminants from the process of manufacturing, including but not limited to serum, albumin, ovalbumin, antibiotics, inactivating agents, formaldehyde, glutaraldehyde, β-propiolactone, gelatin, cell debris, nucleic acids, peptides, amino acids, or growth medium components or any combination thereof. The amount of the excipient may be found in the composition at a percentage that is, is about, is at least, is at least about, is not more than, or is not more than about, 0%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 100% w/w or any percentage by weight in a range defined by any two of the aforementioned numbers.
The term “pharmaceutically acceptable salts” has its plain and ordinary meaning as understood in light of the specification and includes relatively non-toxic, inorganic and organic acid, or base addition salts of compositions or excipients, including without limitation, analgesic agents, therapeutic agents, other materials, and the like. Examples of pharmaceutically acceptable salts, which may be included in any one or more of the formulations comprising the bacteria described herein, include those derived from mineral acids, such as hydrochloric acid and sulfuric acid, and those derived from organic acids, such as ethanesulfonic acid, benzenesulfonic acid, or p-toluenesulfonic acid, and the like. Examples of suitable inorganic bases for the formation of salts include the hydroxides, carbonates, and bicarbonates of ammonia, sodium, lithium, potassium, calcium, magnesium, aluminum, or zinc, and the like. Salts may also be formed with suitable organic bases, including those that are non-toxic and strong enough to form such salts. For example, the class of such organic bases may include but are not limited to mono-, di-, and trialkylamines, including methylamine, dimethylamine, and triethylamine; mono-, di-, or trihydroxyalkylamines including mono-, di-, and triethanolamine; amino acids, including glycine, arginine and lysine; guanidine; N-methylglucosamine; N-methylglucamine; L-glutamine; N-methylpiperazine; morpholine; ethylenediamine; N-benzylphenethylamine; or trihydroxymethyl aminoethane.
Proper formulation is dependent upon the route of administration chosen. Techniques for formulation and administration of the compounds described herein are known to those skilled in the art. Multiple techniques of administering a compound exist in the art including, but not limited to, enteral, oral, rectal, topical, sublingual, buccal, intraaural, epidural, epicutaneous, aerosol, parenteral delivery, including intramuscular, subcutaneous, intra-arterial, intravenous, intraportal, intra-articular, intradermal, peritoneal, intramedullary injections, intrathecal, direct intraventricular, intraperitoneal, intranasal or intraocular injections.
As used herein, a “carrier” has its plain and ordinary meaning as understood in light of the specification and refers to a compound, particle, solid, semi-solid, liquid, or diluent that facilitates the passage, delivery and/or incorporation of a compound to cells, tissues and/or bodily organs.
As used herein, a “diluent” has its plain and ordinary meaning as understood in light of the specification and refers to an ingredient in a pharmaceutical composition that lacks pharmacological activity but may be pharmaceutically necessary or desirable. For example, a diluent may be used to increase the bulk of a potent drug whose mass is too small for manufacture and/or administration. It may also be a liquid for the dissolution of a drug to be administered by injection, ingestion or inhalation. A common form of diluent in the art is a buffered aqueous solution such as, without limitation, phosphate buffered saline that mimics the composition of human blood.
Administered “in combination,” as used herein, means that two (or more) different compositions are delivered to the subject during the course of the subject's affliction with the disorder, e.g., the two or more compositions are delivered after the subject has been diagnosed or selected as one having the disorder and before the disorder has been cured or eliminated. In some embodiments the subject is selected to receive any one or more of the compositions described herein by diagnostic analysis or clinical evaluation or both. For instance, in some embodiments, a subject is screened to determine whether said subject lacks one or more beneficial bacteria or has a reduced amount of said one or more beneficial bacteria prior to receiving an administration of any one or more of the compositions described herein. In some embodiments, the delivery of one therapy is still occurring when the delivery of the second begins, so that there is overlap. This is sometimes referred to herein as “simultaneous” or “concomitant” or “concurrent delivery”. In other embodiments, the delivery of one therapy ends before the delivery of the other therapy begins. This is sometimes referred to herein as “successive” or “sequential delivery.” In embodiments of either case, the therapy is more effective because of combined administration. For example, the second therapy is a more effective, e.g., an equivalent effect is seen with less of the second therapy, or the second therapy reduces symptoms to a greater extent, than would be seen if the second therapy were administered in the absence of the first therapy, or the analogous situation is seen with the first therapy. In some embodiments, delivery is such that the reduction in a symptom, or other parameter related to the disorder is greater than what would be observed with one therapy delivered in the absence of the other. The effect of the two therapies can be partially additive, wholly additive, or greater than additive (e.g., synergistic). The delivery can be such that an effect of the first therapy delivered is still detectable when the second is delivered. “Microbiome” as used herein has its plain and ordinary meaning as understood in light of the specification and refers to a population, e.g., one or more microorganisms that live on a surface of a subject, e.g., in the gut, mouth, skin, and/or elsewhere in a subject. The population may have one or more beneficial functions and/or benefits, relevant to supporting the life of a subject. “Metagenome” refers to the collective genomes of a microbiota or microbiome.
In some embodiments, “nonpathogenic bacteria” refers to bacterial strains, which are not known to cause harm. In some embodiments, nonpathogenic bacteria are not known to cause harm, disease, or death to the subject. Nonpathogenic bacteria may include beneficial bacteria. A beneficial bacterium refers to a live bacterium, which may confer a health benefit on the subject. Beneficial bacteria may be associated with a subject's microbiome, e.g., providing a benefit to a subject's microbiome. For example, beneficial bacteria may compete with pathogenic bacteria, e.g., consuming scarce nutrients, or generating byproducts that are harmful to other organisms, e.g., changing a pH level that is not conducive to the undesirable organism's growth. Beneficial bacteria may provide a benefit by delivering a beneficial product or byproduct to the subject, e.g., a product or byproduct which typically inhibits growth or reproduction of pathogenic bacteria. Beneficial bacteria may additionally or alternatively deliver a product or byproduct which promotes growth and metabolism of other beneficial bacteria.
As used herein, compositions may comprise one or multiple isolates of bacteria. These bacteria may include novel strains and species e.g., any one or more of the bacteria, which comprise a 16S rRNA gene encoding or corresponding to a sequence selected from any one or more of the rDNA sequence of SEQ ID NOS: 1-10 or the complement thereof or any one or more of a sequence having at least 95%, 96%, 97%, 98%, or 99% sequence identity to any one or more of SEQ ID NOS: 1-10 or the complement thereof, as well as, strains selected from any one or more of Absiella, Acetanaerobacterium, Acetatifactor, Acetivibrio, Acetoanaerobium, Acetobacterium, Acholeplasma, Achromobacter, Acidaminococcus, Acidibacillus, Acidiplasma, Acidovorax, Acinetobacter, Actinomyces, Actinomycetaceae, Acutalibacter, Adlercreutzia, Aerococcus, Aeromicrobium, Agathobacter, Agathobaculum, Akkermansi, Algibacter, Algoriella, Algoriphagus, Alicyclobacillus, Alistipes, Alkalibacillus, Alkalibacter, Alkalibacterium, Alkalibaculum, Alkalicoccus, Alkahphilus, Allisonella, Allobaculum, Allofustis, Alloprevotella, Alloscardovia, Alysiella, Aminomonas, Aminomonas, Anaeroarcus, Anaerobacillus, Anaerobacterium, Anaerobium, Anaerobranca, Anaerococcus, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaerolineaceae, Anaeromassilibacillus, Anaeromicrobium, Anaeromusa, Anaeromyxobacter, Anaerorhabdus, Anaerosalibacter, Anaerosphaera, Anaerosporobacter, Anaerostipes, Anaerotignum, Anaerotruncus, Anaerovibrio, Anaerovorax, Aneurinibacillus, Angelakisella, Apibacter, Aquaspirillum, Arabia, Arachidicoccus, Arcobacter, Arcticibacter, Armatimonadia, Arsenicibacter, Asaccharobacter, Asticcacaulis, Atopobacter, Atopobium, Atribacteria, Auricoccus, Azoarcus, Azospira, Bacillaceae, Bacillus, Bacteroidales, Bacteroides, Bacteroidetes, Bariatricus, Barnesiella, Beduini, Bergeriella, Bernardetia, Bhargavaea, Bifidobacterium, Bilophila, Bittarella, Blattabacterium, Blautia, Bordetella, Borrelia, Brachyspira, Brevibacillus, Brevundimonas, Buchnera, Bulleidia, Burkholderiales, Butyricicoccus, Butyricimonas, Butyrivibrio, Caecibacter, Caenibacillus, Caenispirillum, Caldanaerobacter, Caldanaerobius, Caldibacillus, Caldicellulosiruptor, Caldicoprobacter, Caldisalinibacter, Caldisphaera, Calditerricola, Calditerrivibrio, Caloramator, Caloranaerobacter, Caminibacter, Caminicella, Campylobacter, Candidatus Arsenophonus, Candidatus Arthromitus, Candidatus Babela, Candidatus Blochmannia, Candidatus Carsonella, Candidatus Chrysopegis, Candidatus Cloacimonas, Candidatus Dependentiae, Candidatus Desulforudis, Candidatus Desulfovibrio, Candidatus Dorea, Candidatus Evansia, Candidatus Fonsibacter, Candidatus Frackibacter, Candidatus Gastranaerophilus, Candidatus Gracilibacteria, Candidatus Izimaplasma, Candidatus Kine toplastibacterium, Candidatus Kryptonium, Candidatus Liberibacter, Candidatus Pelagibacter, Candidatus Phytoplasma, Candidatus Profftella, Candidatus Promineofilum, Candidatus Purcelliella, Candidatus Saccharibacteria, Candidatus Soleaferrea, Candidatus Stoquefichus, Candidatus Sukia, Candidatus Symbiothrix, Candidatus Tachikawaea, Capnocytophaga, Carboxydocella, Carboxydothermus, Cardiobacterium, Carnobacterium, Catabacter, Catalinimonas, Catellicoccus, Catenabacterium, Caulobacter, Caviibacter, Cellulomonas, Cellulosilyticum, Centipeda, Cetobacterium, Chishuiella, Chitinophaga, Chlorobaculum, Chlorobium, Christensenella, Chryseobacterium, Cloacibacillus, Clostridia, Clostridiaceae, Clostridiales, Clostridium, Cohnella, Colibacter, Collinsella, Consotaella, Coprobacillus, Coprobacter, Coprococcus, Coriobacteriaceae, Corynebacterium, Criibacterium, Culturomica, Cytophaga, Dakarella, Deferribacter, Defluviitalea, Defluviitoga, Dehalobacter, Deinococcus, Dendrosporobacter, Denitrobacterium, Derxia, Desnuesiella, Desulfallas, Desulfarculus, Desulfitibacter, Desulfitobacterium, Desulfobulbus, Desulfocarbo, Desulfococcus, Desulfocurvus, Desulfofarcimen, Desulfofundulus, Desulfomicrobium, Desulfonatronum, Desulfonauticus, Desulfonispora, Desulfosporosinus, Desulfotomaculum, Desulfovibrio, Desulfovirgula, Desulfurella, Desulfuribacillus, Desulfurispora, Desulfurivibrio, Desulfurobacterium, Desulfuromonas, Dethiobacter, Dethiosulfatibacter, Devosia, Dialister, Dielma, Dinoroseobacter, Domibacillus, Dorea, Draconibacterium, Drancourtella, Dubosiella, Duganella, Duodenibacillus, Dysgonamonadaceae, Dysgonomonas, Effusibacillus, Eggerthella, Ehrlichia, Eikenella, Eisenbergiella, Elizabethkingia, Elusimicrobium, Emergencia, Empedobacter, Emticicia, Endomicrobium, Enorma, Enterobacter, Enterococcus, Enterorhabdus, Enteroscipio, Entomoplasma, Epulopiscium, Ereboglobus, Erysipelatoclostridium, Erysipelothrix, Erysipelotrichaceae, Escherichia, Ethanoligenens, Eubacteriaceae, Eubacterium, Ezakiella, Facklamia, Faecalibacterium, Faecalibaculum, Faecalicatena, Faecalicatena, Faecalimonas, Faecalitalea, Fastidiosipila, Fenollaria, Fermentimonas, Fervidicella, Fervidicola, Fibrobacter, Filifactor, Finegoldia, Firmicutes, Flaviramulus, Flavobacteriaceae, Flavobacterium, Flavonifractor, Floricoccus, Fontibacillus, Formivibrio, Formosa, Fournierella, Francisella, Francisellaceae, Fusibacter, Fusicatenibacter, Fusobacterium, Gabonia, Gabonibacter, Garciella, Gemella, Geminocystis, Gemmiger, Geoalkalibacter, Geobacillus, Geobacter, Geofilum, Geopsychrobacter, Geosporobacter, Gilliamella, Gillisia, Globicatella, Gordonibacter, Gorillibacterium, Gracilibacillus, Granulicatella, Haemophilus, Halanaerobium, Halodesulfovibrio, Halomonas, Halonatronum, Haloplasma, Halothiobacillus, Harryflintia, Helcococcus, Helicobacter, Herbaspirillum, Herbinix, Herminiimonas, Hespellia, Holdemania, Hungateiclostridiaceae, Hungateiclostridium, Hungatella, Hydrogenoanaerobacterium, Hydrogenothermus, Hymenobacter, Ideonella, Idiomarina, Ignavibacterium, Ileibacterium, Ilyobacter, Immundisolibacter, Inediibacterium, Inordinaticella, Intestinibacillus, Intestinibacter, Intestinimonas, Isobaculum, Izhakiella, Jeotgalibaca, Jeotgalicoccus, Jonquetella, Kallipyga, Khelaifiella, Khoudiadiopia, Kineothrix, Kingella, Kiritimatiella, Labilibacter, Labilibaculum, Lachnoanaerobaculum, Lachnobacterium, Lachnoclostridium, Lachnospiraceae, Lachnotalea, Lacinutrix, Lacticigenium, Lactobacillus, Lactococcus, Lactomassilus, Lactonifactor, Lagierella, Laribacter, Lascolabacillus, Lawsonibacter, Lebetimonas, Legionella, Lentibacillus, Leptotrichia, Levyella, Libanicoccus, Lihuaxuella, Listeria, Longilinea, Luteimonas, Luteitalea, Lutibacter, Lutibacter, Lysinibacillus, Macellibacteroides, Mageeibacillus, Magnetofaba, Magnetospirillum, Mahella, Mailhella, Mangrovibacterium, Marasmitruncus, Maribacter, Marinifilaceae, Marinifilum, Marinilabilia, Mariniphaga, Marinitoga, Marinobacter, Marinomonas, Marispirochaeta, Marvinbryantia, Massilibacillus, Massilibacterium, Massilibacteroides, Massilimaliae, Massilioclostridium, Massiliomicrobiota, Mediterranea, Mediterraneibacter, Megamonas, Megasphaera, Melghirimyces, Melioribacter, Melissococcus, Merdibacter, Merdimonas, Mesonia, Mesoplasma, Mesorhizobium, Metaprevotella, Methanobrevibacter, Methanocaldococcus, Methanococcus, Methanosphaera, Methanothermococcus, Methanothermus, Methylomonas, Methylophilales, Millionella, Miniphocibacter, Mitsuokella, Mobilibacterium, Modestobacter, Mogibacterium, Monoglobus, Moorella, Moraxella, Mordavella, Mucilaginibacter, Mucinivorans, Mucispirillum, Murdochiella, Muribaculaceae, Muribaculum, Muricauda, Murimonas, Mycolicibacterium, Mycoplasma, Natranaerobius, Natronincola, Nautilia, Ndongobacter, Negativibacillus, Negativibacillus, Neglecta, Neisseria, Neobitarella, Neofamilia, Niameybacter, Niastella, Novispirillum, Novosphingobium, Oceanibaculum, Oceanicaulis, Oceanicella, Oceanithermus, Oceanivirga, Oceanobacillus, Oceanotoga, Odoribacter, Olsenella, Opitutaceae, Opitutus, Orenia, Oribacterium, Ornithinibacillus, Ornithobacterium, Oscillibacter, Oscillochloris, Oscillospiraceae, Ottowia, Oxalobacter, Paenibacillus, Paludibacter, Parabacteroides, Paraclostridium, Paracoccus, Paraeggerthella, Paraliobacillus, Paramaledivibacter, Paraphotobacterium, Paraprevotella, Parascardovia, Parasporobacterium, Parasutterella, Parvimonas, Paucisalibacillus, Pediococcus, Pedobacter, Pelagibacteraceae, Pelosinus, Peptoanaerobacter, Peptoclostridium, Peptoniphilus, Peptostreptococcaceae, Peptostreptococcus, Perlucidibaca, Persephonella, Petrimonas, Petroclostridium, Petrotoga, Phascolarctobacterium, Phocaeicola, Phocea, Phoenicibacter, Photobacterium, Pilibacter, Piscibacillus, Planifilum, Planococcus, Pleomorphomonas, Polaribacter, Polymorphum, Pontibacillus, Porphyromonadaceae, Porphyromonas, Prevotella, Prevotellaceae, Prevotellamassilia, Prochlorococcus, Prolixibacter, Prolixibacteraceae, Propionispira, Propionispora, Prosthecochloris, Proteiniborus, Proteiniclasticum, Proteiniphilum, Proteocatella, Provencibacterium, Pseudoarcobacter, Pseudobutyrivibrio, Pseudoclostridium, Pseudodesulfovibrio, Pseudoflavonifractor, Pseudomonas, Pseudoramibacter, Pseudoscardovia, Pseudoxanthomonas, Psychrilyobacter, Pustulibacterium, Pygmaiobacter, Pyramidobacter, Raoultibacter, Reyranella, Rhizobium, Rhodobacter, Rhodonellum, Rhodopseudomonas, Rhodothermaceae, Rickettsia, Riemerella, Robiginitalea, Robinsoniella, Romboutsia, Roseburia, Rubneribacter, Rubritepida, Ruminiclostridium, Ruminobacter, Ruminococcaceae, Ruminococcus, Rummeliibacillus, Ruthenibacterium, Saccharibacillus, Saccharicrinis, Salegentibacter, Salibacterium, Salinicoccus, Salisaeta, Sanguibacteroides, Sarcina, Sebaldella, Sedimentibacter, Sedimentisphaera, Sediminibacterium, Selenihalanaerobacter, Selenomonas, Sellimonas, Senegalimassilia, Sharpea, Shewanella, Shigella, Shuttleworthia, Siansivirga, Simplicispira, Sinobaca, Sinomicrobium, Sinorhizobium, Slackia, Sneathia, Solimonas, Solirubrobacter, Solitalea, Solobacterium, Sphingobacterium, Sphingomonas, Spiroplasma, Sporanaerobacter, Sporolactobacillus, Sporolituus, Sporomusa, Staphylococcus, Stomatobaculum, Streptobacillus, Streptococcus, Subdoligranulum, Succinatimonas, Succinispira, Succinivibrionaceae, Sulfuricaulis, Sulfurihydrogenibium, Sulfurimonas, Sulfurivirga, Sutterella, Sutterellaceae, Synechococcus, Synergistes, Syntrophomonas, Syntrophus, Tangfeifania, Tannerella, Tenacibaculum, Tenericutes, Tepidanaerobacter, Tepidibacter, Tepidimicrobium, Tepidimicrobium, Tessaracoccus, Thalassomonas, Thalassospira, Thauera, Thermacetogenium, Thermaerobacter, Thermicanus, Thermincola, Thermithiobacillus, Thermoactinomyces, Thermoanaerobacter, Thermoanaerobacteraceae, Thermoanaerobacterales, Thermoanaerobacterium, Thermobacillus, Thermodesulfobacterium, Thermodesulfobium, Thermodesulfovibrio, Thermohalobacter, Thermophagus, Thermosediminibacter, Thermosinus, Thermosipho, Thermotalea, Thermovenabulum, Thioalkalivibrio, Tidjanibacter, Tindallia, Tissierella, Traorella, Treponema, Trichococcus, Tumebacillus, Turicibacter, Turicimonas, Tyzzerella, Ureaplasma, Urinacoccus, Vagococcus, Vallitalea, Varibaculum, Veillonella, Veillonellaceae, Verrucomicrobium, Victivallales, Victivallis, Virgibacillus, Vogesella, Vukanibacillus, Yersinia, Youngiibacter, or Zobellella.
Compositions may be purified to be substantially free of other organisms or to wherein substantially all of the organisms in the composition are a selected organism or community of organisms. For example, compositions can be purified to a predetermined concentration of nonpathogenic bacteria, live bacteria, isolated species of bacteria, a selected community of species of bacteria, or combinations thereof. Compositions may be purified to exclude a selected organism or community of organisms. For example, compositions disclosed herein may be substantially free of pathogenic bacteria, non-live bacteria, ammonia oxidizing bacteria, or combinations thereof.
In some embodiments, the compositions can further comprise one or more prebiotic, stabilizers, antibacterial agents, antifungal agents, or media components. Usual LAB growth factors or “prebiotics”, which has its plain and ordinary meaning as understood in light of the specification, refers to natural growth factors or compounds that induce the growth or activity of microorganisms. Non-limiting examples of prebiotics include skim milk powder (MSK), inulin, fructooligosaccharide, galactooligosaccharide, xylooligosaccharide, lactulose, oligofructose, beta-glucan, isomaltooligosaccharide, guar gum, maltodextrin, arabinooligosaccharide, and resistant starch. Any one or more of the aforementioned prebiotics can be incorporated in any one or more of the compositions described herein. Certain foods are high in prebiotic components, as well, and their contents may be used to enhance the growth or activity of microorganisms. Non-limiting examples of high-prebiotic foods include chicory root, dandelion greens, Jerusalem artichoke, garlic, onions, leeks, asparagus, bananas, barley, oats, apples, konjac root, cocoa, burdock root, flaxseeds, yacon root, jicama root, wheat bran, and seaweed. Any one or more of the aforementioned high-prebiotic foods can be incorporated in any one or more of the compositions described herein.
A “stabilizer” has its plain and ordinary meaning as understood in light of the specification and refers to any compound or material that confers improved stability properties on the one or more microorganism so that probiotics may be developed, stored, and distributed in a wide variety of circumstances while maintaining a useful shelf-life. Non-limiting examples of stabilizers include sugars, sugar alcohols, proteins, amino acids, and fats/lipids. In some embodiments, the stabilizer may be raffinose, soybean oligosaccharides, fructooligosaccharides, galactooligosaccharides, galactosyl lactose, palatinose, lactulose, lactitol, xylitol, sorbitol, mannitol, trehalose, glucose, sucrose, fructose, maltose, milk, milk powders, whey, whey protein concentrates, casein, casein hydrolysates, lactoferrin, lactoperoxidase, lactoglobulins, glycomacropeptides, lacto-saccharides, lacto-lipids, or short chain fatty acids including acetic, propionic, butyric, isobutyric, valeric, isovaleric, or caproic acids. Any one or more of the aforementioned stabilizers can be incorporated in any one or more of the compositions described herein.
An “antibacterial agent”, also known as an “antibiotic,” has its plain and ordinary meaning as understood in light of the specification and refers to a compound or substance with the ability to lower the growth, replication, infection, or spread of bacteria. In some cases, the antibacterial kills the bacteria. Antibacterial agents may be broad spectrum (targeting many species of bacteria) or narrow spectrum (targeting one or few species of bacteria). Many mechanisms of action exist for antibacterial agents, including cell cycle inhibition, disruption of cell surface formation, nutrient uptake inhibition, inhibition of protein synthesis, inhibition of lipid synthesis, inhibition of nucleic acid synthesis, antimetabolic activity, protein-targeting activity, protein degradation, regulation of enzymes, disruption of DNA repair, altering cell surface permeability, and desiccation. Non-limiting examples of antibacterial agents include aminoglycosides, amoxicillin, ampicillin, azithromycin, bacteriocin, bacitracin, beta-lactams, carbapenems, cefaclor, cefdinir, cefotaxime, ceftazidime, ceftriaxone, cefuroxime, cephalexin, cephalosporin, chloramphenicol, ciprofloxacin, clarithromycin, clavulanate, clindamycin, clotrimazole, dalbavancin, demeclocycline, dicloxacillin, doxycycline, eravacycline, erythromycin, fluconazole, furazolidone, lansoprazole, levofloxacin, lincomycin, linezolid, macrolides, metronidazole, minocycline, monobactams, moxifloxacin, nitroimidazole, omadacycline, oritavancin, oxacillin, penem, penicillin, penicillin V potassium, polymyxins, quinolones, rifabutin, rifampin, streptogramins, sulfamethoxazole, sulfasalazine, sulfonamides, telavancin, tetracycline, tinidazole, trimethoprim, or vancomycin. Any one or more of the aforementioned antibiotics can be incorporated in any one or more of the compositions described herein.
An “antifungal agent” has its plain and ordinary meaning as understood in light of the specification and refers to a compound or substance with the ability to lower the growth, replication, infection, or spread of fungi. In some cases, the antifungal agent kills the fungus. Antifungal agents may be broad spectrum (targeting many species of fungi) or narrow spectrum (targeting one or few species of fungi). Many mechanisms of action exist for antifungal agents, including cell cycle inhibition, ergosterol synthesis inhibition, inhibition of heat shock proteins, disruption of spindle and cytoplasmic microtubule function, inhibition of chitin synthesis, disruption of cell surface formation, physicochemical interactions with fungal membrane sterols, nutrient uptake inhibition, inhibition of macromolecular synthesis, inhibition of protein synthesis, inhibition of lipid synthesis, accumulation of squalene, inhibition of nucleic acid synthesis, antimetabolic activity, protein-targeting activity, protein degradation, regulation of enzymes, disruption of DNA repair, altering cell surface permeability, and desiccation. Non-limiting examples of antibacterial agents include amphotericin B, anidulafungin, azoles, benzoic acid, butaconazole, butenafine, capsofungin, ciclopiroxolamine, clotrimazole, econazole, fluconazole, flucyosine, 5-fluorocytosine, griseofulvin, hamycin, isavuconazole, isoconazole, itraconazole, ketoconazole, micafungin, miconazole, naftifine, natamycin, nystatin, pneumocandins, polyenes, posaconazole, ravuconazole, salicylic acid, selenium sulfide, sulconazole, sertaconazole, terconazole, terbinafine, tolnaftate, undecylenic acid, or voriconazole. Any one or more of the aforementioned antifungal agents can be incorporated in any one or more of the compositions described herein.
A “media component”, also referred to simply as “media” or “medium,” as used herein has its plain and ordinary meaning as understood in light of the specification and refers to a substance that provides nutrients for microorganisms to grow and culture. A media component can either be liquid, or solid through the addition of agar. Media can be classified into the six broad categories: basal media, enriched media, selective media, indicator media, transport media, and storage media. Non-limiting examples of media, a component of which can be included in any one or more of the formulations described herein, include Yeast Peptone Dextrose (YPD), Lysogeny broth (LB), Luria LB, Lennox LB, Miller LB, Synthetic defined growth media (SD), Yeast minimal media (YMM), Yeast nitrogen base (YNB), Minimal salts (M9), Terrific broth, Terrific broth (modified), Hanahan's Broth (SOB Medium), SOC Medium, 2X YT medium, NZCYM Broth, Acetic acid Bacterium Media (AA), Acetomicrobium faecalis Media (AF), AATCC Bacteriostasis Media, Blood Heart Infusion Media (BHI), TSA Blood Media, Bifidus Selective Medium Broth (BSM), Fastidious Anaerobe media+blood (FAA), Gifu Anaerobic Broth, Hektoen Enteric Media, Lactobacilli deMan, Rogosa & Sharpe Media, Chopped Meat Media, Mueller-Hinton, Minimal mucin media, Modified Reinforced Clostridial Media, deMan, Rogosa & Sharpe Media, Phenylethyl Alcohol, Reinforced Clostridial Media, Rich Mucin Media, TSB with Hemin and Menadione, Tryptic Soy Broth (TSB), BHI plus Inulin, or Supplemented Brain Heart Infusion. For a listing of desired media components, which can be incorporated into any one or more of the formulations set forth herein, see TABLE 2. Any one or more of the media components of TABLE 2 can be incorporated in any one or more of the compositions described herein and such compositions can be used in any one or more of the methods described herein. In some embodiments, the isolate or composition or both, which may or may not contain any one or more media components, stabilizers, or a prebiotic as described herein, are lyophilized, spray dried, or freeze-dried. This can be performed using any standard method to one skilled in the art.
In some embodiments, the compositions described herein are formulated for oral delivery. Such formulations of the compositions described herein include a powder, liquid, beverage capsule, caplet, spray, or food e.g. those designed for clinical nutrition, a food or beverage supplement or adjuvant designed either for human or animal consumption. Dairy food products or beverages including fermented milks, fresh cheeses or yogurts or their dried or freeze-dried equivalents represent suitable delivery systems or compositions to incorporate any one or more of the bacteria or compositions described herein with or without any one or more of the prebiotics, media components, or stabilizers described herein. As e.g., food supplement or adjuvant powdered milk or milk derivatives matrixes loaded with the selected probiotics proved quite convenient. If ever necessary, said powdered matrixes can be further packaged as e.g. gelatin or cellulose capsules, gelules or tablets. These compositions can further comprise one or more additional lactic acid bacteria and/or further additives, including pH stabilizers, viscosity stabilizers, preservatives, antioxidants, colorants or flavors.
The following examples illustrate only some of the alternatives of the invention and are not intended to constitute any limitation or restriction thereof.
Additional embodiments are disclosed in further detail in the following examples, which are not in any way intended to limit the scope of the claims. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent approaches that have been found to function well in the practice of the invention, and thus can be considered to constitute examples of modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments that are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.
As disclosed herein, stool samples were collected from healthy human donors at least 18 years of age without acute diseases and infections and without history of major diseases, especially gastrointestinal diseases. The donors were given a self-collecting device and instructions (Fisher Scientific 02-544-208) to collect stool samples. Within 20 minutes from collection, the sample was placed in a refrigerator at 4° C. before processing the same day. Stool samples were processed in an anaerobic chamber. A pea sized sample was taken from inner layers of the stool sample and homogenized using 25 mL of 1×PBS. The stool homogenate was then diluted 1000-fold. Diluted stool homogenate was placed in selective media agar plates inside an anaerobic chamber (TABLE 1).
The bacteria were allowed to grow at 37° C. for 24-72 hours. Colonies were streaked onto new fresh quad plates using the same media at 37° C. inside an anaerobic chamber for another 24-72 hours. Then this re-streak was repeated two more times. Next, cell pellets were collected and stored in glycerol at −80° C. for future use. Formulations of the media used are outlined in TABLE 2 below. It will be understood that the agar component is optional and used in cases of bacterial growth in solid culture instead bacterial growth in liquid culture.
Acetomicrobium Faecalis
As disclosed herein, the cell pellets grown and isolated from human subject stool samples pursuant to the aforementioned examples, were thawed, then sequenced for variation in the 16S ribosomal RNA gene to identify the species of each pellet. 742 unique strains of bacteria were identified in the human subjects (TABLE 3). Of these, 5 were selected as being particularly enriched in healthy individuals, and these strains were novel isolates, whose 16S genes were <97% identical to known bacteria (TABLE 4). Another 5 were identified as novel isolates, whose 16S genes were <99% identical to known bacteria (TABLE 5).
Bacteroides sp. 4_3_47FAA
Bacteroides caccae CL03T12C61
Parabacteroides sp. D13
Bacteroides vulgatus str. 3775 SL(B) 10
Bacteroides sp. 1_1_30
Bacteroides sp. HMSC067B03
Bacteroides sp. AF25-17LB
Bacteroides sp. AM37-9
Bacteroides sp. OF03-11BH
Bacteroides sp. AF32-8BH
Bacteroides uniformis CL03T00C23
Bacteroides sp. HMSC073E02
Butyricimonas sp. Marseille-P4593
Bacteroides sp. AF20-13LB
Bacteroides thetaiotaomicron VPI-5482
Parabacteroides sp. 2_1_7
Bacteroides sp. 2_2_4
Bacteroides sp. AF15-14LB
Bacteroides vulgatus ATCC 8482
Bacteroides finegoldii DSM 17565
Bacteroides sp. D22
Bacteroides ovatus SD CMC 3f
Parabacteroides merdae CL03T12C32
Bacteroides vulgatus dnLKV7
Bacteroides ovatus CL02T12C04
Bacteroides massiliensis B84634 =
Bacteroides ovatus
Bacteroides dorei DSM 17855
Bacteroides ovatus CL03T12C18
Bacteroides caecimuris
Bacteroides sartorii
Parabacteroides sp. SN4
Bacteroides sp. AM07-18
Bacteroides sp. 2_1_22
Bacteroides vulgatus CL09T03C04
Bacteroides stercoris CC31F
Alistipes sp. AF14-19
Bacteroides sp. AF25-38AC
Bacteroides uniformis ATCC 8492
Parabacteroides sp. D26
Mediterranea massiliensis
Parabacteroides sp. AM44-16
Bacteroides eggerthii 1_2_48FAA
Bacteroides ovatus 3_8_47FAA
Bacteroides xylanisolvens
Parabacteroides distasonis
Bacteroides sp. AM16-15
Bacteroides sp. AR29
Bacteroides sp. D20
Bacteroides uniformis str. 3978 T3 i
Bacteroides bouchesdurhonensis
Bacteroides stercoris ATCC 43183
Bacteroides sp. 3_1_23
Bacteroides uniformis dnLKV2
Bacteroides sp. AF39-16AC
Bacteroides finegoldii CL09T03C10
Oscillibacter sp. PEA192
Bacteroides sp. AM32-11AC
Bacteroides cellulosilyticus
Bacteroides sp. AF29-11
Bacteroides sp. 3_1_19
Oscillibacter sp. KLE 1728
Bacteroides sp. AM16-13
Parabacteroides merdae ATCC 43184
Bacteroides sp. AF26-7BH
Parabacteroides sp. AF27-14
Bacteroides sp. AF34-31BH
Parabacteroides distasonis ATCC 8503
Alistipes putredinis DSM 17216
Bacteroides sp. 3_1_13
Bacteroides plebeius DSM 17135
Bacteroides coprocola DSM 17136
Alistipes shahii WAL 8301
Alistipes sp. AM16-43
Alistipes finegoldii DSM 17242
Roseburia inulinivorans DSM 16841
Oscillospiraceae bacterium VE202-24
Faecalibacterium cf. prausnitzii
Bacteroides sp. HMSC068A09
Bacteroides sp. KFT8
Faecalibacterium sp. AF27-11BH
Faecalibacterium prausnitzii A2-165
Parabacteroides sp. AF19-14
Bacteroides fragilis 3_1_12
Bacteroides sp. D2
Faecalibacterium sp. AM43-5AT
Parabacteroides johnsonii CL02T12C29
Bacteroides sp. AF27-33
Bacteroides fragilis str. 3976T8
Blautia obeum
Faecalibacterium prausnitzii M21/2
Lachnospiraceae bacterium
Alistipes onderdonkii WAL 8169 =
Alistipes obesi
Faecalibacterium sp. OM04-11BH
Blautia sp. Marseille-P2398
Tannerella sp. 6_1_58FAA_CT1
Odoribacter splanchnicus DSM 20712
Fusicatenibacter saccharivorans
Bacteroides fragilis str. 2-F-2 #4
Faecalibacterium sp. OF03-6AC
Clostridiales bacterium CCNA10
Faecalibacterium sp. AF10-46
Bacteroides sp. AM23-12
Roseburia intestinalis L1-82
Subdoligranulum sp. APC924/74
Bacteroides eggerthii DSM 20697
Roseburia faecis
Faecalibacterium sp. AF28-13AC
Clostridium sp. ATCC BAA-442
Lachnospiraceae bacterium GAM79
Parabacteroides distasonis str. 3776 Po2 i
Prevotella sp. 109
Gemmiger formicilis
Alistipes senegalensis JC50
Tannerella sp. AF04-6
Bacteroides thetaiotaomicron dnLKV9
Roseburia hominis A2-183
Bacteroides mediterraneensis
Roseburia sp. TF10-5
Bacteroides cellulosilyticus
Bacteroides sp. 2_1_33B
Ruminococcus sp. AM42-11
Bacteroides coprophilus DSM 18228 =
Bacteroides fluxus YIT 12057
Bacteroides intestinalis DSM 17393
Ruminococcaceae bacterium TF06-43
Bacteroides fragilis CL05T12C13
Clostridium sp. AM34-9AC
Prevotella lascolaii
Clostridium sp. AF36-18BH
Culturomica massiliensis
Clostridium sp. AF34-10BH
Alistipes sp. Marseille-P5997
Parabacteroides johnsonii DSM 18315
Ruminococcus sp. TF11-2AC
Lawsonibacter asaccharolyticus
Oscillibacter sp. ER4
Bacteroides nordii CL02T12C05
Parabacteroides sp. CH2-D42-20
Bacteroides ndongoniae
Odoribacter sp. AF15-53
Alistipes sp. AF48-12
Bacteroides sp. AF14-46
Ruminococcaceae bacterium AF10-16
Firmicutes bacterium AF36-3BH
Firmicutes bacterium AM55-24TS
Clostridium sp. AF46-12NS
Bacteroides fragilis HMW 610
Tannerella sp. AM09-19
Paraprevotella clara YIT 11840
Bacteroides fragilis YCH46
Subdoligranulum sp. 4_3_54A2FAA
Clostridiaceae bacterium AF18-31LB
Bacteroides faecichinchillae JCM
Clostridium sp. AM22-11AC
Clostridiales bacterium Choco116
Bacteroides fragilis HMW 616
Bacteroides oleiciplenus YIT 12058
Clostridiales bacterium VE202-03
Subdoligranulum sp. OF01-18
Bacteroides gallinarum DSM 18171 =
Firmicutes bacterium OM08-11AC
Dorea longicatena DSM 13814
Coprococcus comes ATCC 27758
Ruminococcaceae bacterium D16
Bacteroides sp. AM16-24
Firmicutes bacterium TM09-10
Ruthenibacterium lactatiformans
Firmicutes bacterium AM59-13
Bacteroides acidifaciens
Firmicutes bacterium AF22-6AC
Eubacterium sp. AF22-9
Firmicutes bacterium AF16-15
Firmicutes bacterium AF36-19BH
Bacteroides galacturonicus
Bacteroides sp. OF04-15BH
Dorea formicigenerans ATCC 27755
Sanguibacteroides justesenii
Eubacterium sp. AM46-8
Anaerotruncus colihominis DSM 17241
Bacteroides clarus YIT 12056
Butyricicoccus sp. AM28-25
Lachnospira pectinoschiza
Clostridium sp. M62/1
Bacteroides congonensis
Blautia obeum ATCC 29174
Eubacterium ventriosum ATCC 27560
Prevotellamassilia timonensis
Eubacterium sp. AM49-13BH
Odoribacter sp. AM16-33
Clostridiaceae bacterium TF01-6
Ruminococcaceae bacterium AM28-23LB
Lachnospiraceae bacterium AM48-27BH
Clostridium phoceensis
Butyricicoccus sp. AM27-36
Bacteroides sp. AF39-11AC
Eubacterium ramulus ATCC 29099
Roseburia sp. OF03-24
Bacteroides salyersiae WAL 10018 =
Ruminococcus sp. AM16-34
Lactobacillus rogosae
Lachnospiraceae bacterium 3_1_46FAA
Parabacteroides sp. TM07-1AC
Bacteroides nordii WAL 11050 = JCM
Lachnoclostridium sp. SNUG30386
Intestinimonas butyriciproducens
Dorea formicigenerans 4_6_53AFAA
Subdoligranulum sp. AM23-21AC
Bacteroides togonis
Subdoligranulum sp. AM16-9
Lachnospiraceae bacterium OF11-28
Coprococcus catus
Dorea longicatena AGR2136
Ruminococcaceae bacterium cv2
Clostridiaceae bacterium OM08-6BH
Firmicutes bacterium AF25-13AC
Clostridiales bacterium KLE1615
Dorea sp. AGR2135
Blautia wexlerae DSM 19850
Roseburia sp. OM04-10AA
Paraprevotella xylaniphila YIT 11841
Lachnospiraceae bacterium 8_1_57FAA
Ruminococcaceae bacterium KLE1738
Lachnospiraceae bacterium 1_1_57FAA
Roseburia sp. AM23-20
Parabacteroides goldsteinii
Dorea sp. Marseille-P4042
Pseudoflavonifractor sp. Marseille-P3106
Parabacteroides sp. AF17-3
Tyzzerella sp. Marseille-P3062
Blautia massiliensis
Clostridium sp. OM08-29
Butyricicoccus sp. AM29-23AC
Clostridium sp. OF03-18AA
Lachnospiraceae bacterium OM04-12BH
Roseburia sp. AF25-13LB
Flavonifractor plautii 1_3_50AFAA
Prevotella stercorea DSM 18206
Butyrivibrio crossotus DSM 2876
Parabacteroides sp. AF48-14
Butyricicoccus sp. GAM44
Coprobacter secundus
Blautia sp. SG-772
Alistipes sp. CHKCI003
Clostridiaceae bacterium AF42-6
Bacteroides sp. AM10-21B
Subdoligranulum variabile DSM 15176
Coprobacillus sp. AM28-15LB
Burkholderiales bacterium 1_1_47
Bacteroides timonensis
Agathobaculum butyriciproducens
Barnesiella intestinihominis YIT 11860
Parasutterella excrementihominis YIT
Ruminococcus sp. AF16-40
Intestinimonas massiliensis
Clostridium sp. AM49-4BH
Bacteroides stercorirosoris JCM 17103
Clostridium sp. AF36-4
Burkholderiales bacterium
Ruminococcus bromii L2-63
Ruminococcus bicirculans
Ruminococcus sp. AM28-29LB
Alistipes timonensis JC136
Ruminococcus lactaris ATCC 29176
Clostridium sp. AF37-5
Bacteroides sp. 14(A)
Ruminococcus sp. AF16-50
Bacteroides ilei
Parabacteroides sp. An277
Angelakisella massiliensis
Bacteroides cellulosilyticus DSM 14838
Blautia sp. KLE 1732
Phascolarctobacterium faecium DSM
Clostridiaceae bacterium AF31-3BH
Clostridium sp. AM34-11AC
Ruminococcus sp. AF19-15
Bacteroides salanitronis DSM 18170
Ruminococcus sp. AM28-13
Butyricimonas virosa DSM 23226
Prevotella sp. Marseille-P4119
Clostridiaceae bacterium AF29-16BH
Prevotella sp. MGM2
Ruminococcus sp. AF26-25AA
Flavonifractor plautii ATCC 29863
Clostridium sp. SN20
Bacteroides sp. OM08-11
Ruminococcus sp. AF17-11
Ruminococcus sp. 5_1_39BFAA
Butyricimonas sp. An62
Firmicutes bacterium AM29-6AC
Ruminococcus sp. AF34-12
Blautia sp. AM28-10
Ruminococcus sp. OM05-7
Clostridiales bacterium AM23-16LB
Tyzzerella nexilis DSM 1787
Bacteroides pyogenes JCM 10003
Blautia sp. SF-50
Clostridiales bacterium VE202-13
Alistipes sp. Marseille-P2431
Clostridium sp. AF12-19
Blautia sp. AF17-9LB
Barnesiella viscericola DSM 18177
Ruminococcus faecis JCM 15917
Ruminococcus sp. AF37-20
Ruminococcus sp. AM34-10LB
Parabacteroides bouchesdurhonensis
Parabacteroides sp. Marseille-P3668
Ruminococcus sp. AF43-11
Butyricicoccus sp. AF10-3
Ruminococcus sp. AM31-32
Firmicutes bacterium AF19-2LB
Roseburia sp. AF20-18LB
Blautia sp. AM42-2
Butyricicoccus sp. AM32-19
Blautia sp. AF14-40
Ruminococcus sp. AF37-3AC
Akkermansia muciniphila ATCC BAA-835
Prevotella sp. P5-126
Prevotella sp. MGM1
Clostridium sp. OM05-6BH
Bacteroides sp. HPS0048
Roseburia sp. AF42-8
Ruminococcus sp. AM36-18
Parabacteroides goldsteinii dnLKV18
Butyricicoccus sp. AM05-1
Ruminococcus sp. AF17-12
Ruminococcus sp. AF42-10
Eubacterium sp. AF15-50
Blautia sp. AF19-1
Pseudoflavonifractor capillosus ATCC
Blautia sp. TM10-2
Ruminococcus sp. OM02-16LB
bacterium LF-3
Negativibacillus massiliensis
Clostridiaceae bacterium AF02-42
Roseburia sp. AM16-25
Butyricicoccus sp. AF15-40
Ruminococcus sp. AF18-29
Roseburia sp. AF15-21
Barnesiella sp. An22
Clostridiaceae bacterium AM27-36LB
Alistipes indistinctus YIT 12060
Bacteroides barnesiae DSM 18169 =
Bilophila wadsworthia 3_1_6
Butyricicoccus sp. AM18-35
Bilophila wadsworthia ATCC 49260
Blautia sp. BCRC 81119
Ruminococcus sp. AF31-8BH
Clostridium sp. AF28-12
Holdemania filiformis DSM 12042
Butyricicoccus sp. AF35-5AC
Eubacterium sp. AF17-7
Faecalitalea cylindroides T2-87
Bacteroides sp. An269
Parabacteroides sp. AF14-59
Blautia sp. AF22-5LB
Ruminococcus sp. OF05-2BH
Roseburia sp. AF12-17LB
Ruminococcus sp. AM31-15AC
Clostridium sp. AM27-31LB
Ruminococcus sp. AM43-6
Ruminococcus sp. AM54-1NS
Dialister invisus DSM 15470
Parabacteroides gordonii DSM 23371
Clostridiales bacterium AF36-10
Roseburia sp. OM03-18
Ruminococcus sp. AF25-19
Ruminococcus sp. AM12-48
Muribaculaceae bacterium DSM
Blautia sp. OF03-15BH
Clostridia bacterium UC5.1-2H11
Erysipelotrichaceae bacterium
Clostridium sp. TF06-15AC
Ruminococcus sp. AF17-1AC
Blautia sp. OF03-13
Lachnospiraceae bacterium TM07-2AC
Clostridium sp. AF27-2AA
Ruminococcus sp. AM47-2BH
Blautia sp. OM05-6
Ruminococcus sp. AF21-11
Prevotella sp. 885
Clostridium sp. SS2/1
Clostridium sp. AM25-23AC
Parabacteroides chinchillae
Blautia sp. AF26-2
Prevotella sp. AM42-24
Ruminococcus sp. AM26-12LB
Coprobacter fastidiosus NSB1
Ruminococcus sp. AF19-29
Desulfotomaculum sp. OF05-3
Alistipes ihumii AP11
Anaeromassilibacillus sp. Marseille-
Eubacterium sp. AF34-35BH
Mediterraneibacter sp. KCTC 15684
Lachnospiraceae bacterium
Ruminococcus sp. OM04-4AA
Blautia sp. AF34-10
Neglecta timonensis
Monoglobus pectinilyticus
Dorea sp. AM58-8
Clostridium sp. AF02-29
Bacteroides sp. An19
Eubacterium sp. OM08-24
Ruminococcus sp. TM09-4
Clostridium sp. AM33-3
Blautia sp. OM07-19
Ruminococcus callidus ATCC 27760
Blautia sp. AF32-4BH
Fournierella massiliensis
Clostridium sp. AM30-24
Firmicutes bacterium OM04-13BH
Prevotella sp. P4-51
Odoribacter laneus YIT 12061
Anaeromassilibacillus sp. An250
Clostridium sp. AF43-10
Clostridium sp. AM46-21
Clostridium sp. AF37-5AT
Neobitarella massiliensis
Dorea sp. AF36-15AT
Bifidobacterium adolescentis L2-32
Phocea massiliensis
Blautia sp. AF25-12LB
Clostridium sp. AF15-49
Erysipelotrichaceae bacterium 6_1_45
Prevotella sp. TF12-30
Clostridium sp. AF24-2LB
Clostridium sp. AF27-5AA
Clostridia bacterium UC5.1-2F7
Intestinibacillus sp. Marseille-P4005
Blautia sp. AF19-10LB
Clostridium sp. AM27-28
Clostridium sp. AT4
Prevotella sp. P3-122
Ruminococcus sp. OM06-36AC
Collinsella aerofaciens ATCC 25986
Bifidobacterium stercoris JCM 15918
Blautia sp. AM16-16B
Clostridium sp. AF20-7
Collinsella sp. TF05-9AC
Clostridium sp. TF11-13AC
Blautia sp. OM06-15AC
Ruminococcus sp. OM07-7
Tidjanibacter massiliensis
Clostridium sp. AM45-5
Anaerotignum lactatifermentans DSM
Bacteroides sp. An51A
Ruminococcus sp. AM27-11LB
Coprococcus sp. AF38-1
Bilophila sp. 4_1_30
Ruminococcus sp. AM23-1
Prevotella sp. AM23-5
Firmicutes bacterium AF12-30
Blautia sp. TF10-30
Ruminococcus sp. AF33-11BH
Bifidobacterium longum NCC2705
Alistipes sp. Marseille-P5061
Clostridiaceae bacterium OF09-1
Firmicutes bacterium AM10-47
Bifidobacterium adolescentis ATCC
Bifidobacterium longum subsp. longum
Bifidobacterium adolescentis DSM
Clostridium sp. AM42-36
Ruminococcus sp. AF25-17
Ruminococcus sp. AM34-9LB
Collinsella sp. 4_8_47FAA
Bifidobacterium longum subsp. longum
Alistipes sp. An54
Blautia sp. AF19-13LB
Blautia sp. AF19-34
Lachnospiraceae bacterium
Prevotella bivia DSM 20514
Clostridia bacterium UC5.1-1D10
Clostridium sp. AF32-12BH
Prevotella copri DSM 18205
Prevotella sp. P2-180
Ruminococcus sp. AF17-22AC
Ruminococcus sp. B05
Porphyromonas sp. COT-108 OH2963
Mordavella sp. Marseille-P3756
Firmicutes bacterium AM43-11BH
Anaerostipes hadrus DSM 3319
Coprococcus sp. AF16-5
Ruminococcus sp. AF20-12LB
Clostridium sp. L2-50
Sutterella wadsworthensis 3_1_45B
Sutterella wadsworthensis HGA0223
Oscillibacter sp. PC13
Prevotella sp. P3-120
Blautia sp. AM23-13AC
Clostridium sp. AF50-3
Butyricicoccus sp. AM42-5AC
Dorea sp. OM02-2LB
Clostridium sp. AF23-8
Ruminococcus sp. AF27-11AA
Ruminococcus sp. AM45-2
Clostridium sp. 7_3_54FAA
Clostridium sp. OF09-36
Lachnoclostridium sp. SNUG30099
Ruminococcaceae bacterium AM07-15
Blautia sp. AM29-29
Clostridium sp. AF29-8BH
Ruminococcus sp. AF12-5
Clostridium sp. AF20-17LB
Blautia sp. TF11-31AT
Ruminococcus sp. AM54-14NS
Ruminococcus sp. AF14-10
Ruminococcus sp. AF45-4BH
Prevotella sp. AM34-19LB
Lachnospiraceae bacterium AM21-21
Faecalibacterium sp. An122
Alistipes sp. An66
Gabonia massiliensis
Lachnospiraceae bacterium AM10-38
Asaccharobacter celatus
Pseudoflavonifractor sp. An184
Lachnospiraceae bacterium TF01-11
Lachnoclostridium sp. SNUG30370
Clostridium sp. AM09-51
Ruminococcus sp. AF25-28AC
Ruminococcus sp. AM36-17
Anaeromassilibacillus sp. Marseille-
Parabacteroides timonensis
Muribaculum sp. An287
Coprococcus sp. AF16-22
Coprococcus eutactus ATCC 27759
Clostridiales bacterium VE202-27
Clostridium sp. AM42-4
Bacteroides helcogenes P 36-108
Ruminococcus sp. AM36-2AA
Pediococcus acidilactici D3
Mediterranea sp. An20
Rikenella microfusus DSM 15922
Prevotella sp. P4-76
Lachnotalea sp. AF33-28
Akkermansia sp. KLE1605
Prevotella sp. P5-108
Coprococcus sp. AF19-8AC
Ruminococcus sp. AF21-42
Lachnospiraceae bacterium AM26-1LB
Blautia sp. Marseille-P3087
Faecalibacterium sp. An192
Bacteroides sp. AF16-49
Clostridium sp. OF09-10
Alistipes inops
Barnesiella sp. An55
Ruminococcus sp. AM29-12LB
Romboutsia timonensis
Fusicatenibacter sp.
Pseudoflavonifractor sp. AF19-9AC
Ruminococcus champanellensis
Haemophilus sp. HMSC061E01
Ruminococcus sp. AF46-10NS
Ruminococcus sp. AM49-10BH
Ruminococcus sp. OF02-6
Bifidobacterium pseudocatenulatum
Flavonifractor sp. An306
Blautia wexlerae AGR2146
Massilioclostridium coli
Eubacterium sp. 3_1_31
Prevotella buccalis DNF00985
Flavonifractor sp. An135
Haemophilus sp. HMSC068C11
Roseburia sp. AM59-24XD
Ruminococcus sp. AM22-14LB
Ruminococcus sp. AM46-18
Haemophilus sp. HMSC71H05
Clostridium sp. AF35-15
Dorea sp. AF24-7LB
Ruminococcus sp. OM08-7
Clostridium sp. AF21-20LB
Streptococcus thermophilus JIM 8232
Eubacterium sp. TM06-47
Clostridium sp. AM16-23
Ruminococcus sp. AM32-17LB
Ruminococcus sp. OM08-9BH
Prevotella bivia DNF00320
Ruminococcaceae bacterium D5
Butyricicoccus pullicaecorum 1.2
Coprobacillus sp. AF31-1BH
Ruminococcus sp. AM57-5
Parabacteroides goldsteinii DSM
Firmicutes bacterium OM07-11
Acidaminococcus intestini RyC-MR95
Sutterella wadsworthensis
Holdemania sp. Marseille-P2844
Lachnospiraceae bacterium Choco86
Adlercreutzia equolifaciens DSM 19450
Bacteroidales bacterium KA00344
Clostridium sp. OM05-5BH
Ruminococcus sp. AF24-16
Anaeromassilibacillus sp. Marseille-
Coprobacillus cateniformis
Lachnospiraceae bacterium OF09-6
Clostridium sp. ATCC 29733
Prevotella sp. P4-65
Ruminococcus sp. AM33-14
Haemophilus sp. HMSC066D02
Anaeromassilibacillus sp. An172
Flavonifractor sp. An91
Firmicutes bacterium AM31-12AC
Clostridium sp. AM18-55
Bifidobacterium longum subsp. longum
Roseburia sp. OM02-15
Holdemanella biformis DSM 3989
Haemophilus parainfluenzae ATCC
Haemophilus sp. CCUG 60358
Metaprevotella massiliensis
Lachnospiraceae bacterium AM25-27
Ruminococcus sp. AM27-16
Phascolarctobacterium succinatutens
Eggerthella sp. 1_3_56FAA
Prevotella buccalis ATCC 35310
Clostridiales bacterium VE202-16
Parabacteroides sp. AM08-6
Collinsella sp. AF25-2LB
Clostridium sp. AF34-13
Faecalibacterium sp. An121
Bifidobacterium longum subsp. suis
Collinsella sp. AF28-5AC
Lachnospiraceae bacterium TF10-8AT
Coprococcus sp. OM04-5BH
Haemophilus parainfluenzae T3T1
Prevotella ihumii
Parabacteroides sp. 426-9
Eubacterium sp. AM28-29
Coprobacillus sp. AF13-15
Ruminococcus sp. AF32-2AC
Bifidobacterium catenulatum DSM
Bifidobacterium bifidum PRL2010
Parabacteroides sp. AF18-52
Collinsella sp. AM34-10
Erysipelotrichaceae bacterium 2_2_44A
Eggerthella lenta DSM 2243
Holdemania massiliensis AP2
Flavonifractor sp. An100
Victivallales bacterium CCUG 44730
Dielma fastidiosa
Flavonifractor sp. An10
Gemmiger sp. An50
Gemmiger sp. An87
Butyricimonas sp. Marseille-P3923
Christensenella minuta
Faecalitalea cylindroides ATCC 27803
Haemophilus sp. HMSC61B11
Achromobacter sp. ATCC35328
Bacteroides sp. An279
Coprobacillus sp. AF21-8LB
Anaeromassilibacillus sp. An200
Ruminococcus sp. AF42-9BH
Ruminococcaceae bacterium
Ruminococcus sp. AF41-9
Clostridium sp. AF12-41
Lachnospiraceae bacterium AM40-2BH
Clostridium sp. Marseille-P3244
Collinsella sp. AM38-1BH
Alistipes sp. An116
Lachnoclostridium sp. Anl4
Flavonifractor sp. An82
Dorea sp. Marseille-P4003
Ruminococcus sp. AF19-4LB
Absiella dolichum DSM 3991
Hungatella hathewayi DSM 13479
Haemophilus parainfluenzae HK262
Haemophilus sp. HMSC073C03
Eubacterium coprostanoligenes
Anaerotruncus rubiinfantis
Anaerofilum sp. An201
Ruminococcus sp. AF14-5
Eisenbergiella massiliensis
Lachnoclostridium edouardi
Enterobacter sp. EC-NT1
Clostridium sp. AF17-2
Coprobacillus sp. TF10-10
Ruminococcus sp. AF31-14BH
Lachnospiraceae bacterium
Lachnospiraceae bacterium OM02-26
Blautia hydrogenotrophica DSM 10507
Ruminococcus sp. AM58-7XD
Lachnospiraceae bacterium AM23-7LB
Ruminococcus sp. AM40-10AC
Clostridium sp. OM07-10AC
Odoribacter sp. OF09-27XD
Erysipelotrichaceae bacterium
Prevotella melaninogenica D18
Candidatus Stoquefichus sp. KLE1796
Blautia sp. Marseille-P3201T
Clostridium sp. AF15-31
Alloprevotella tannerae ATCC 51259
Veillonella rogosae JCM 15642
Anaerotruncus sp. AT3
Clostridium sp. OF10-22XD
Escherichia coli 083:H1 str. NRG 857C
Veillonella sp. AF42-16
Erysipelotrichaceae bacterium AF19-
Coprobacillus sp. 8_1_38FAA
Turicibacter sp. H121
Gordonibacter pamelaeae 7-10-1-b
Methanobrevibacter smithii TS145A
Clostridium sp. KLE 1755
Eubacterium sp. TM05-53
Ruminococcus sp. AM18-15
Lachnospiraceae bacterium AM25-17
Acetivibrio ethanolgignens
Prevotella sp. P5-92
Catenibacterium mitsuokai DSM 15897
Blautia hansenii DSM 20583
Escherichia coli 025b:H4
Bifidobacterium kashiwanohense JCM
Clostridia bacterium UC5.1-1D1
Bacteroides sp. An322
Bacteroides sp. Marseille-P3684
Dialister sp. Marseille-P5638
Lachnospiraceae bacterium OF09-
Ruminococcus sp. AF25-23LB
Coprobacillus sp. 8_2_54BFAA
Clostridium sp. FS41
Anaerotruncus sp. 22A2-44
Butyricimonas sp. Marseille-P2440
Bifidobacterium sp. N4G05
Coprobacillus sp. AF17-11AC
Bacteroides salyersiae WAL 10018 = DSM 18765 = JCM 12988
Paraprevotella xylaniphila YIT 11841
Acidaminococcus intestini RyC-MR95
Bifidobacterium adolescentis DSM 20087
Bifidobacterium adolescentis ATCC 15703
Bacteroides sp. HMSC068A09
Odoribacter sp. AF15-53
Bacteroides sp. 4_3_47FAA
Parabacteroides sp. CH2-D42-20
Coprococcus comes ATCC 27758
This application claims the benefit of U.S. Provisional Application No. 63/190,142, filed May 18, 2021, which is hereby expressly incorporated by reference in its entirety.
| Number | Name | Date | Kind |
|---|---|---|---|
| 6696057 | Bojrab | Feb 2004 | B1 |
| 8906668 | Henn | Dec 2014 | B2 |
| 9314489 | Kelly et al. | Apr 2016 | B2 |
| 9463208 | Hlavka | Oct 2016 | B2 |
| 9585920 | Kovarik et al. | Mar 2017 | B2 |
| 9610308 | Borody | Apr 2017 | B2 |
| 9669059 | Wang | Jun 2017 | B2 |
| 10052353 | Honda et al. | Aug 2018 | B2 |
| 20160271189 | Cutcliffe | Sep 2016 | A1 |
| 20170065647 | Kim | Mar 2017 | A1 |
| 20170304374 | Honig et al. | Oct 2017 | A1 |
| 20180221286 | Kabadi et al. | Aug 2018 | A1 |
| 20180353554 | Henn et al. | Dec 2018 | A1 |
| 20220047647 | Honda | Feb 2022 | A1 |
| Number | Date | Country |
|---|---|---|
| WO 2018075886 | Apr 2018 | WO |
| WO-2020054728 | Mar 2020 | WO |
| Entry |
|---|
| Duranti et al. Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis, Scientific Reports 6:23971, 2016, DOI: 10.1038/srep23971 (Year: 2016). |
| Seq ID No. 10—ATCC 15703 Alignment (Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) “Basic local alignment search tool.” J. Mol. Biol. 215:403-410), search performed Mar. 1, 2023. (Year: 2023). |
| Basholli-Salihu, et al., “Effect of lyoprotectants on β-glucosidase activity and viability of Bifidobacterium infantis after freeze-drying and storage in milk and low pH juices.” LWT—Food Science and Technology 57 (2014) 276-282. |
| Number | Date | Country | |
|---|---|---|---|
| 20230017769 A1 | Jan 2023 | US |
| Number | Date | Country | |
|---|---|---|---|
| 63190142 | May 2021 | US |
