Microbiological Consortium for Disease Treatment

Abstract

Providing a microbiological consortium for disease treatment. [Solution] The present invention provides a microbial consortium capable of stably engrafting in the digestive tract of a target and degrading disease-related metabolites, and a method of using the same. A microbial consortium for administration to an animal is disclosed herein, comprising a plurality of active microorganisms and an effective amount of a supporting community of microorganisms. In some embodiments, the plurality of active microorganisms metabolize a first metabolite to produce one or more metabolites, the first metabolite being the cause or contributing factor of a disease in the animal.

Description

[Technical Field]

[0001] Cross-reference of related applications This application claims the benefit and priority of U.S. Provisional Patent Application No. 62 / 987,757, filed on 10 March 2020, and the disclosure of that Provisional Application is incorporated herein by reference in its entirety for all purposes.

[0002] Sequence List This application includes a sequence listing submitted electronically in ASCII format, which is incorporated herein by reference in its entirety. The ASCII copy, created on 10 March 2021, is named FBI-002WO_SL.txt and has a size of 878,406 bytes.

[0003] Field of Invention The present invention generally relates to a microbial consortium for administration to animals to degrade disease-related metabolic substrates. [Background technology]

[0004] background The gastrointestinal tract contains various biological niches along its longitudinal length, and these niches have different physical, chemical, and nutritional compositions. As a result of these diverse conditions, specific microbial communities are established in particular biological niches. The microbial species that make up specific microbial communities respond well to their local environment and produce numerous bioactive molecules, which facilitate colonization of the host, intermicrobial communication, nutrient metabolism, and the incorporation or elimination of competing microbial species. To further complicate matters, microbial species and strains within the human GI tract are quite diverse between individuals, which is thought to be due to numerous factors, including genetic characteristics, diet, use of antibiotics and antifungals, surgical interventions (e.g., gastric bypass / colectomy), the presence of inflammatory bowel disease and / or irritable bowel syndrome, as well as other environmental influences. However, despite this inter-individual diversity, the functional characteristics of various human gut microbiota are relatively consistent among healthy adults, including the central metabolic pathways involved in carbohydrate metabolism, amino acid metabolism, fermentation, and oxidative phosphorylation.

[0005] Modulation of microbial species within the GI tract by the use of antibiotics, antifungals, and more recently, fecal microbiota transplantation ("FMT"), has become a clinically studied approach for the treatment and / or prevention of certain diseases and disorders. For example, Dodd et al. (Nature, 2007, 551: 648-652) studied gnotobiotic mice that act on intestinal permeability and systemic immunity. FMT has been proposed as a therapeutic method to modulate the levels of aromatic amino acid metabolites in the serum. In further examples, the administration of bacterial compositions has also been proposed as a method for treating Clostridium difficile infection, ulcerative colitis, cholestatic diseases, and hyperoxaluria (see, for example, U.S. Patent Application Publication 2018 / 0353554, WO2019 / 036510, and U.S. Patent Reissue 39,585). As modalities for treating various diseases and / or conditions, there is a need for microbial compositions containing multiple microbial species that possess improved therapeutic efficacy and the ability to efficiently engraft and proliferate within the host, and to metabolize pathogenic substances into non-pathogenic metabolites within various biological niches of the GI tube of different individuals and within diverse GI environments. [Prior art documents] [Patent Documents]

[0006] [Patent Document 1] U.S. Patent Application Publication No. 2018 / 0353554 [Patent Document 2] International Publication No. 2019 / 036510 [Patent Document 3] U.S. Reissue Patent No. 39,585 [Overview of the project] [Means for solving the problem]

[0007] Summary of the Invention A microbial consortium for administration to animals is disclosed herein, comprising a plurality of active microorganisms and an effective amount of supporting microbial communities. In some embodiments, the plurality of active microorganisms metabolize a first metabolite to produce one or more metabolites, the first metabolite being the cause or contributing factor of a disease in the animal.

[0008] In some embodiments, the supporting microbial community includes between 1 and 300 microbial strains, under the following conditions: 1) Conditions under which a supporting microbial community metabolizes one or more metabolites produced by multiple active microorganisms, and one or more metabolites inhibit the metabolism of a first metabolic substrate by one or more of the multiple active microorganisms. 2) Conditions that increase the flow rate of the precursor of the first metabolic substrate into the biochemical pathway that converts the precursor into metabolites other than the first metabolic substrate, 3) Conditions under which a microbial support community, when administered to an animal, improves one or more properties of multiple active microorganisms selected from the group consisting of a) colonization in the gastrointestinal tract, b) biomass, c) metabolism of the first metabolic substrate, and d) long-term stability, compared to administration of active microorganisms in the absence of the microbial support community, and 4) Microbial support communities ferment polysaccharides into one or more of the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H2 and CO2; ferment amino acids into one or more of the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, fluoretate, 3-(1H-indole-3-yl)propanoate, 5-aminopentanoate, H2, H2S and CO2; methane from H2 and CO2; methane from formate and H2; acetate from H2 and CO2. Conditions for catalyzing one or more reactions selected from the group consisting of acetate from uremate and H2, acetate and sulfide from H2, CO2 and sulfate, propionate and CO2 from succinate, succinate from H2 and fumarate, succinate from uremate and fumarate, succinate from lactate, butyrate, acetate, H2 and CO2, uncoupling of conjugated bile acids to produce primary bile acids, conversion of cholic acid (CA) to 7-oxocholic acid, conversion of 7-oxocholic acid to 7-betacholic acid (7-betaCA), conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA). It satisfies one, two, three, or four of the following conditions.

[0009] In some embodiments, the first metabolic substrate metabolic activity of at least one of multiple active microorganisms is significantly different when measured in a standardized substrate metabolic assay at two pH values ​​in the range of 4–8, and the difference between the two pH values ​​is at least 1 pH unit.

[0010] In some embodiments, the metabolic activity of a first metabolite for at least one of several active microorganisms is significantly different when measured in a standardized substrate metabolism assay at two first metabolite concentrations within 100-fold of each other, and when the difference between the two first metabolite concentrations is at least 1.2-fold.

[0011] In some embodiments, the supporting microbial community comprises at least three, at least four, at least five, or six phyla selected from Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, and Euryarchaeota.

[0012] In some embodiments, the supporting microbial community includes one or more of the subclades Bacteroidales, Clostridiales, Erysipelotrichales, Negativicutes, Coriobacteriia, Bifidobacteriales, or Methanobacteriales.

[0013] In some embodiments, the first metabolic substrate is an oxalate. In some embodiments, a microbial support community catalyzes the synthesis of methane from formates and H2.

[0014] In some embodiments, the active microorganisms include Oxalobacter formigenes. In some embodiments, the supporting communities of the microorganisms include Bacteroidetes and Euryarchaeota. In some embodiments, the supporting communities of the microorganisms include Bacteroides and Methanobrevibacter. In further embodiments, the supporting communities of the microorganisms include Bacteroides thetaiotaomicron and / or Bacteroides vulgatus, as well as Methanobrevibacter smithii.

[0015] In some embodiments, a supporting microbial community metabolizes one or more metabolites produced by multiple active microorganisms, and one or more metabolites inhibit the metabolism of multiple active microorganisms.

[0016] In some embodiments, microbial support communities, when administered to animals, enhance one or more properties of multiple active microorganisms selected from the group consisting of colonization in the gastrointestinal tract, biomass, metabolism of the first metabolite, and long-term stability, compared to administration of multiple active microorganisms in the absence of microbial support communities.

[0017] In some embodiments, the support community is Fermentation of polysaccharides into one or more of the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H2, and CO2. Fermentation of amino acids into one or more of the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, floleate, 3-(1H-indole-3-yl)propanoate, 5-aminopentanoate, H2, H2S, and CO2. Synthesis of methane from H2 and CO2, methane from formate and H2, acetate from H2 and CO2, acetate from formate and H2, acetate and sulfides from H2, CO2 and sulfate, propionate and CO2 from succinate, succinate from H2 and fumarate; synthesis of one or more of the group consisting of succinate from formate and fumarate, and synthesis of butyrate, acetate, H2 and CO2 from lactate, and Decoupling of conjugated bile acids for the production of primary bile acids, conversion of cholic acid (CA) to 7-oxocholic acid, conversion of 7-oxocholic acid to 7-betacholic acid (7-betaCA), conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA). It catalyzes one or more reactions selected from the group consisting of the following.

[0018] In some embodiments, the supporting community of microorganisms includes between 20 and 200 microbial strains. In some embodiments, the supporting community includes at least four phyla selected from the group consisting of Bacteroidetes, Firmicutes, Actinobacteria, and Proteobacteria. In some embodiments, the supporting community includes Ruminococcus, Clostridium, Bacteroides, Neglecta, Bifidobacterium, Egerthella, Clostridiaceae, Parabacteroides, Bilophila, Dorea, Collinsella, and Faecalibacterium.

[0019] In some embodiments, the supporting community includes Ruminococcus bromii, Clostridium citroniae, Bacteroides salyersiae, Neglecta timonensis, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides thetaiotaomicron, Eggerthella lenta, Clostridiaceae sp., Bifidobacterium dentium, Parabacteroides merdae, Bilophila wadsworthia, Bacteroides caccae, Dorea longicatena, Collinsella aerofaciens, Clostridium scindens, Faecalibacterium prausnitzii, Clostridium symbiosum, and Bacteroides vulgatus.

[0020] In some embodiments, the supporting community includes Acidaminococcus, Akkermansia, Alistipes, Anaerofustis, Anaerostipes, Anaerotruncus, Bacteroides, Barnesiella, Bifidobacterium, Bilophila, Blautia, Butyricimonas, Catabacter hongkongensis, Clostridiaceae, Clostridiales, Clostridium, Collinsella, Coprococcus, Dialister, Dielma, Dorea, Eggerthella, Eisenbergiella, Eubacterium, Faecalibacterium, Fusicatenibacter saccharivorans, Gordonibacter pamelaeae, Holdemanella, Hungatella, Lachnoclostridium, Lachnospiraceae, Lactobacillus, Longicatena, Megasphaera, Methanobrevibacter, Monoglobus, Neglecta, Parabacteroides, Paraprevotella, Parasutterella, Phascolarctobacterium, Porphyromonas, Roseburia hominis, Ruminococcaceae, Ruminococcus, Ruthenibacterium, Senegalimassilia, Sutterella, and Turicibacter.

[0021] In some embodiments, the supporting community is: Acidaminococcus intestine, Akkermansia muciniphila, Alistipes onderdonkii, Alistipes putredinis, Alistipes senegalensis, Alistipes shahii, Alistipes sp., Alistipes timonensis, Anaerofustis stercorihominis, Anaerostipes hadrus, Anaerotruncus massiliensis, Bacteroides caccae, Bacteroides coprocola, Bacteroides faecis, Bacteroides finegoldii, Bacteroides fragilis, Bacteroides kribbi, Bacteroides massiliensis, Bacteroides nordii, Bacteroides ovatus, Bacteroides salyersiae, Bacteroides stercorirosoris, Bacteroides stercoris, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bacteroides xylanisolvens, Barnesiella intestinihominis, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium catenulatum, Bifidobacterium dentium, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bilophila wadsworthia, Blautia faecis, Blautia hydrogenotrophica, Blautia massiliensis, Blautia obeum, Blautia wexlerae, Butyricimonas faecihominis, Catabacter hongkongensis, Clostridiaceae sp., Clostridiales sp., Clostridium aldenense, Clostridium bolteae, Clostridium citroniae, Clostridium clostridioforme, Clostridium fessum, Clostridium scindens, Collinsella aerofaciens, Coprococcus comes, Coprococcus eutactus, Dialister invisus, Dialister succinatiphilus, Dielma fastidiosa, Dorea formicigenerans, Dorea longicatena, Eggerthella lenta, Eisenbergiella tayi, Eubacterium eligens, Eubacterium hallii, Eubacterium rectale, Eubacterium siraeum, Eubacterium ventriosum, Eubacterium xylanophilum, Faecalibacterium prausnitzii, Fusicatenibacter saccharivorans, Gordonibacter pamelaeae, Holdemanella biformis, Hungatella effluvia, Lachnoclostridium pacaense, Lachnospiraceae sp., Lactobacillus rogosae, Longicatena caecimuris, Megasphaera massiliensis, Methanobrevibacter smithii, Monoglobus pectinolyticus, Neglecta timonensis, Parabacteroides distasonis, Parabacteroides merdae, Paraprevotella clara, Parasutterella excrementihominis, Phascolarctobacterium faecium, Porphyromonas asaccharolytica, Roseburia hominis, Ruminococcaceae sp., Ruminococcus bromii, Ruminococcus faecis, Ruthenibacterium lactatiformans, Senegalimassilia anaerobia, Sutterella massiliensis, Sutterella wadsworthensis, and Turicibacter sanguinis.

[0022] In some embodiments, the supporting microbial communities include Akkermansia, Alistipes, Anaerostipes, Bacteroides, Bifidobacterium, Bilophila, Blautia, Clostridium, Collinsella aerofaciens, Coprococcus, Dialister, Dorea, Eggerthella, Eisenbergiella, Eubacterium, Faecalibacterium, Fusicatenibacter, Gordonibacter, Holdemanella, Hungatella, Lachnoclostridium, Lachnospiraceae, Lactobacillus, Monoglobus, Neglecta, Parabacteroides, Paraprevotella, Parasutterella, Phascolarctobacterium, Porphyromonas, Roseburia, Ruminococcaceae, Ruminococcus, Ruthenibacterium, and Sutterella.

[0023] In some embodiments, the supporting community of microorganisms is Akkermansia muciniphila, Alistipes onderdonkii, Alistipes putredinis, Alistipes shahii, Alistipes timonensis, Anaerostipes hadrus, Bacteroides caccae, Bacteroides fragilis, Bacteroides kribbi, Bacteroides koreensis, Bacteroides massiliensis, Bacteroides nordii, Bacteroides salyersiae, Bacteroides stercorirosoris, Bacteroides stercoris, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bacteroides xylanisolvens, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Bifidobacterium dentium, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bilophila wadsworthia, Bilophila wadsworthia, Blautia faecis, Blautia obeum, Blautia wexlerae, Clostridium aldenense, Clostridium bolteae, Clostridium citroniae, Clostridium clostridioforme, Clostridium fessum, Clostridium scindens, Collinsella aerofaciens, Coprococcus comes, Coprococcus eutactus, Dialister invisus, Dialister succinatiphilus, Dorea formicigenerans, Dorea longicatena, Eggerthella lenta, Eisenbergiella tayi, Eubacterium eligens, Eubacterium rectale, Faecalibacterium prausnitzii, Fusicatenibacter saccharivorans, Gordonibacter pamelaeae, Holdemanella biformis, Hungatella effluvia, Lachnoclostridium pacaense, Lachnospiraceae sp., Lactobacillus rogosae, Monoglobus pectinilyticus, Neglecta timonensis, Parabacteroides distasonis, Parabacteroides merdae, Paraprevotella clara, Parasutterella excrementihominis, Phascolarctobacterium faecium, Porphyromonas asaccharolytica, Roseburia hominis, Ruminococcaceae sp., Ruminococcus bromii, Ruminococcus This includes, or consists of, faecis, Ruthenibacterium lactatiformans, Sutterella massiliensis, and Sutterella wadsworthensis.

[0024] In some embodiments, the microbial consortium or microbial support community includes 20-200, 70-80, 80-90, 100-110, or 150-160 microbial strains.

[0025] In some embodiments, the supporting microbial community includes between 100 and 150 microbial strains.

[0026] In some embodiments, the multiple active microorganisms and their supporting communities are selected from a group of microorganisms, each containing a 16S sequence that is at least 80% identical, at least 90% identical, or at least 97% identical to any one of the microorganisms listed in Tables 4, 22, 23, 20, 16, 17, 18, or 19.

[0027] In some embodiments, the multiple active microorganisms and their supporting communities consist of groups of microorganisms, each containing a 16S sequence that is at least 80% identical, at least 90% identical, or at least 97% identical to any one of the microorganisms listed in Tables 22, 23, 20, 16, 17, 18, or 19.

[0028] In some embodiments, the first metabolic substrate activity for one of several active microorganisms is significantly different from the first metabolic substrate activity for at least one other of the several active microorganisms when measured under the same conditions in a standardized substrate metabolism assay.

[0029] In some embodiments, one of the multiple active microorganisms has a higher first metabolic substrate activity at a lower pH compared to at least one other of the multiple active microorganisms at the same lower pH. In some embodiments, one of the multiple active microorganisms has a higher first metabolic substrate activity at a lower pH compared to the first metabolic substrate activity of the same active microorganism at a higher pH. In some embodiments, the lower pH is 4.5 ± 0.5.

[0030] In some embodiments, one of the multiple active microorganisms has a higher first metabolite metabolic activity at a higher pH compared to at least one other of the multiple active microorganisms at the same higher pH. In some embodiments, one of the multiple active microorganisms has a higher first metabolite metabolic activity at a higher pH compared to the first metabolite metabolic activity of the same active microorganism at a lower pH. In some embodiments, the higher pH is 7.5 ± 0.5.

[0031] In some embodiments, one of the multiple active microorganisms has higher primary substrate metabolic activity at lower pH, and another of the multiple active microorganisms has higher primary substrate metabolic activity at higher pH. In some embodiments, the difference between the two pH values ​​is at least 1.5, 2.0, 2.5, 3.0, 3.5, or 4.0 pH units.

[0032] In some embodiments, one of several active microorganisms has a higher first metabolite metabolic activity at a lower first metabolite concentration compared to the first metabolite metabolic activity of at least one other of the several active microorganisms when measured under the same conditions in a standardized substrate metabolism assay. In some embodiments, one of several active microorganisms has a higher first metabolite metabolic activity at a lower first metabolite concentration compared to the first metabolite metabolic activity of the same active microorganism at a higher first metabolite concentration. In some embodiments, one of several active microorganisms has a higher first metabolite metabolic activity at a higher first first metabolite concentration compared to the first metabolite metabolic activity of at least one other of the several active microorganisms when measured under the same conditions in a standardized substrate metabolism assay. In some embodiments, one of several active microorganisms has a higher first metabolite metabolic activity at a lower first metabolite concentration compared to the first metabolite metabolic activity of the same active microorganism at a higher first metabolite concentration.

[0033] In some embodiments, one of several active microorganisms has higher first metabolite metabolic activity at a lower first metabolite concentration, and one of several active microorganisms has higher first metabolite metabolic activity at a higher first metabolite concentration. In some embodiments, the difference between two first metabolite concentrations is at least 1.2, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, or greater than 100.

[0034] In some embodiments, the microbial consortium of the present invention comprises multiple active microorganisms comprising 2 to 200 microbial strains. In a particular embodiment, the multiple active microorganisms comprise 2 to 20 microbial strains.

[0035] In some embodiments of the present invention, the first metabolite is an oxalate. In some embodiments, one or more metabolites are selected from the group consisting of formates and carbon dioxide (CO2). In some embodiments, at least one of a plurality of active microorganisms has higher oxalate metabolic activity at 0.75 mM oxalate compared to the oxalate metabolic activity of at least one other of the plurality of active microorganisms when measured under the same conditions in a standardized oxalate metabolic assay. In some embodiments, one of the plurality of active microorganisms has higher oxalate metabolic activity at 0.75 mM oxalate compared to the oxalate metabolic activity of the same active microorganism at higher oxalate concentrations. In some embodiments, at least one of the plurality of active microorganisms has higher oxalate metabolic activity at 40 mM oxalate compared to the oxalate metabolic activity of at least one other of the plurality of active microorganisms when measured under the same conditions in a standardized oxalate metabolic assay. In some embodiments, one of the plurality of active microorganisms has higher oxalate metabolic activity at 40 mM oxalate compared to the oxalate metabolic activity of the same active microorganism at lower oxalate concentrations. In some embodiments, one of the multiple active microorganisms has higher primary substrate metabolic activity with 0.75 mM oxalate, and another of the multiple active microorganisms has higher primary substrate metabolic activity with 40 mM oxalate.

[0036] In some embodiments, the standardized substrate metabolism assay includes the analysis of a sample microbial culture using a colorimetric enzyme assay to measure the activity of oxalate oxidase in a culture sample containing a microbial consortium, the culture sample containing three or more microbial strains in a suitable culture medium incubated for 1 to 120 hours at a pH of 3.5 to 8.0 and a temperature of 35°C to 40°C in the presence of oxalate at a concentration of 0.5 mM to 50 mM.

[0037] In some embodiments, the standardized substrate metabolism assay includes liquid chromatography-mass spectrometry, and the culture sample comprises three or more microbial strains in a suitable culture medium incubated for 1 to 120 hours at a temperature of 35°C to 40°C at a pH of 3.5 to 8.0 in the presence of oxalates at a concentration of 0.5 mM to 50 mM.

[0038] In some embodiments, the microbial consortium of the present invention further includes fermentative microorganisms that metabolize a fermentation substrate into one or more fermentation products; and synthetic microorganisms that catalyze synthetic reactions that combine one or more metabolites and one or more fermentation products to produce one or more synthetic products.

[0039] In some embodiments, one or more fermentation products are a second metabolite for multiple active microorganisms or a third metabolite for a synthetic microorganism. In some embodiments, one or more synthetic products are a second metabolite for multiple active microorganisms or a fourth metabolite for a fermentation microorganism. In some embodiments, the fermentation substrate is a polysaccharide, and one or more fermentation products are selected from the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H2, and CO2. In some embodiments, the fermentation substrate is an amino acid, and one or more fermentation products are selected from the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, floleate, 3-(1H-indole-3-yl)propanoate, 5-aminopentanoate, H2, H2S, and CO2.

[0040] In some embodiments, the reactions catalyzed by synthetic microorganisms are selected from the group consisting of the synthesis of methane from H2 and CO2, methane from formate and H2, acetate from H2 and CO2, acetate from formate and H2, acetate and sulfides from H2, CO2 and sulfate, propionate and CO2 from succinate, succinate from H2 and fumarate; succinate from formate and fumarate, and butyrate, acetate, H2 and CO2 from lactate.

[0041] In some embodiments, when administered to animals consuming a high-oxalate diet, the microbial consortium significantly reduces the oxalate concentration in a sample selected from the group consisting of blood, serum, feces, or urine, compared to a sample collected from a corresponding control animal consuming a high-oxalate diet but not administered the microbial consortium.

[0042] In some embodiments, the multiple active microorganisms include three microbial strains. In some embodiments, the multiple active microorganisms include three Proteobacteria strains. In some embodiments, the multiple active microorganisms include three Oxalobacter formigenes strains.

[0043] In some embodiments, the first metabolic substrate is a bile acid. For example, in some embodiments, the bile acid is lithocholic acid (LCA) or deoxycholic acid (DCA). In some embodiments, one or more metabolites produced by multiple active microorganisms are secondary bile acids. For example, in some embodiments, the secondary bile acid is selected from the group consisting of isolithocholic acid (iso-LCA) or isodeoxycholic acid (iso-DCA). In some embodiments, the microbial support community enhances the conversion of one or more conjugated bile acids selected from the group consisting of taurochenodeoxycholic acid (TCDCA), glycochenodeoxycholic acid (GCDCA), taurocholic acid (TCA), and glycocholic acid (GCA) to cholic acid (CA) or chenodeoxycholic acid (CDCA). In some embodiments, the microbial support community enhances the conversion of CA to 7-betacholic acid (7-beta-CA). In other embodiments, microbial support communities enhance the conversion of CDCA to ursodeoxycholic acid (UDCA).

[0044] In some embodiments, at least one of the multiple active microorganisms has higher bile acid metabolic activity at a bile acid concentration of 0.1 mM compared to the bile acid metabolic activity of at least one other of the multiple active microorganisms when measured under the same conditions in a standardized bile acid metabolism assay. In some embodiments, at least one of the multiple active microorganisms has higher bile acid metabolic activity at a bile acid concentration of 0.1 mM compared to the bile acid metabolic activity of the same active microorganism at higher bile acid concentrations. In some embodiments, at least one of the multiple active microorganisms has higher bile acid metabolic activity at a bile acid concentration of 10 mM compared to the bile acid metabolic activity of at least one other of the multiple active microorganisms when measured under the same conditions in a standardized bile acid metabolism assay. In some embodiments, at least one of the multiple active microorganisms has higher bile acid metabolic activity at a bile acid concentration of 10 mM compared to the bile acid metabolic activity of the same active microorganism at lower bile acid concentrations. In some embodiments, one of the multiple active microorganisms has higher bile acid metabolic activity at 0.1 mM bile acid, and another of the multiple active microorganisms has higher bile acid metabolic activity at 10 mM bile acid.

[0045] In some embodiments, the standardized substrate metabolism assay includes determining the bile acid profile in a cultured sample containing a microbial consortium using liquid chromatography-mass spectrometry, wherein the cultured sample contains three or more microbial strains in a suitable culture medium incubated for 1 to 96 hours at a pH of 3.5 to 8.0 and a temperature of 35°C to 40°C in the presence of bile acids at concentrations of 0.1 mM to 10 mM.

[0046] In some embodiments, the multiple active microorganisms include one or more phyla selected from Firmicutes and Actinobacteria. In some embodiments, the multiple active microorganisms include one or more strains selected from Eggerthella lenta and Clostridium scindens.

[0047] In some embodiments, the microbial consortium of the present invention is 1 × 106 ~1 × 10 13 It is administered as a prescribed dose within the range of total colony-forming units (CFU) / kg.

[0048] In some embodiments, the microbial consortium, when administered to an animal, reduces the concentration of the first metabolite in the animal.

[0049] In some embodiments, animals serve as experimental models for diseases.

[0050] This disclosure also provides pharmaceutical compositions comprising a microbial consortium and a pharmaceutically acceptable carrier or excipient.

[0051] The Disclosure also provides a method for treating subjects diagnosed with or at risk of having a metabolic disease or condition selected from the group consisting of primary hyperoxaluria, secondary hyperoxaluria, cholestatic diseases (e.g., primary sclerosing cholangitis, primary biliary cholangitis, progressive familial intrahepatic cholestasis, or non-alcoholic steatohepatitis), and multiple sclerosis, using the microbial consortium of the present invention.

[0052] In some embodiments, administration of the pharmaceutical composition disclosed herein reduces the level of a first metabolite in a subject by at least 20%, at least 40%, at least 60%, or at least 80% compared to an untreated control subject or to the level of the first metabolite in the subject before administration. In some embodiments, the first metabolite is an oxalate. In other embodiments, the first metabolite is DCA or LCA. In some embodiments, the level of the first metabolite is determined from a blood, serum, fecal, or urine sample. [Brief explanation of the drawing]

[0053] [Figure 1] Figure 1 shows bar graphs of % in vitro growth inhibition of support strains in the presence of 0.5% oxalate (black bar graph) or 0.125% oxalate (white bar graph) in the culture medium.

[0054] [Figure 2A] Figure 2A shows a bar graph of in vitro oxalate metabolic activity of active microbial strains cultured for 72 hours in Mega Media containing 7.5 mM oxalate (black bar graph) or 750 μM oxalate (white bar graph) at pH 7.5. Figure 2B shows a bar graph of in vitro oxalate metabolic activity of active microbial strains cultured for 72 hours in Chopped Meat Media containing 7.5 mM oxalate (black bar graph) or 750 μM oxalate (white bar graph) at pH 7.5. [Figure 2B] Same as above.

[0055] [Figure 3A] Figure 3A shows a bar graph of the in vitro oxalate metabolic activity of active microbial strains cultured for 72 hours in Mega Media containing 7.5 mM oxalate at pH 4.5 (black bar graph) or 7.2 (white bar graph). Figure 3B shows a bar graph of the in vitro oxalate metabolic activity of active microbial strains cultured for 72 hours in Chopped Meat Media containing 7.5 mM oxalate at pH 4.5 (black bar graph) or 7.2 (white bar graph). [Figure 3B] Same as above.

[0056] [Figure 4A]Figure 4A shows bar graphs of in vitro oxalate levels (measured by absorbance 595) in microbial cultures containing only Oxalobacter formigenes, only the active strain, only the support strain, or both the active and support strains in Mega Media. Figure 4B shows bar graphs of in vitro oxalate levels (measured by absorbance 595) in microbial cultures containing only Oxalobacter formigenes, only the active strain, only the support strain, or both the active and support strains in Chopped Meat Medium at pH 7.2. Absorbance 595 was measured at the start of microbial culture incubation with 7.5 mM oxalate (t=0 hours, black bar graph) and after 72 hours of incubation with 7.5 mM oxalate (t=72 hours, white bar graph). [Figure 4B] Same as above.

[0057] [Figure 5] Figure 5 shows the percentage body weight gain (Figure 5A) and food consumption (Figure 5B) of gnotobiotic Balb / c mice treated with a normal or high-oxalate diet and forced oral administration of non-established or Oxalobacter formigenes only, active strain only (active organism), support strain only (supporter), or both active and support strains (complete community).

[0058] [Figure 6] Figure 6 shows the urinary oxalate concentrations of gnotobiotic Balb / c mice fed a normal (no oxalate) (Figure 6A) or high-oxalate (oxalate supplemented) (Figure 6B) diet, and treated by forced oral administration of non-established (control), Oxalobacter formigenes only (formigenes), active strain only (active organism), support strain only (supporter), or both active and support strains (active organism + supporter).

[0059] [Figure 7-1]Figure 7 shows serum liver enzyme / function levels in gnotobiotic Balb / c mice treated with normal (non-bold) or high-oxalic acid (bold) diets and by forced oral administration of Oxalobacter formigenes only (O. formigenes), active strain only (active), support strain only (support), both active and support strains (active + support), or saline vehicle control (saline). ALT = alanine transaminase (Figure 7A), AST = aspartate transaminase (Figure 7B), ALB = albumin (Figure 7C), ALP = alanine phosphatase (Figure 7D), A / G ratio = albumin / globulin ratio (Figure 7E), TBIL = total bilirubin (Figure 7F), GGT = gamma-glutamyltransferase (Figure 7G), TP = prothrombin time (Figure 7H). [Figure 7-2] Same as above. [Figure 7-3] Same as above. [Figure 7-4] Same as above.

[0060] [Figure 8-1] Figure 8 shows serum renal enzyme / function levels in gnotobiotic Balb / c mice treated with normal (non-bold) or high-oxalic acid (bold) diets and by forced oral administration of Oxalobacter formigenes only (O. formigenes), active strain only (active organism), support strain only (supporter), both active and support strains (active organism + supporter), or saline vehicle control (saline). UREA = urea (Figure 8A), CREA = creatinine (Figure 8B), PHOS = phosphorus (Figure 8C), CA = calcium (Figure 8D), CL = chloride (Figure 8E), NA = sodium (Figure 8F), K = potassium (Figure 8G), GLOB = globulin (Figure 8H). [Figure 8-2] Same as above. [Figure 8-3] Same as above. [Figure 8-4] Same as above.

[0061] [Figure 9-1]Figure 9 shows serum triglyceride (TRIG, Figure 9A), cholesterol (CHOL, Figure 9B), glucose (GLUC, Figure 9C), and creatine kinase (CK, Figure 9D) levels in gnotobiotic Balb / c mice treated with normal (non-bold) or high-oxalic acid (bold) diets by forced oral administration of Oxalobacter formigenes alone (O. formigenes), active strain only (active), support strain only (support), both active and support strains (active + support), or saline vehicle control. [Figure 9-2] Same as above.

[0062] [Figure 10-1] Figure 10 shows the microbial species in fecal samples collected at the time of forced oral administration or 2 weeks after forced oral administration from gnotobiotic Balb / c mice that were fed a normal (control; Figures 10A, 10B, and 10C) or high-oxalic acid (High-Ox; Figures 10D, 10E, and 10F) diet and treated with the active strain only (active organism; Figures 10A and 10D), the support strain only (support; Figures 10B and 10E), or the active strain and support strain (active organism + support; Figures 10C and 10F). [Figure 10-2] Same as above.

[0063] [Figure 11] Figure 11 shows bar graphs of in vitro oxalate levels (measured by LC-MS) in microbial cultures containing donor-derived strains grown for 120 hours in YCFAC basic medium at either pH 7.0 (white bars), pH 6.0 (gray bars), or pH 5.0 (black bars). The residual % oxalate is calculated by comparing it to the amount of oxalate present at the start of the assay (2 mM). Oxalate levels in O. formigenes cultures (FBI00067) at pH 6.0 and pH 7.0 were below the detection limit at the end of the assay (<1.9% and <1.7% residual oxalate, respectively).

[0064] [Figure 12A]Figure 12 shows the growth of donor-derived O. formigenes strains cultured for 144 hours in YCFAC basic medium supplemented with the indicated oxalate concentrations (0 mM, 2 mM, 40 mM, 80 mM, 120 mM, 160 mM) (x axis). The cultures were monitored by turbidity (OD600; y axis). Figures 12A-C show the growth of the indicated strains at pH 7.0, Figures 12D-F show the growth of the indicated strains at pH 6.0, and Figures 12G-I show the growth of the indicated strains at pH 5.0. [Figure 12B] Same as above. [Figure 12C] Same as above. [Figure 12D] Same as above. [Figure 12E] Same as above. [Figure 12F] Same as above. [Figure 12G] Same as above. [Figure 12H] Same as above. [Figure 12I] Same as above.

[0065] [Figure 13] Figure 13 shows urinary oxalate levels in sterile C57Bl / 6NTac mice (n=4 per condition) treated with a low-complexity, high-oxalate diet and either non-established (-) or forced oral administration of one of the five candidate microbial consortia (I-V) or proof-of-concept consortia (+).

[0066] [Figure 14] Figure 14 shows urinary oxalate levels in sterile C57Bl / 6NTac mice (n=4 per condition) treated with highly complex samples, oxalate-supplemented drinking water, or forced oral administration of one of five candidate microbial consortia (I-V) or a positive control consortium (+).

[0067] [Figure 15]Figure 15 shows urinary oxalate levels in sterile C57Bl / 6NTac mice (n=4 per condition) colonized with a non-oxalate-controlled human microbiome before testing. Mice were given highly complex samples, supplied with oxalate-supplemented drinking water, and the human microbiome was removed by antibiotic treatment, leaving them non-colonized (-), or re-colonized by forced oral administration with one of a collection of donor strains ("suggested oxalate degraders only"), including five candidate microbial consortia (I-V), a positive control consortium containing commercially available strains (+), or three O. formigenes strains and an additional set of strains provisionally classified as oxalate-degrading.

[0068] [Figure 16] Figure 16 shows the diversity of microbial strains in the mouse fecal samples from Figure 15 (measured by metagenomic sequencing).

[0069] [Figure 17] Figure 17 shows the relative (Figure 17A) and absolute (Figure 17B) abundances of O. formigenes in the feces of germ-free mice treated only with candidate microbial consortia (I-V) or support communities lacking O. formigenes.

[0070] [Figure 18] Figure 18 shows the concentrations of various bile acid compounds (including TCA, CA, and DCA) in cultures of commercially available strains incubated at 37°C for 24 hours with the addition of 100 μM TCA. [Modes for carrying out the invention]

[0071] Detailed explanation Disclosed herein are microbial consortia for administration to animals, comprising a plurality of active microorganisms that metabolize a first metabolite that causes or contributes to disease in animals. The microbial consortia disclosed herein further comprise an effective amount of supporting microorganisms that metabolize one or more metabolites produced by the plurality of active microorganisms, the one or more metabolites which inhibit the metabolism of the plurality of active microorganisms. These microbial consortia are advantageous in that, when administered to animals, they have improved properties compared to the administration of the plurality of active microorganisms alone. The improved properties of the microbial consortia include one or more of the following: improved engraftment in the gastrointestinal tract, increased biomass, increased metabolism of the first metabolite, and improved long-term stability.

[0072] To facilitate understanding of this invention, several terms and phrases are defined below.

[0073] As used herein, the terms “a” and “an” mean “one or more” and include plural forms, unless the context is appropriate.

[0074] As used herein, the term “active microorganism” refers to a microorganism that expresses one or more metabolic enzymes in sufficient quantities to metabolize a substrate that causes or contributes to disease in an animal.

[0075] As used herein, the term “biomass” refers to the total mass of one or more microorganisms or consortia within a given area or volume.

[0076] As used herein, the term “microbial consortium” means a mixture of two or more microbial strains such that one microbial strain in the mixture exerts a beneficial or desired effect on another microbial strain in the mixture.

[0077] As used herein, the term “engraftment in the gastrointestinal tract” refers to the establishment of one or more microorganisms or microbial consortia in one or more niches of the gastrointestinal tract that were not present with one or more microorganisms or microbial consortia prior to administration of one or more microorganisms or microbial consortia. Engraftment in the gastrointestinal tract may be temporary or persistent.

[0078] As used herein, the term “effective amount” refers to an amount sufficient to achieve a beneficial or desired result. In some embodiments, an effective amount is an improved engraftment of one or more active microorganisms in the gastrointestinal tract, an increase in the biomass of one or more active microorganisms, an increase in the metabolism of a first metabolite, or an improvement in long-term stability.

[0079] As used herein, the term “fermentable microorganism” refers to a microorganism that expresses one or more enzymes in sufficient quantities to catalyze a fermentation reaction in the gastrointestinal niche.

[0080] As used herein, the term “long-term stability” means that one or more microorganisms, or a microbial consortium, can maintain engraftment and metabolic activity in one or more niches of the gastrointestinal tract despite transient or prolonged environmental changes in the gastrointestinal tract niches.

[0081] As used herein, the terms “metabolism,” “metabolizing,” “metabolization,” or their variant spellings refer to the biochemical conversion of a metabolic substrate into a metabolite. In some embodiments, metabolism includes isomerization.

[0082] As used herein, the term “microorganism” refers to microbial organisms, including but not limited to bacteria, archaea, protists, and unicellular fungi.

[0083] As used herein, the term “microbial consortium” refers to a preparation of two or more microorganisms in which the metabolite of one of the two or more microorganisms is a metabolic substrate for one of the other microorganisms constituting the consortium.

[0084] As used herein, the term “pharmaceutical composition” refers to a combination of an activator and an inactive or active carrier that makes the composition particularly suitable for therapeutic use in vivo or ex vivo.

[0085] As used herein, the term “pharmaceutically acceptable carrier” refers to any of the standard pharmaceutical carriers, e.g., phosphate-buffered salt solutions, water, emulsions (e.g., oil / water or water / oil emulsions), and various types of wetting agents. The composition may also include stabilizers and preservatives. For examples of carriers, stabilizers, and adjuvants, see, for example, Martin, Remington's Pharmaceutical Sciences, 15 th Ed. Mack Publ. Co., Easton, See PA

[1975] .

[0086] As used herein, “significantly” or “significant” refers to a change or modification of a measurable parameter that is statistically significant to the extent determined according to the appropriate statistically relevant test. For example, in some embodiments, a change or modification is significant if it is statistically significant according to, for example, a Student's t-test, a chi-squared test, or a Mann-Whitney test.

[0087] As used herein, the term “standardized substrate metabolic assay” refers to an experimental assay known to those skilled in the art, used to quantify the amount of substrate converted to a metabolite.

[0088] As used herein, the term “subject” refers to an organism to be treated by the microbial consortiums and compositions described herein. Such organisms preferably include, but are not limited to, mammals (e.g., mice, monkeys, horses, cattle, pigs, dogs, cats and similar), and more preferably include humans.

[0089] As used herein, the term “supporting community” refers to one or more microbial strains that, when administered with active microorganisms, enhance one or more properties of the active microorganisms, selected from the group consisting of colonization in the gastrointestinal tract, biomass, metabolic substrate metabolism, and long-term stability.

[0090] As used herein, the term “synthetic microorganism” refers to a microorganism that expresses one or more enzymes in an amount sufficient to catalyze a combination of one or more metabolites produced by active microorganisms and one or more fermentation products produced by fermentative microorganisms in the gastrointestinal niche.

[0091] In the context of two or more nucleic acid or polypeptide sequences, the term “identity” or “sequence identity” percentage refers to two or more sequences or subsequences that have a specified percentage of nucleotide or amino acid residues that are identical when compared and aligned to the greatest extent possible, measured using one of the sequence comparison algorithms described below (e.g., BLASTP and BLASTN, or other algorithms available to those skilled in the art), or by visual inspection. Depending on the application, the “identity” percentage may be present across regions of the sequences being compared, for example, across functional domains, or alternatively, across the entire length of the two sequences to be compared.

[0092] For sequence comparison, typically one sequence acts as the reference sequence compared to the test sequence. When using a sequence comparison algorithm, the test and reference sequences are input into a computer, subsequence coordinates are specified as needed, and sequence algorithm program parameters are specified. The sequence comparison algorithm then calculates the sequence identity percentage of the test sequence to the reference sequence based on the specified program parameters.

[0093] The optimal sequence alignment for comparison is, for example, as described in Smith & Waterman, Adv. Appl. According to the local homology algorithm in Math. 2:482 (1981), Needleman & Wunsch, J. Computer implementations of these algorithms (Wisconsin) were performed using the homology alignment algorithm of Mol. Biol. 48:443 (1970) and the similarity search method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988). This can be done by GAP, BESTFIT, FASTA, and TFASTA (as described in the Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.) or by visual inspection (see Ausubel et al., infra for general information).

[0094] One example of a suitable algorithm for determining sequence identity and sequence similarity percentages is the BLAST algorithm described in Altschul et al., J. Mol. Biol. 215:403-410 (1990). Software for performing BLAST analysis is publicly available through the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov / ).

[0095] When used by reference, 16S rRNA sequences have a sequence identity of at least 97% that indicates a high probability that two microbial strains belong to the same species, while 16S rRNA sequences with less than 97% sequence identity indicate a high probability that two microbial strains belong to different species, and 16S rRNA sequences with less than 95% sequence identity indicate a high probability that two microbial strains belong to distinctly different genera (Stackebrandt E., and Goebel, BM, Int J Syst Bact, 44 (1994) 846-849).

[0096] Throughout this specification, where a composition is described as having, including or comprising, a particular component, or where a process and method is described as having, including or comprising, a particular step, it is further intended that there are compositions of the present invention that are essentially composed of or consist of the described component, and processes and methods of the present invention that are essentially composed of or consist of the described processing step.

[0097] Generally, the composition that defines the percentage is based on weight, unless otherwise specified. Furthermore, if a variable element is not defined, the existing definition of that variable element prevails. Biological niche

[0098] The present invention provides a microbial consortium capable of colonizing one or more niches in the digestive tract, where it can metabolize substrates that cause or contribute to disease in animals. These niches comprise specific microbial communities whose composition differs due to several environmental factors, including, but not limited to, specific physical compartments of the digestive tract in which the microbial communities reside, the chemical and physicochemical properties of the habitat, the metabolic substrate composition of the habitat, and other coexisting microbial species. physical partition

[0099] The digestive tract consists of several physical compartments. For example, the human digestive tract includes the oral cavity, pharynx, esophagus, stomach, small intestine (duodenum, jejunum, ileum), cecum, large intestine (ascending colon, transverse colon, descending colon), and rectum. In addition, the pancreas, liver, gallbladder, and associated ducts constitute compartments of the human digestive tract. Each of these compartments has, for example, variable anatomical shape and dimensions, air permeability, water content, mucus secretion levels, presence of antimicrobial peptides in the lumen, and the presence or absence of peristalsis. Furthermore, different digestive compartments have different pH levels. In humans, the pH of the oral cavity, upper stomach, lower stomach, duodenum, jejunum, ileum, and colon ranges from 6.5–7.5, 4.0–6.5, 1.5–4.0, 7.0–8.5, 4.0–7.0, and 4.0–7.0, respectively. The compartments of the digestive tract have different oxygen load levels, and these levels are subject to considerable variability. For example, the partial oxygen pressure in the lumen of the mouse stomach has been measured at approximately 58 mmHg, while the partial oxygen pressure in the lumen of the distal sigmoid colon has been measured at approximately 3 mmHg (He et al., 1999). The oxygen level of the digestive tract greatly influences the biochemical pathways utilized by symbiotic microorganisms. For example, symbiotic bacteria utilize aerobic respiration at oxygen concentrations above 5 mbar O2, anaerobic respiration between 1 and 5 mbar O2, and fermentation at O2 concentrations below 1 mbar. The sensitivity of microorganisms to O2 levels, as well as their ability to perform metabolic reactions under aerobic and / or anaerobic conditions, influence which microbial species colonize specific compartments of the digestive tract. metabolic compartments

[0100] In addition to the various physical and chemical environments that contribute to the gastrointestinal niche, different niches contain different metabolic substrates.

[0101] Metabolic substrates that may be present in the gastrointestinal niche are not limited to these, but include oxalates, fructans, inulin, glucuronoxylan, arabinoxylan, glucomannan, β-mannan, dextran, starch, arabinan, xyloglucan, galacturonan, β-glucan, galactomannan, rhamnogalacturonan I, rhamnogalacturonan II, arabinogalactan, mucin O-linked glycans, yeast α-mannan, yeast β-glucan, chitin, alginate, porphyrin, laminarin, carrageenan, agarose, alternan, levan, xanthan gum, galactooligosaccharides, hyaluronan, chondrointin sulfate, dermatan sulfate, heparin sulfate, keratan sulfate, and phenyx. Examples include rualanine, tyrosine, tryptophan, leucine, valine, isoleucine, glycine, proline, asparagine, glutamine, aspartate, glutamate, cysteine, lysine, arginine, serine, methionine, alanine, arginine, histidine, ornithine, citrulline, carnitine, hydroxyproline, cholic acid, chenodeoxycholic acid, taurochenodeoxycholic acid, glycochenodeoxycholic acid, cholesterol, cinnamic acid, coumaric acid, sinapic acid, ferulic acid, caffeic acid, quinic acid, chlorogenic acid, catechin, epicatechin, gallic acid, pyrogallol, catechol, quercetin, myricetin, campherol, luteolin, apigenin, naringenin, and hesperidin. Microbial Consortium

[0102] The present invention provides a microbial consortium comprising multiple active microorganisms and an effective amount of supporting microbial communities. In some embodiments, the microbial consortium comprises 3 to 500 microbial strains. For example, in some embodiments, the microbial consortium consists of 3-500, 4-500, 5-500, 6-500, 7-500, 8-500, 9-500, 10-500, 11-500, 12-500, 13-500, 14-500, 15-500, 16-500, 17-500, 18-500, 19-500, 20-500, 21-500, 22-500, 23-500, 24-500, 25-500, 30-500, 35-500, 40-500, 45-500, 50-500, 60-500, and 70-500. 80-500, 90-500, 100-500, 110-500, 120-500, 130-500, 140-500, 150-500, 160-500, 170-500, 180-500, 190-500, 200-500, 210-500, 220-500, 230-500, 240-500, 250-500, 260-500, 270-500, 280-500, 290-500, 300-500, 400-500, 3-300, 4-300, 5-300, 6-300, 7-300, 8-300, 9- 300, 10-300, 11-300, 12-300, 13-300, 14-300, 15-300, 16-300, 17-300, 18-300, 19-300, 20-300, 21-300, 22-300, 23-300, 24-300, 25-300, 30-300, 35-300, 40-300, 45-300, 50-300, 60-300, 70-300, 80-300, 90-300, 100-300, 110-300, 120-300, 130-300, 140-300, 150-300, 16 0-300, 170-300, 180-300, 190-300, 200-300, 210-300, 220-300, 230-300, 240-300, 250-300, 260-300, 270-300, 280-300, 290-300, 3-250, 4-250, 5-250, 6-250, 7-250, 8-250, 9-250, 10-250, 11-250, 12-250, 13-250, 14-250, 15-250, 16-250, 17-250, 18-250, 19-250, 20-250,21~250、22~250、23~250、24~250、25~250、30~250、35~250、40~250、45~250、50~250、60~250、70~250、80~250、90~250、100~250、110~250、120~250、130~250、140~250、150~250、160~250、170~250、180~250、190~250、200~250、210~250、220~250、230~250、240~250、3~200、4~200、5~200、6~200、7~200、8~200、9~200、10~200、11~200、12~200、13~200、14~200、15~200、16~200、17~200、18~200、19~200、20~200、21~200、22~200、23~200、24~200、25~200、30~200、35~200、40~200、45~200、50~200、60~200、70~200、80~200、90~200、100~200、110~200、120~200、130~200、140~200、150~200、160~200、170~200、180~200、190~200、3~150、4~150、5~150、6~150、7~150、8~150、9~150、10~150、11~150、12~150、13~150、14~150、15~150、16~150、17~150、18~150、19~150、20~150、21~150、22~150、23~150、24~150、25~150、30~150、35~150、40~150、45~150、50~150、60~150、70~150、80~150、90~150、100~150、110~150、120~150、130~150、140~150、3~100、4~100、5~100、6~100、7~100、8~100、9~100、10~100、11~100、12~100、13~100、14~100、15~100、16~100、17~100、18~100、19~100、20~100、21~100、22~100、23~100、24~100、25~100、30~100、35~100、40~100、45~100、50~100、60~100、70~100、80~100、90~100、3~75、4~75、5-75, 6-75, 7-75, 8-75, 9-75, 10-75, 11-75, 12-75, 13-75, 14-75, 15-75, 16-75, 17-75, 18-75, 19-75, 20-75, 21-75, 22-75, 23-75, 24-75, 25-75, 30-75, 35-75, 40-75, 45-75, 50-75, 60-75, 70-75, 3-50, 4-50, 5-50, 6-50, 7-50, 8-50, 9-50, 10-50, 11-50, 12-50, 13-50, 14-50 Includes microbial strains of 15-50, 16-50, 17-50, 18-50, 19-50, 20-50, 21-50, 22-50, 23-50, 24-50, 25-50, 30-50, 35-50, 40-50, 45-50, 3-25, 4-25, 5-25, 6-25, 7-25, 8-25, 9-25, 10-25, 11-25, 12-25, 13-25, 14-25, 15-25, 16-25, 17-25, 18-25, 19-25, 20-25, 21-25, 22-25, 23-25, or 24-25. For example, in some embodiments, the microbial consortium includes about 20 to about 200, about 70 to about 80, about 80 to about 90, about 100 to about 110, or about 150 to about 160 microbial strains.

[0103] In some embodiments, the microbial consortium described herein includes microbial strains having a relative abundance of approximately 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, 5%, 1%, 0.1%, 0.01%, 0.001%, 0.0001%, 0.00001%, or 0.000001% of the total microbial consortium. In some embodiments, the relative abundance of a microbial strain is determined by metagenomic sequencing and calculated as the percentage of readings classified as identified microbial strains, divided by genome size. For example, in some embodiments, the relative abundance of the microbial strains of the present invention is determined by metagenomic shotgun sequencing. active microorganisms

[0104] The microbial consortium of the present invention comprises multiple active microorganisms capable of metabolizing a first metabolite that causes or contributes to disease in animals. In some embodiments, the present invention provides a microbial consortium capable of metabolizing the first metabolite at a pH in the range of 4 to 8. For example, in some embodiments, one or more of the multiple active microorganisms are present at pH ranges of 4 to 8, 4.2 to 8, 4.4 to 8, 4.6 to 8, 4.8 to 8, 5 to 8, 5.2 to 8, 5.4 to 8, 5.6 to 8, 5.8 to 8, 6 to 8, 6.2 to 8, 6.4 to 8, 6.6 to 8, 6.8 to 8, 7 to 8, 7.2 to 8, 7.4 to 8, 7.6 to 8, 7.8 to 8, 4 to 7, 4.2 to 7, 4.4 to 7, 4.6 to 7, 4.8 to 7, 5 to 7, 5.2 to 7, The first metabolic substrate can be metabolized at pH levels within the range of 5.4~7, 5.6~7, 5.8~7, 6~7, 6.2~7, 6.4~7, 6.6~7, 6.8~7, 4~6, 4.2~6, 4.4~6, 4.6~6, 4.8~6, 5~6, 5.2~6, 5.4~6, 5.6~6, 5.8~6, 4~6, 4.2~6, 4.4~6, 4.6~6, 4.8~6, 5~6, 5.2~6, 5.4~6, 5.6~6, or 5.8~6.

[0105] In some embodiments, the multiple active microorganisms include one microbial strain having significantly different first metabolic substrate metabolic activity in a standard substrate metabolic assay performed at two pH values ​​differing by 1 pH unit and within a pH range of 4–8. In some embodiments, the difference between the two pH values ​​is 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.2, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, or 4.0 pH units. For example, in some embodiments, a single microbial strain has a first metabolic substrate activity that is significantly different in standard substrate metabolism assays at pH 4 and pH 8, pH 5 and pH 8, pH 6 and pH 8, pH 7 and pH 8, pH 4 and pH 7, pH 5 and pH 7, pH 6 and pH 7, pH 4 and pH 6, pH 5 and pH 6, or pH 4 and pH 5.

[0106] As used herein, “lower pH” refers to a pH in a standardized substrate metabolism assay that is lower than another pH value. For example, a standardized substrate metabolism assay performed at pH 4.5 has a lower pH than a standardized substrate metabolism assay performed at pH 7.5. As used herein, “higher pH” refers to a pH in a standardized substrate metabolism assay that is higher than another pH value. For example, a standardized substrate metabolism assay performed at pH 7.5 has a higher pH than a standardized substrate metabolism assay performed at pH 4.5.

[0107] As used herein, “higher primary metabolite metabolic activity” means either the primary metabolite metabolic activity of a microbial strain that is higher than the primary metabolite metabolic activity of the same microbial strain under different conditions, or / or the primary metabolite metabolic activity of a microbial strain that is higher than the primary metabolite metabolic activity of a different microbial strain under the same conditions.

[0108] In some embodiments, the multiple active microorganisms include two microbial strains having significantly different first metabolite metabolic activities. For example, in some embodiments, one of the multiple active microorganisms has a significantly higher first metabolite metabolic activity at a lower pH compared to the first metabolite metabolic activity of another microbial strain among the multiple active microorganisms at the same lower pH. In some embodiments, one of the multiple active microorganisms has a significantly higher first metabolite metabolic activity at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 compared to the first metabolite metabolic activity of another microbial strain among the multiple active microorganisms at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5, respectively. In some embodiments, one of the multiple active microorganisms has a significantly higher first metabolite metabolic activity at a higher pH compared to the first metabolite metabolic activity of another microbial strain among the multiple active microorganisms at the same higher pH. In some embodiments, one of the multiple active microorganisms has a significantly higher first metabolic substrate metabolic activity at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 compared to the first metabolic substrate metabolic activity of another microbial strain among the multiple active microorganisms at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0, respectively.

[0109] In some embodiments, one of several active microorganisms has a significantly higher first metabolite metabolic activity at lower pH levels compared to its first metabolite metabolic activity at higher pH levels. For example, in some embodiments, one of several active microorganisms has a significantly higher first metabolite metabolic activity at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 than it has at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0. In some embodiments, one of several active microorganisms has a significantly higher first metabolite metabolic activity at higher pH levels compared to its first metabolite metabolic activity at lower pH levels. For example, in some embodiments, one of the multiple active microorganisms has a first metabolic activity at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 that is significantly higher than the first metabolic activity it has at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5.

[0110] In some embodiments, the multiple active microorganisms include active microorganisms having higher first metabolite metabolic activity at lower pH and other microorganisms having higher first metabolite metabolic activity at higher pH. For example, in some embodiments, the multiple active microorganisms include active microorganisms having higher first metabolite metabolic activity at pH 4.0 and other microorganisms having higher first metabolite metabolic activity at pH 7.5. In some embodiments, the multiple active microorganisms include active microorganisms having higher first metabolite metabolic activity at pH 4.0 and other microorganisms having higher first metabolite metabolic activity at pH 7.6. In some embodiments, the multiple active microorganisms include active microorganisms having higher first metabolite metabolic activity at pH 4.0 and other microorganisms having higher first metabolite metabolic activity at pH 7.7. In some embodiments, the multiple active microorganisms include active microorganisms having higher first metabolite metabolic activity at pH 4.0 and other microorganisms having higher first metabolite metabolic activity at pH 7.8. In some embodiments, the active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 4.0 and another microorganism having a higher first metabolite metabolic activity at pH 7.9. In some embodiments, the active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 4.0 and another microorganism having a higher first metabolite metabolic activity at pH 8.0. In some embodiments, the active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 4.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.5. In some embodiments, the active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 4.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.6. In some embodiments, the active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 4.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.7. In some embodiments, the active microorganisms include active microorganisms having higher first metabolite metabolic activity at pH 4.5 and other microorganisms having higher first metabolite metabolic activity at pH 7.8.In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 4.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.9. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 4.5 and another microorganism having a higher first metabolite metabolic activity at pH 8.0. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 5.0 and another microorganism having a higher first metabolite metabolic activity at pH 7.5. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 5.0 and another microorganism having a higher first metabolite metabolic activity at pH 7.6. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 5.0 and another microorganism having a higher first metabolite metabolic activity at pH 7.7. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 5.0 and another microorganism having a higher first metabolite metabolic activity at pH 7.8. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 5.0 and another microorganism having a higher first metabolite metabolic activity at pH 7.9. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 5.0 and another microorganism having a higher first metabolite metabolic activity at pH 8.0. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 5.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.5. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 5.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.6. In some embodiments, the active microorganisms include active microorganisms having higher first metabolite metabolic activity at pH 5.5 and other microorganisms having higher first metabolite metabolic activity at pH 7.7.In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 5.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.8. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 5.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.9. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 5.5 and another microorganism having a higher first metabolite metabolic activity at pH 8.0. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.0 and another microorganism having a higher first metabolite metabolic activity at pH 7.5. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.0 and another microorganism having a higher first metabolite metabolic activity at pH 7.6. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.0 and another microorganism having a higher first metabolite metabolic activity at pH 7.7. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.0 and another microorganism having a higher first metabolite metabolic activity at pH 7.8. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.0 and another microorganism having a higher first metabolite metabolic activity at pH 7.9. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.0 and another microorganism having a higher first metabolite metabolic activity at pH 8.0. In some embodiments, the multiple active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.5. In some embodiments, the active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.5, and another microorganism having a higher first metabolite metabolic activity at pH 7.6.In some embodiments, the active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.7. In some embodiments, the active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.8. In some embodiments, the active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.5 and another microorganism having a higher first metabolite metabolic activity at pH 7.9. In some embodiments, the active microorganisms include an active microorganism having a higher first metabolite metabolic activity at pH 6.5 and another microorganism having a higher first metabolite metabolic activity at pH 8.0.

[0111] In some embodiments, the multiple active microorganisms include one microbial strain having a significantly different first metabolite metabolic activity in a standard substrate metabolism assay performed at a first metabolite concentration compared to its first metabolite metabolic activity in a standard substrate metabolism assay performed at a different first metabolite concentration, where the difference between the two first metabolite concentrations is no more than 100 times. In some embodiments, the difference between the two first metabolite concentrations is 1.2 times. For example, in some embodiments, the difference between the two first metabolite concentrations is at least 1.2 times, 1.4 times, 1.6 times, 1.8 times, 2.0 times, 4 times, 6 times, 8 times, 10 times, 20 times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90 times, or 100 times, or greater.

[0112] As used herein, “lower primary metabolic substrate concentration” refers to a substrate concentration in a standardized substrate metabolism assay that is lower in value compared to another substrate concentration. “Higher primary metabolic substrate concentration” refers to a substrate concentration in a standardized substrate metabolism assay that is higher in value compared to another substrate concentration.

[0113] In some embodiments, the multiple active microorganisms include two microbial strains having significantly different first metabolite metabolic activity. For example, in some embodiments, one of the multiple active microorganisms has a significantly higher first metabolite metabolic activity at a lower first metabolite concentration compared to the first metabolite metabolic activity of another microbial strain among the multiple active microorganisms at the same lower first metabolite concentration. In some embodiments, one of the multiple active microorganisms has a significantly higher first metabolite metabolic activity at a higher first metabolite concentration compared to the first metabolite metabolic activity of another microbial strain among the multiple active microorganisms at the same higher first metabolite concentration.

[0114] In some embodiments, one of several active microorganisms has a significantly higher first metabolite metabolic activity at a lower first metabolite concentration compared to its first metabolite metabolic activity at a higher first metabolite concentration.

[0115] In some embodiments, the multiple active microorganisms include active microorganisms having higher first metabolite metabolic activity at lower first metabolite concentrations, and other microorganisms having higher first metabolite metabolic activity at higher first metabolite concentrations. For example, in some embodiments, the difference between the lower first metabolite concentration and the higher first metabolite concentration is at least 1.2, 1.4, 1.6, 1.8, 2.0, 4, 6, 8, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100, or greater.

[0116] In some embodiments, the multiple active microorganisms include two microbial strains having significantly different growth rates. For example, in some embodiments, one of the multiple active microorganisms has a significantly higher growth rate at a lower pH compared to the growth rate of another microbial strain of the multiple active microorganisms at the same lower pH. In some embodiments, one of the multiple active microorganisms has a significantly higher growth rate at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 compared to the growth rate of another microbial strain of the multiple active microorganisms at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5, respectively. In some embodiments, one of the multiple active microorganisms has a significantly higher growth rate at a higher pH compared to the growth rate of another microbial strain of the multiple active microorganisms at the same higher pH. In some embodiments, one of the multiple active microorganisms has a significantly higher growth rate at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 compared to the growth rate of another microbial strain among the multiple active microorganisms at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0, respectively.

[0117] In some embodiments, one of several active microorganisms has a significantly higher growth rate at lower pH compared to its growth rate at higher pH. For example, in some embodiments, one of several active microorganisms has a significantly higher growth rate at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 than it has at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0. In some embodiments, one of several active microorganisms has a significantly higher growth rate at higher pH compared to its growth rate at lower pH. For example, in some embodiments, one of several active microorganisms has a significantly higher growth rate at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 than it has at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5.

[0118] In some embodiments, a group of active microorganisms includes one strain that, when cultured in a medium containing a specific concentration of a first metabolite, has a significantly higher growth rate compared to the growth rate of another strain of the group of active microorganisms cultured in the same medium containing the same concentration of the first metabolite. In some embodiments, the difference between the two growth rates is at least 0.2, at least 0.4, at least 0.6, at least 0.8, at least 1.0, at least 1.2, at least 1.4, at least 1.6, at least 1.8, or at least 2.0.

[0119] In some embodiments, the first metabolic substrate may be selected from, but is not limited to, oxalates and bile acids (e.g., litcholic acid (LCA), deoxycholic acid (DCA)).

[0120] In some embodiments, the disclosure provides a microbial consortium comprising multiple active microorganisms capable of metabolizing a first metabolite to one or more metabolites. For example, in some embodiments, one or more metabolites may be selected from, but are not limited to, formates, CO2, and secondary bile acids (e.g., 3-oxo-deoxycholic acid (3-oxoDCA), 3-oxo-lithocholic acid (3-oxoLCA), isolithocholic acid (isoLCA), or isodeoxycholic acid (isoDCA)). In some embodiments, the multiple active microorganisms may comprise 2 to 200 microbial strains. For example, in some embodiments, the microbial consortium includes 2-10, 2-15, 2-20, 2-25, 2-30, 2-35, 2-40, 2-45, 2-50, 2-75, 2-100, 2-125, 2-150, 2-175, or 2-200 active microbial strains. In certain embodiments, the multiple active microorganisms may include 2-20 microbial strains. Oxalate-metabolic active microorganisms

[0121] In one embodiment, the disclosure provides a microbial consortium comprising multiple active microorganisms that metabolize oxalates. In some embodiments, each of the multiple active microorganisms that metabolize oxalates expresses a sufficient amount of one or more enzymes involved in oxalate metabolism. For example, in some embodiments, one or more active microorganisms express formyl-CoA transferase (Frc), oxalate-formate exchange transporter (e.g., OxIT), and oxalyl-CoA decarboxylase (e.g., OxC), and / or oxalate decarboxylase (e.g., OxD).

[0122] In some embodiments, the multiple active microorganisms that metabolize oxalates include 2 to 20 oxalate-metabolizing microbial strains. For example, in some embodiments, the microbial consortium includes 2 to 20, 3 to 20, 4 to 20, 5 to 20, 6 to 20, 7 to 20, 8 to 20, 9 to 20, 10 to 20, 11 to 20, 12 to 20, 13 to 20, 14 to 20, 15 to 20, 16 to 20, 17 to 20, 18 to 20, 19 to 20, 2 to 18, 3 to 18, 4 to 18, 5 to 18, 6 to 18, 7 to 18, 8 to 18, 9 to 18 , 10~18, 11~18, 12~18, 13~18, 14~18, 15~18, 16~18, 17~18, 2~16, 3~16, 4~16, 5~16, 6~16, 7~16, 8~16, 9~16, 10~16, 11~16, 12~16, 13~16, 14~16, 15~16, 2~14, 3~14, 4~14, 5~14, 6~14, 7~14, 8~14, 9~14, 1 0-14, 11-14, 12-14, 13-14, 2-13, 3-13, 4-13, 5-13, 6-13, 7-13, 8-13, 9-13, 10-13, 11-13, 12-13, 2-12, 3-12, 4-12, 5-12, 6-12, 7-12, 8-12, 9-12, 10-12, 11-12, 2-12, 3-12, 4-12, 5-12, 6-12, 7-12, 8-1 The 2, 9-12, 10-12, 11-12, 2-10, 3-10, 4-10, 5-10, 6-10, 7-10, 8-10, 9-10, 2-10, 3-10, 4-10, 5-10, 6-10, 7-10, 8-10, 9-10, 2-8, 3-8, 4-8, 5-8, 6-8, 7-8, 2-6, 3-6, 4-6, 5-6, 2-4, or 3-4 oxalate-metabolizing microbial strains are included. In some embodiments, the multiple active microorganisms may include three oxalate-metabolizing microbial strains. In some embodiments, the multiple active microorganisms consist of three oxalate-metabolizing microbial strains.

[0123] In some embodiments, the plurality of active microorganisms that metabolize oxalate include Oxalobacter formigenes, Bifidobacterium sp., Bifidobacterium dentium, Dialister invisus, Lactobacillus acidophilus, Lactobacillus gasseri, Lactobacillus helveticus, Lactobacillus reuteri, Eggerthella lenta, Lactobacillus rhamnosus, Enterococcus faecalis, Enterococcus gallinarum, Enterococcus faecium, Providencia rettgeri, Streptococcus thermophilus, Lactobacillus plantarum, Lactobacillus casei, Lactobacillus salivarius, Lactobacillus johnsii, Bifidobacterium infantis, Bifidobacterium animalis, Clostridium sporogenes, Leuconostoc It may include one or more microbial species selected from, but not limited to, *Lactis* and *Leuconostoc mesenteroides*.

[0124] In some embodiments, the active microorganisms that metabolize oxalates include Bifidobacterium dentium ATCC 27678, Enterococcus faecalis HM-432, and Lactobacillus helveticus. DSM 20075, Bifidobacterium dentium ATCC 27680, Lactobacillus acidophilus ATCC 4357, Lactobacillus reuteri HM-102, Bifidobacterium dentium DSM 20221, Lactobacillus acidophilus DSM 20079. Lactobacillus rhamnosus ATCC 53103. Bifidobacterium dentium DSM 20436. Lactobacillus acidophilus DSM 20242. Lactobacillus rhamnosus DSM 20245. Bifidobacterium sp.HM-868、Lactobacillus gasseri ATCC 33323、Lactobacillus rhamnosus DSM 8746、Dialister invisus DSM 15470、Lactobacillus gasseri DSMZ 107525、Lactobacillus rhamnosus HM-106、Eggerthella lenta ATCC 43055、Lactobacillus gasseri DSMZ 20077. Oxalobacter formigenes ATCC 35274. Eggerthella slow DSM 2243. Lactobacillus gasseri HM-104. Oxalobacter formigenes DSM 4420. Enterococcus faecalis HM-202 HM-644、およびOxalobacter formigenes The HM-1 is a very smooth and smooth This is a 2-year-old manufacturer.

[0125] In some embodiments, the multiple active microorganisms include Oxalobacter formigenes strains having 16S sequences that are at least 80% identical to SEQ ID NO: 67, SEQ ID NO: 133, or SEQ ID NO: 289. In some embodiments, the multiple active microorganisms include Oxalobacter formigenes strains having 16S sequences that are at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 67, SEQ ID NO: 133, or SEQ ID NO: 289.

[0126] In some embodiments, the multiple active microorganisms include Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 67, and Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 133. In some embodiments, the multiple active microorganisms include Oxalobacter formigenes strains having a 16S sequence at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 67, and Oxalobacter formigenes strains having a 16S sequence at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 133.

[0127] In some embodiments, the multiple active microorganisms include Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 133, and Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 289. In some embodiments, the multiple active microorganisms include Oxalobacter formigenes strains having a 16S sequence at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 133, and Oxalobacter formigenes strains having a 16S sequence at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 289.

[0128] In some embodiments, the multiple active microorganisms include Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 67, and Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 289. In some embodiments, the multiple active microorganisms include Oxalobacter formigenes strains having a 16S sequence at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 67, and Oxalobacter formigenes strains having a 16S sequence at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 289.

[0129] In some embodiments, the multiple active microorganisms include Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 67, Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 133, and Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 289. In some embodiments, the multiple active microorganisms include Oxalobacter formigenes strains having a 16S sequence identical to at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of the 16S sequence of SEQ ID NO: 67, Oxalobacter formigenes strains having a 16S sequence identical to at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of the 16S sequence of SEQ ID NO: 133, and Oxalobacter formigenes strains having a 16S sequence identical to at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of the 16S sequence of SEQ ID NO: 289.

[0130] In some embodiments, the multiple active microorganisms consist of Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 67, Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 133, and Oxalobacter formigenes strains having a 16S sequence at least 80% identical to SEQ ID NO: 289. In some embodiments, the multiple active microorganisms include Oxalobacter formigenes strains having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to SEQ ID NO: 67, Oxalobacter formigenes strains having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to SEQ ID NO: 133, and Oxalobacter formigenes strains having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to SEQ ID NO: 289. It consists of the formigenes strain.

[0131] As used herein, “substantially metabolizing oxalate,” “substantial metabolism of oxalate,” and these alternative expressions refer to a substantially significant reduction in the amount of oxalate in an in vitro assay (e.g., as described in Example 3). In some embodiments, one or more of several active microorganisms can substantially metabolize oxalate at a pH in the range of 4–8. For example, in some embodiments, one or more of the multiple active microorganisms are present in the following order: 4-8, 4.2-8, 4.4-8, 4.6-8, 4.8-8, 5-8, 5.2-8, 5.4-8, 5.6-8, 5.8-8, 6-8, 6.2-8, 6.4-8, 6.6-8, 6.8-8, 7-8, 7.2-8, 7.4-8, 7.6-8, 7.8-8, 4-7, 4.2-7, 4.4-7, 4.6-7, 4.8-7, 5-7, 5.2-7, 5. The oxalates can be substantially metabolized at pH levels within the ranges of 4-7, 5.6-7, 5.8-7, 6-7, 6.2-7, 6.4-7, 6.6-7, 6.8-7, 4-6, 4.2-6, 4.4-6, 4.6-6, 4.8-6, 5-6, 5.2-6, 5.4-6, 5.6-6, 5.8-6, 4-6, 4.2-6, 4.4-6, 4.6-6, 4.8-6, 5-6, 5.2-6, 5.4-6, 5.6-6, or 5.8-6.

[0132] In some embodiments, the multiple active microorganisms include a single microbial strain having significantly different oxalate metabolic activity in a standard oxalate metabolism assay performed at two pH values ​​that differ by at least 1 pH unit and within a pH range of 4 to 8. For example, in some embodiments, a single microbial strain has significantly different oxalate metabolic activity in a standard oxalate metabolism assay at pH 4 and pH 8, pH 5 and pH 8, pH 6 and pH 8, pH 4 and pH 7, pH 5 and pH 7, pH 6 and pH 7, pH 4 and pH 6, pH 5 and pH 6, or pH 4 and pH 5.

[0133] In some embodiments, oxalate metabolic activity is detected using a standard oxalate metabolic assay. For example, in some embodiments, oxalate metabolic activity is detected using a colorimetric enzyme assay that measures the activity of oxalate oxidase. In certain embodiments, the relative change in the amount of oxalate present in the culture medium inoculated with the microbial strain is measured using a commercially available oxalate assay kit (e.g., Sigma-Aldrich, catalog number MAK315). In some embodiments, oxalate metabolic activity is detected using liquid chromatography-mass spectrometry (LC-MS / MS). In some embodiments, the relative change in the amount of oxalate present is compared with the amount of oxalate present at the start of inoculation (i.e., t=0) to the amount of oxalate present at 2, 4, 6, 8, 10, 12, 14, 16, 18, 24, 30, 36, 48, 60, 72, 84, 96, 120, or 144 hours after inoculation.

[0134] As used herein, “higher oxalate metabolic activity” means either the oxalate metabolic activity of a microbial strain that is higher than the oxalate metabolic activity of the same microbial strain under different conditions, or / or the oxalate metabolic activity of a microbial strain that is higher than the oxalate metabolic activity of a different microbial strain under the same conditions.

[0135] In some embodiments, the multiple active microorganisms include two microbial strains having significantly different oxalate metabolic activity. For example, in some embodiments, one of the multiple active microorganisms has significantly higher oxalate metabolic activity at a lower pH compared to the oxalate metabolic activity of another microbial strain of the multiple active microorganisms at the same lower pH. In some embodiments, one of the multiple active microorganisms has significantly higher oxalate metabolic activity at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 compared to the oxalate metabolic activity of another microbial strain of the multiple active microorganisms at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5, respectively. In some embodiments, one of the multiple active microorganisms has significantly higher oxalate metabolic activity at a higher pH compared to the oxalate metabolic activity of another microbial strain of the multiple active microorganisms at the same higher pH. In some embodiments, one of the multiple active microorganisms has significantly higher oxalate metabolic activity at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 compared to the oxalate metabolic activity of another microbial strain among the multiple active microorganisms at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0, respectively.

[0136] In some embodiments, one of several active microorganisms has significantly higher oxalate metabolic activity at lower pH levels compared to its oxalate metabolic activity at higher pH levels. For example, in some embodiments, one of several active microorganisms has significantly higher oxalate metabolic activity at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5 than it has at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0. In some embodiments, one of several active microorganisms has significantly higher oxalate metabolic activity at higher pH levels compared to its oxalate metabolic activity at lower pH levels. For example, in some embodiments, one of several active microorganisms has significantly higher oxalate metabolic activity at pH 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 than it has at pH 4.0, 4.5, 5.0, 5.5, 6.0, or 6.5.

[0137] In some embodiments, the multiple active microorganisms include active microorganisms having higher oxalate metabolic activity at lower pH and other microorganisms having higher oxalate metabolic activity at higher pH. For example, in some embodiments, the multiple active microorganisms include active microorganisms having higher oxalate metabolic activity at pH 4.0 and other microorganisms having higher oxalate metabolic activity at pH 7.5. In some embodiments, the multiple active microorganisms include active microorganisms having higher oxalate metabolic activity at pH 4.0 and other microorganisms having higher oxalate metabolic activity at pH 7.6. In some embodiments, the multiple active microorganisms include active microorganisms having higher oxalate metabolic activity at pH 4.0 and other microorganisms having higher oxalate metabolic activity at pH 7.7. In some embodiments, the multiple active microorganisms include active microorganisms having higher oxalate metabolic activity at pH 4.0 and other microorganisms having higher oxalate metabolic activity at pH 7.8. In some embodiments, the multiple active microorganisms include active microorganisms having higher oxalate metabolic activity at pH 4.0 and other microorganisms having higher oxalate metabolic activity at pH 7.9. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 4.0 and another microorganism having higher oxalate metabolic activity at pH 8.0. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 4.5 and another microorganism having higher oxalate metabolic activity at pH 7.5. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 4.5 and another microorganism having higher oxalate metabolic activity at pH 7.6. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 4.5 and another microorganism having higher oxalate metabolic activity at pH 7.7. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 4.5 and another microorganism having higher oxalate metabolic activity at pH 7.8.In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 4.5 and another microorganism having higher oxalate metabolic activity at pH 7.9. In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 4.5 and another microorganism having higher oxalate metabolic activity at pH 8.0. In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.0 and another microorganism having higher oxalate metabolic activity at pH 7.5. In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.0 and another microorganism having higher oxalate metabolic activity at pH 7.6. In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.0 and another microorganism having higher oxalate metabolic activity at pH 7.7. In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.0 and another microorganism having higher oxalate metabolic activity at pH 7.8. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.0 and another microorganism having higher oxalate metabolic activity at pH 7.9. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.0 and another microorganism having higher oxalate metabolic activity at pH 8.0. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.5 and another microorganism having higher oxalate metabolic activity at pH 7.5. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.5 and another microorganism having higher oxalate metabolic activity at pH 7.6. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.5 and another microorganism having higher oxalate metabolic activity at pH 7.7.In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.5 and another microorganism having higher oxalate metabolic activity at pH 7.8. In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.5 and another microorganism having higher oxalate metabolic activity at pH 7.9. In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 5.5 and another microorganism having higher oxalate metabolic activity at pH 8.0. In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.0 and another microorganism having higher oxalate metabolic activity at pH 7.5. In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.0 and another microorganism having higher oxalate metabolic activity at pH 7.6. In some embodiments, the multiple active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.0 and another microorganism having higher oxalate metabolic activity at pH 7.7. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.0 and another microorganism having higher oxalate metabolic activity at pH 7.8. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.0 and another microorganism having higher oxalate metabolic activity at pH 7.9. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.0 and another microorganism having higher oxalate metabolic activity at pH 8.0. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.5 and another microorganism having higher oxalate metabolic activity at pH 7.5. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.5 and another microorganism having higher oxalate metabolic activity at pH 7.6.In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.5 and another microorganism having higher oxalate metabolic activity at pH 7.7. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.5 and another microorganism having higher oxalate metabolic activity at pH 7.8. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.5 and another microorganism having higher oxalate metabolic activity at pH 7.9. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at pH 6.5 and another microorganism having higher oxalate metabolic activity at pH 8.0.

[0138] In some embodiments, one or more of the multiple active microorganisms can substantially metabolize oxalates at oxalate concentrations ranging from about 0.75 mM to about 40 mM. For example, in some embodiments, one or more of the multiple active microorganisms can substantially metabolize oxalates at concentrations ranging from about 0.75 mM to about 40 mM, about 1 mM to about 40 mM, about 2.5 mM to about 40 mM, about 5 mM to about 40 mM, about 7.5 mM to about 40 mM, about 10 mM to about 40 mM, about 15 mM to about 40 mM, about 20 mM to about 40 mM, about 25 mM to about 40 mM, about 30 mM to about 40 mM, and about 0.75 mM to about 30 mM. M, approximately 1mM to approximately 30mM, approximately 2.5mM to approximately 30mM, approximately 5mM to approximately 30mM, approximately 7.5mM to approximately 30mM, approximately 10mM to approximately 30mM, approximately 15mM to approximately 30mM, approximately 20mM to approximately 30mM, approximately 25mM to approximately 30mM, approximately 0.75mM to approximately 25mM, approximately 1mM to approximately 25mM, approximately 2.5mM to approximately 25mM, approximately 5mM to approximately 25mM, approximately 7.5mM to approximately 25mM, approximately 10mM to approximately 25mM, approximately 15mM to approximately 25mM, approximately 20mM to approximately 25mM, approximately 0.75mM to approximately 20mM, approximately 1mM to approximately 20mM, approximately 2.5mM to approximately 20mM, approximately 5mM to approximately 20mM, approximately 7.5mM to approximately 20mM, approximately 10mM to approximately 20mM, approximately 15mM to approximately 20mM, approximately 0.75mM to approximately 15mM, approximately 1mM to approximately 15mM, approximately 2.5mM to approximately 15mM, approximately 5mM to approximately 15mM, approximately 7 It can substantially metabolize oxalates with oxalate concentrations in the following ranges: 0.5 mM to approximately 15 mM, approximately 10 mM to approximately 15 mM, approximately 0.75 mM to approximately 10 mM, approximately 1 mM to approximately 10 mM, approximately 2.5 mM to approximately 10 mM, approximately 5 mM to approximately 10 mM, approximately 7.5 mM to approximately 10 mM, approximately 0.75 mM to approximately 5 mM, approximately 1 mM to approximately 5 mM, approximately 2.5 mM to approximately 5 mM, or approximately 0.75 mM to approximately 1 mM.

[0139] In some embodiments, multiple active microorganisms include one microbial strain having significantly different oxalate metabolic activity in a standard in vitro oxalate metabolic assay (e.g., as described in Example 3) at a certain oxalate concentration compared to its oxalate metabolic activity in a standard in vitro oxalate metabolic assay performed at different oxalate concentrations, where the difference between the two oxalate concentrations is within 100 times. For example, in some embodiments, one microbial strain has oxalate concentrations of approximately 0.75 mM and approximately 40 mM, approximately 1 mM and approximately 40 mM, approximately 2.5 mM and approximately 40 mM, approximately 5 mM and approximately 40 mM, approximately 7.5 mM and approximately 40 mM, approximately 10 mM and approximately 40 mM, approximately 15 mM and approximately 40 mM, approximately 20 mM and approximately 40 mM, approximately 25 mM and approximately 40 mM, approximately 30 mM and approximately 40 mM, approximately 0.75 mM and approximately 30 mM, approximately 1 mM and approximately 30 mM, approximately 2.5 mM and approximately 30 mM, approximately 5 mM and approximately 30 mM, approximately 7.5 mM and approximately 30 mM, approximately 10 mM and approximately 30 mM, approximately 15 mM and approximately 30 mM, approximately 20 mM and approximately 30 mM, approximately 25 mM and approximately 30 mM, approximately 0.75 mM and approximately 25 mM, approximately 1 mM and approximately 25 mM, approximately 2.5 mM and approximately 25 mM, approximately 5 mM and approximately 25 mM, approximately 7.5 mM and approximately 25 mM, approximately 10 mM and approximately 25 mM, Approximately 15mm and approximately 25mm, approximately 20mm and approximately 25mm, approximately 0.75mm and approximately 20mm, approximately 1mm and approximately 20mm, approximately 2.5mm and approximately 20mm, approximately 5mm and approximately 20mm, approximately 7.5mm and approximately 20mm, approximately 10mm and approximately 20mm, approximately 15mm and approximately 20mm, approximately 0.75mm and approximately 15mm, approximately 1mm and approximately 15mm, approximately 2.5mm and approximately 15mm, approximately 5mm and approximately 15mm, approximately 7.5mm and approximately In standard oxalate metabolism assays performed at 15 mM, approximately 10 mM and approximately 15 mM, approximately 0.75 mM and approximately 10 mM, approximately 1 mM and approximately 10 mM, approximately 2.5 mM and approximately 10 mM, approximately 5 mM and approximately 10 mM, approximately 7.5 mM and approximately 10 mM, approximately 0.75 mM and approximately 5 mM, approximately 1 mM and approximately 5 mM, approximately 2.5 mM and approximately 5 mM, or approximately 0.75 mM and approximately 1 mM, it exhibits significantly different oxalate metabolic activity.

[0140] In some embodiments, the multiple active microorganisms include two microbial strains having significantly different oxalate metabolic activity. For example, in some embodiments, one of the multiple active microorganisms has significantly higher oxalate metabolic activity at lower oxalate concentrations compared to the oxalate metabolic activity of another microbial strain among the multiple active microorganisms at the same lower oxalate concentration. In some embodiments, one of the multiple active microorganisms has significantly higher oxalate metabolic activity at oxalate concentrations of 0.75 mM, 1 mM, 2.5 mM, 5 mM, or 7.5 mM, compared to the oxalate metabolic activity of another microbial strain among the multiple active microorganisms at the same higher oxalate concentration. In some embodiments, one of the multiple active microorganisms has significantly higher oxalate metabolic activity at higher oxalate concentrations compared to the oxalate metabolic activity of another microbial strain among the multiple active microorganisms at the same higher oxalate concentration. In some embodiments, one of several active microorganisms has significantly higher oxalate metabolic activity at oxalate concentrations of 15 mM, 20 mM, 25 mM, 30 mM, or 40 mM compared to the oxalate metabolic activity of another strain of the several active microorganisms at oxalate concentrations of 15 mM, 20 mM, 25 mM, 30 mM, or 40 mM, respectively.

[0141] In some embodiments, one of several active microorganisms has significantly higher oxalate metabolic activity at lower oxalate concentrations compared to its oxalate metabolic activity at higher oxalate concentrations. For example, in some embodiments, one of several active microorganisms has significantly higher oxalate metabolic activity at 0.75 mM, 1 mM, 2.5 mM, 5 mM, or 7.5 mM oxalate concentrations than it has at 15 mM, 20 mM, 25 mM, 30 mM, or 40 mM oxalate concentrations. In some embodiments, one of several active microorganisms has significantly higher oxalate metabolic activity at higher oxalate concentrations compared to its oxalate metabolic activity at lower oxalate concentrations. For example, in some embodiments, one of several active microorganisms has significantly higher oxalate metabolic activity at 15 mM, 20 mM, 25 mM, 30 mM, or 40 mM oxalate concentrations than it has at 0.75 mM, 1 mM, 2.5 mM, 5 mM, or 7.5 mM oxalate concentrations.

[0142] In some embodiments, the active microorganisms include active microorganisms having higher oxalate metabolic activity at lower oxalate concentrations and other active microorganisms having higher oxalate metabolic activity at higher oxalate concentrations. For example, in some embodiments, the active microorganisms include active microorganisms having higher oxalate metabolic activity at about 0.75 mM oxalate and other active microorganisms having higher oxalate metabolic activity at about 40 mM oxalate. In some embodiments, the active microorganisms include active microorganisms having higher oxalate metabolic activity at 1 mM oxalate and other active microorganisms having higher oxalate metabolic activity at about 40 mM oxalate. In some embodiments, the active microorganisms include active microorganisms having higher oxalate metabolic activity at 2.5 mM oxalate and other active microorganisms having higher oxalate metabolic activity at about 40 mM oxalate. In some embodiments, the active microorganisms include active microorganisms having higher oxalate metabolic activity at 5 mM oxalate and other active microorganisms having higher oxalate metabolic activity at about 40 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 7.5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 40 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 0.75 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 30 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 1 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 30 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 2.5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 30 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 30 mM oxalate.In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 7.5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 30 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 0.75 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 25 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 1 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 25 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 2.5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 25 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 25 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 7.5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 25 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 0.75 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 20 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 1 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 20 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 2.5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 20 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 20 mM oxalate.In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 7.5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 20 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 0.75 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 15 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 1 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 15 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 2.5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 15 mM oxalate. In some embodiments, the active microorganisms include an active microorganism having higher oxalate metabolic activity at 5 mM oxalate and another active microorganism having higher oxalate metabolic activity at about 15 mM oxalate. In some embodiments, the active microorganisms include active microorganisms having higher oxalate metabolic activity at 7.5 mM oxalate and other active microorganisms having higher oxalate metabolic activity at about 15 mM oxalate.

[0143] In some embodiments, when tested in an in vitro oxalate metabolism assay (for example, as described in Example 3 below), the multiple active microorganisms of the present invention significantly reduce the concentration of oxalates present in the sample by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, or at least 80%.

[0144] In some embodiments, the multiple active microorganisms of the present invention significantly reduce the concentration of oxalates present in blood, serum, bile, feces, or urine samples by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, or at least 80% compared to untreated control subjects or pre-administration levels. The concentration of oxalates in blood, serum, bile, feces, or urine samples can be measured using liquid chromatography-mass spectrometry (LC-MS), as described in Example 4 below. Active microorganisms that modify bile salts

[0145] The non-conjugated primary bile acids cholic acid (CA) and chenodeoxycholic acid (CDCA) are substrates for 7α-dehydroxylation by selected members of the gut microbiota. As shown below, 7α-dehydroxylation converts CA and CDCA to litcholic acid (LCA) and deoxycholic acid (DCA), respectively. LCA and DCA are secondary bile acids associated with adverse health outcomes. [ka]

[0146] In some embodiments, the microbial consortium disclosed herein comprises microbial strains having robust 3α-hydroxysteroid dehydrogenase (3α-HSDH) and 3β-hydroxysteroid dehydrogenase (3β-HSDH) activity. As shown below, 3α-HSDH and 3β-HSDH convert DCA and LCA to isoDCA and isoLCA, respectively, which are alternative secondary bile acids. [ka]

[0147] In some embodiments, the microbial consortium provided herein comprises multiple active microorganisms expressing 3α-HSDH selected from one or more of Eggerthella lenta, Ruminococcus gnavus, Clostridium perfringens, Peptostreptococcus productus, and Clostridium scindens. In some embodiments, the microbial consortium provided herein comprises multiple active microorganisms expressing 3β-HSDH selected from one or more of Peptostreptococcus productus, Clostridium innocuum, and Clostridium scindens.

[0148] In some embodiments, the multiple active microorganisms include one or more microbial strains selected from Eggethella lenta strains having a 16S sequence at least 80% identical to SEQ ID NO: 30, Eggethella lenta strains having a 16S sequence at least 80% identical to SEQ ID NO: 96, Eggethella lenta strains having a 16S sequence at least 80% identical to SEQ ID NO: 170, Eggethella lenta strains having a 16S sequence at least 80% identical to SEQ ID NO: 201, or Clostridum scindens strains having a 16S sequence at least 80% identical to SEQ ID NO: 87.

[0149] In some embodiments, the multiple active microorganisms include Eggethella lenta strains having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to SEQ ID NO: 30; Eggethella lenta strains having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to SEQ ID NO: 96; and Eggethella lenta strains having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to SEQ ID NO: 170. The collection includes one or more microbial strains selected from Eggethella lenta strains having a 16S sequence identical to at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of the 16S sequence to Eggethella lenta strain, SEQ ID NO: 201, or Clostridum scindens strains having a 16S sequence identical to at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of the 16S sequence to SEQ ID NO: 87.

[0150] In some embodiments, the multiple active microorganisms include two microbial strains having significantly different bile acid metabolic activity. For example, in some embodiments, one of the multiple active microorganisms has significantly higher bile acid metabolic activity at lower bile acid concentrations compared to the bile acid metabolic activity of another microbial strain among the multiple active microorganisms at the same lower bile acid concentration. In some embodiments, one of the multiple active microorganisms has significantly higher bile acid metabolic activity at bile acid concentrations of 0.1 mM, 0.2 mM, 0.3 mM, 0.4 mM, 0.5 mM, 0.6 mM, 0.7 mM, 0.8 mM, 0.9 mM, and 1.0 mM compared to the bile acid metabolic activity of another microbial strain among the multiple active microorganisms at oxalate concentrations of 0.1 mM, 0.2 mM, 0.3 mM, 0.4 mM, 0.5 mM, 0.6 mM, 0.7 mM, 0.8 mM, 0.9 mM, or 1.0 mM, respectively. In some embodiments, one of several active microorganisms has significantly higher bile acid metabolic activity at higher bile acid concentrations compared to the bile acid metabolic activity of another strain of the several active microorganisms at the same higher bile acid concentration. In some embodiments, one of several active microorganisms has significantly higher bile acid metabolic activity at bile acid concentrations of 5.0 mM, 5.5 mM, 6.0 mM, 6.5 mM, 7.0 mM, 7.5 mM, 8.0 mM, 8.5 mM, 9.0 mM, 9.5 mM, or 10.0 mM compared to the oxalate metabolic activity of another strain of the several active microorganisms at oxalate concentrations of 5.0 mM, 5.5 mM, 6.0 mM, 6.5 mM, 7.0 mM, 7.5 mM, 8.0 mM, 8.5 mM, 9.0 mM, 9.5 mM, or 10.0 mM, respectively.

[0151] In some embodiments, one of several active microorganisms has significantly higher bile acid metabolic activity at lower bile acid concentrations compared to its bile acid metabolic activity at higher bile acid concentrations. For example, in some embodiments, one of several active microorganisms has significantly higher bile acid metabolic activity at bile acid concentrations of 0.1 mM, 0.2 mM, 0.3 mM, 0.4 mM, 0.5 mM, 0.6 mM, 0.7 mM, 0.8 mM, 0.9 mM, or 1.0 mM than it has at bile acid concentrations of 5.0 mM, 5.5 mM, 6.0 mM, 6.5 mM, 7.0 mM, 7.5 mM, 8.0 mM, 8.5 mM, 9.0 mM, 9.5 mM, or 10.0 mM. In some embodiments, one of several active microorganisms has significantly higher bile acid metabolic activity at higher bile acid concentrations compared to its bile acid metabolic activity at lower bile acid concentrations. For example, in some embodiments, one of several active microorganisms has significantly higher bile acid metabolic activity at bile acid concentrations of 5.0 mM, 5.5 mM, 6.0 mM, 6.5 mM, 7.0 mM, 7.5 mM, 8.0 mM, 8.5 mM, 9.0 mM, 9.5 mM, or 10.0 mM than it has at bile acid concentrations of 0.1 mM, 0.2 mM, 0.3 mM, 0.4 mM, 0.5 mM, 0.6 mM, 0.7 mM, 0.8 mM, 0.9 mM, or 1.0 mM.

[0152] In some embodiments, the multiple active microorganisms include active microorganisms having higher bile acid metabolic activity at lower bile acid concentrations and other active microorganisms having higher bile acid metabolic activity at higher bile acid concentrations. For example, in some embodiments, the multiple active microorganisms include active microorganisms having higher bile acid metabolic activity at about 0.1 mM bile acid and other active microorganisms having higher bile acid metabolic activity at about 10 mM bile acid. In some embodiments, the multiple active microorganisms include active microorganisms having higher bile acid metabolic activity at about 0.2 mM bile acid and other active microorganisms having higher bile acid metabolic activity at about 10 mM bile acid. In some embodiments, the multiple active microorganisms include active microorganisms having higher bile acid metabolic activity at about 0.3 mM bile acid and other active microorganisms having higher bile acid metabolic activity at about 10 mM bile acid. In some embodiments, the multiple active microorganisms include active microorganisms having higher bile acid metabolic activity at about 0.4 mM bile acid and other active microorganisms having higher bile acid metabolic activity at about 10 mM bile acid. In some embodiments, the active microorganisms include an active microorganism having higher bile acid metabolic activity at approximately 0.5 mM bile acid, and another active microorganism having higher bile acid metabolic activity at approximately 10 mM bile acid. In some embodiments, the active microorganisms include an active microorganism having higher bile acid metabolic activity at approximately 0.1 mM bile acid, and another active microorganism having higher bile acid metabolic activity at approximately 7.5 mM bile acid. In some embodiments, the active microorganisms include an active microorganism having higher bile acid metabolic activity at approximately 0.2 mM bile acid, and another active microorganism having higher bile acid metabolic activity at approximately 7.5 mM bile acid. In some embodiments, the active microorganisms include an active microorganism having higher bile acid metabolic activity at approximately 0.3 mM bile acid, and another active microorganism having higher bile acid metabolic activity at approximately 5.0 mM bile acid. In some embodiments, the active microorganisms include an active microorganism having higher bile acid metabolic activity at approximately 0.4 mM bile acid, and another active microorganism having higher bile acid metabolic activity at approximately 7.5 mM bile acid.In some embodiments, the active microorganisms include an active microorganism having higher bile acid metabolic activity at approximately 0.1 mM bile acid, and another active microorganism having higher bile acid metabolic activity at approximately 5.0 mM bile acid. In some embodiments, the active microorganisms include an active microorganism having higher bile acid metabolic activity at approximately 0.2 mM bile acid, and another active microorganism having higher bile acid metabolic activity at approximately 5.0 mM bile acid. In some embodiments, the active microorganisms include an active microorganism having higher bile acid metabolic activity at approximately 0.3 mM bile acid, and another active microorganism having higher bile acid metabolic activity at approximately 5.0 mM bile acid. In some embodiments, the active microorganisms include an active microorganism having higher bile acid metabolic activity at approximately 0.4 mM bile acid, and another active microorganism having higher bile acid metabolic activity at approximately 5.0 mM bile acid. In some embodiments, the active microorganisms include an active microorganism having higher bile acid metabolic activity at approximately 0.5 mM bile acid, and another active microorganism having higher bile acid metabolic activity at approximately 5.0 mM bile acid.

[0153] In some embodiments, when tested with a standard in vitro bile acid metabolism assay, the multiple active microorganisms of the present invention significantly reduce the concentrations of lithoholic acid (LCA) and / or deoxycholic acid (DCA) present in the sample by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, or at least 80%.

[0154] In some embodiments, the multiple active microorganisms of the present invention significantly reduce the concentrations of LCA and / or DCA present in blood, serum, bile, feces, or urine samples when administered to a subject by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, or at least 80% compared to an untreated control or pre-administration levels. Microbial support communities

[0155] The microbial consortium of the present invention further includes a microbial support community that enhances the properties of one or more of the multiple active microorganisms. For example, in some embodiments, the microbial support community enhances the colonization of multiple active microorganisms in the digestive tract. In other embodiments, the microbial support community enhances the biomass of multiple active microorganisms. In other embodiments, the microbial support community enhances the metabolism of a first metabolic substrate by multiple active microorganisms. In other embodiments, the microbial support community enhances the long-term stability of multiple active microorganisms.

[0156] The microbial support communities disclosed herein metabolize one or more metabolites produced by multiple active microorganisms, and one or more metabolites inhibit the metabolism of multiple active microorganisms. For example, in some embodiments, the microbial support community metabolizes formate produced by multiple active microorganisms, and the presence of formate inhibits the metabolism of oxalate by multiple active microorganisms. In some embodiments, the microbial support community of the present invention catalyzes the fermentation of polysaccharides to one or more from the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H2, and CO2. In some embodiments, the microbial support community catalyzes the fermentation of amino acids into one or more of the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, floleate, 3-(1H-indole-3-yl)propanoate, 5-aminopentanoate, H2, H2S, and CO2. In some embodiments, the supporting community catalyzes the synthesis of one or more of the group consisting of methane from H2 and CO2, methane from formate and H2, acetate from H2 and CO2, acetate from formate and H2, acetate and sulfides from H2, CO2 and sulfate, propionate and CO2 from succinate, succinate from H2 and fumarate; succinate from formate and fumarate, and butyrate, acetate, H2 and CO2 from lactate. In some embodiments, the supporting community of the present invention catalyzes the decoupling of conjugated bile acids for the production of primary bile acids, the conversion of cholic acid (CA) to 7-oxocholic acid, the conversion of 7-oxocholic acid to 7-betacholic acid (7-betaCA), the conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and / or the conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA).

[0157] The microbial support community of the present invention includes microbial strains between 1 and 300. For example, in some embodiments, the microbial support community includes strains between 1 and 300, between 5 and 300, between 10 and 300, between 15 and 300, between 20 and 300, between 30 and 300, between 40 and 300, between 50 and 300, between 60 and 300, between 70 and 300, between 80 and 300, between 90 and 300, between 100 and 300, between 110 and 300, between 120 and 300, between 130 and 300, between 140 and 300, between 150 and 300, between 160 and 300, between 170 and 300, between 180 and 300, between 190 and 300, between 200 and 300, and 2 Between 10 and 300, between 220 and 300, between 230 and 300, between 240 and 300, between 250 and 300, between 260 and 300, between 270 and 300, between 280 and 300, between 290 and 300, between 1 and 250, between 5 and 250, between 10 and 250, between 15 and 250, between 20 and 250, between 30 and 250, between 40 and 250, between 50 and 250, between 60 and 250, between 70 and 250, between 80 and 250, between 90 and 250, between 100 and 250, between 110 and 250, between 120 and 250, between 130 and 250, between 140 and 25 Between 0, between 150 and 250, between 160 and 250, between 170 and 250, between 180 and 250, between 190 and 250, between 200 and 250, between 210 and 250, between 220 and 250, between 230 and 250, between 240 and 250, between 1 and 200, between 5 and 200, between 10 and 200, between 15 and 200, between 20 and 200, between 30 and 200, between 40 and 200, between 50 and 200, between 60 and 200, between 70 and 200, between 80 and 200, between 90 and 200, between 100 and 200, between 110 and 200, between 120 and 200, 1 Between 30 and 200, between 140 and 200, between 150 and 200, between 160 and 200, between 170 and 200, between 180 and 200, between 190 and 200, between 1 and 150, between 5 and 150, between 10 and 150, between 15 and 150, between 20 and 150, between 30 and 150, between 40 and 150, between 50 and 150, between 60 and 150, between 70 and 150, between 80 and 150, between 90 and 150, between 100 and 150, between 110 and 150, between 120 and 150, between 130 and 150, between 140 and 150, between 1 and 100, between 5 and 100,The microbial community includes microbial strains between 10 and 100, between 15 and 100, between 20 and 100, between 30 and 100, between 40 and 100, between 50 and 100, between 60 and 100, between 70 and 100, between 80 and 100, between 90 and 100, between 1 and 50, between 5 and 50, between 10 and 50, between 15 and 50, between 20 and 50, between 30 and 50, or between 40 and 50. For example, in some embodiments, the supporting microbial community includes microbial strains of about 20 to about 200, about 70 to about 80, about 80 to about 90, about 100 to about 110, or about 150 to about 160.

[0158] In some embodiments, the supporting community of microorganisms includes at least one, at least two, at least three, at least four, or at least five species from the following phyla: Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, and Euryarchaeota. In some embodiments, the supporting community of microorganisms includes at least one, at least two, at least three, at least four, or at least five species from the following subclades: Bacteroidales, Clostridiales, Erysipelotrichales, Negativicutes, Coriobacteriia, Bifidobacteriales, and Methanobacteriales.

[0159] In some embodiments, the supporting community of the microorganisms of the present invention consumes one or more metabolites derived from a diet rich in animal components. For example, in some embodiments, the supporting community of the microorganisms of the present invention consumes one or more of the following metabolites: α-mannan, acetate, agarose, alanine, arabinan, arabinogalactan, arabinoxylan, arginine, asparagine, aspartate, β-glucan, benzoic acid, carrageenan, catechol, chlorogenic acid, chondroitin sulfate, cysteine, dextran, enterodiol, flavan-3-ol, flavanone, flavone, flavonol, fole Formates, galactomannan, galacturonan, galacturonate, glucomannan, glutamine, glycine, hyaluronan, hydrogen, hydroxyproline, inulin, isoflavone, lactate, laminarin, leucine, levan, methionine, mucin O-linked glycans, phenylalanine, proline, rhamnogalacturonan I, rhamnogalacturonan II, secoisolariciresinol diglycoside, serine, starch, tyrosine, valine, xyloglucan, and xylooligosaccharides. In some embodiments, the microbial support community is designed to maximize the number of metabolites derived from the host diet that the support community can consume.

[0160] In some embodiments, the supporting community of the microorganism of the present invention consumes one or more of the following dietary, host-derived, or microbial metabolites: thiamine, methanol, indole-3-acetate, L-glutamate, L-ornithine, niacin, 2-oxybutyrate, betaine, D-fructuronate, D-gluconate, D-tagaturonate, D-turanose, inosine, glycine, histidine, L-idonate, isoleucine, serine, N-acetyl-D-mannosamine N, nitrate, thymidine, uridine, butyrate, propanoate, indole, glutamine, inositol, arginine, aspartate, malate, oxalate, phenol, succinate, ethanol, hydrogen, formate, lactate, aminobenzoate, lyxose, isomaltose, phenylalanine, tyrosine, pyruvate, mannitol, sorbitol, D-tagalose, glycerol, leucine, N-acetylgalactosamine, isovalerate, vir Otin, isobutyrate, 2-methylbutyrate, D-galactosamine, glycolytocholate, valine, melibiose, taurolitocholate, menaquinone, chenodeoxycholic acid, cholic acid, glycochenodeoxycholate, glycocholate, glycodeoxycholate, thiosulfate, pyridoxal, bicarbonate, N-acetyl-D-glucosamine, sulfate, riboflavin, methionine, N-acetylneuraminic acid, ribose, D-galacturonate, ta Urochenodeoxycholate, taurocholate, arabinose, rhamnose, pantothenic acid, xylooligosaccharides, acetate, D-glucuronic acid, cysteine, adenosylcobalamin, sucrose, trehalose, urea, xylose, cellobiose, mannose, L-fucose, D-galactose, D-glucosamine, D-psicose, fructooligosaccharides, carbon dioxide, maltose, ammonia, raffinose, dextrin, lactose, glucose, and fructose.

[0161] In some embodiments, the supporting community of the microorganism of the present invention produces one or more of the following metabolites: dimethylamine, folic acid, butylamine, phenylethylamine, 1,2-propanediol, acetone, trimethylamine, putrescine, tyramine, 4-aminobutyrate, valerate, 1,2-ethanediol, methylamine, phenylacetate, spermidine, hydrogen sulfide, linoleic acid, formaldehyde, trimethylamine N-oxide, cadaverine, alanine, threonine, methane, and pentanol.

[0162] In some embodiments of the present invention, the proprietary dosage forms of the microorganism consortium of this disclosure contain active microorganisms and supporting microorganisms in colony-type unit (CFU) ratios of about 5:1, 4:1, 3:1, 2:1, 1:1, 1:2, 1:3, 1:4, and 1:5. In some embodiments, the proprietary dosage forms of the microorganism consortium of this disclosure contain active microorganisms and supporting microorganisms in total CFU amounts of about one order of magnitude, two orders of magnitude, three orders of magnitude, four orders of magnitude, five orders of magnitude, six orders of magnitude, seven orders of magnitude, eight orders of magnitude, nine orders of magnitude, or ten orders of magnitude relative to each other.

[0163] In some embodiments, the supporting microbial communities include Absiella dolichum, Bacteroides uniformis, Eubacterium siraeum, Acidaminococcus fermentans, Bacteroides vulgatus, Eubacterium ventriosum, Acidaminococcus sp., Bacteroides xylanisolvens, Faecalibacterium prausnitzii, and Adlercreutzia. equolifaciens, Bifidobacterium breve, Granulicatella adiacens, Akkermansia muciniphila, Bifidobacterium catenulatum, Holdemanella biformis, Alistipes finegoldii, Bifidobacterium pseudocatenulatum, Holdemania filiformis, Alistipes indistinctus, Bilophila wadsworthia, Hungatella hathewayi, Alistipes onderdonkii, Blautia hansenii, Intestinibacter bartlettii, Alistipes putredinis, Blautia hydrogenotrophica, Intestinimonas butyriciproducens, Alistipes senegalensis, Blautia obeum, Lactobacillus ruminis, Alistipes shahii, Blautia sp., Marvinbryantia formatexigens, Anaerobutyricum hallii, Blautia wexlerae, Megasphaera, Anaerofustis stercorihominis, Butyricimonas virosa, Methanobrevibacter smithii, Anaerostipes caccae, Butyrivibrio crossotus, Anaerotruncus colihominis, Catenibacterium mitsuokai, Bacteroides caccae, Clostridium asparagiforme, Bacteroides cellulosilyticus, Clostridium bolteae, Mitsuokella multacida, Bacteroides coprocola, Clostridium hiranonis, Odoribacter splanchnicus, Bacteroides coprophilus, Clostridium hylemonae, Olsenella uli, Bacteroides dorei, Clostridium leptum, Oscillibacter sp., Bacteroides dorei, Clostridium methylpentosum, Parabacteroides distasonis, Bacteroides eggerthii, Clostridium orbiscindens, Parabacteroides johnsonii, Bacteroides finegoldii, Clostridium saccharolyticum, Parabacteroides merdae, Bacteroides fragilis, Clostridium scindens, Parabacteroides sp., Bacteroides intestinalis, Clostridium sp., Prevotella buccalis, Bacteroides ovatus, Prevotella copri, Bacteroides pectinophilus, Roseburia inulinivorans, Bacteroides plebeius, Clostridium spiroforme, Ruminococcus gauvreauii, Bacteroides rodentium, Collinsella aerofaciens, Ruminococcus gnavus, Collinsella stercoris, Ruminococcus lactaris, Coprococcus comes, Ruminococcus torques, Coprococcus eutactus, Slackia exigua, Desulfovibrio piger, Slackia heliotrinireducens, Dorea formicigenerans, Solobacterium moorei, Dorea longicatena, Streptococcus salivarius subsp.The list may include one or more microbial strains selected from, but not limited to, Thermophilus, Bacteroides stercoris, Ethanoligenens harbinense, Subdoligranulum variabile, Bacteroides thetaiotaomicron, Eubacterium rectale, Turicibacter sanguinis, and Tyzzerella nexilis.

[0164] In some embodiments, the supporting community of microorganisms includes Absiella dolichum DSM 3991, Bilophila wadsworthia ATCC 49260, Intestinibacter bartlettii DSM 16795, Acidaminococcus fermentans DSM 20731, Bilophila wadsworthia DSM 11045, Intestinimonas butyriciproducens DSM 26588, Acidaminococcus sp. HM-81, Blautia hansenii DSM 20583, Lactobacillus amylovorus DSM 20552, Adlercreutzia equolifaciens DSM 19450, Blautia hydrogenotrophica DSM 10507, Lactobacillus casei subsp.casei ATCC 393, Akkermansia muciniphila ATCC BAA-835, Blautia obeum DSMZ 25238, Lactobacillus casei subsp.casei ATCC 39539, Alistipes finegoldii DSM 17242, Blautia sp. HM-1032, Lactobacillus crispatus HM-370, Alistipes indistinctus DSM 22520, Blautia wexlerae DSM 19850, Lactobacillus johnsonii HM-643, Alistipes onderdonkii DSM 19147, Butyricimonas virosa DSM 23226, Lactobacillus parafarraginis HM-478, Alistipes putredinis DSM 17216, Butyrivibrio crossotus DSM 2876, Lactobacillus plantarum ATCC 14917, Alistipes senegalensis DSM 25460, Catenibacterium mitsuokai DSM 15897, Lactobacillus plantarum ATCC 202195, Alistipes shahii DSM 19121, Cetobacterium somerae DSM 23941, Lactobacillus ruminis ATCC 25644, Anaerobutyricum hallii DSM 3353, Clostridium asparagiforme DSM 15981, Lactobacillus ruminis DSM 20404, Anaerococcus lactolyticus DSM 7456, Clostridium bolteae DSM 15670, Lactobacillus ultunensis DSM 16048, Anaerofustis stercorihominis DSM 17244, Clostridium bolteae HM-1038, Lactococcus lactis Berridge DSM 20729, Anaerostipes caccae DSM 14662, Clostridium bolteae HM-318, Marvinbryantia formatexigens DSM 14469, Anaerotruncus colihominis DSM 17241, Clostridium cadaveris HM-1040, Megasphaera indica DSM 25562, Bacteroides caccae ATCC 43185, Clostridium citroniae HM-315, Megasphaera sp. DSM 102144、Bacteroides caccae HM-728、Clostridium hiranonis DSM 13275、Methanobrevibacter smithii DSM 11975、Bacteroides cellulolyticus DSM 14838、Clostridium hylemonas DSM 15053、Methanobrevibacter smithii DSM 2374、Bacteroides cellulolyticus HM-726、Clostridium harmless HM-173、Methanobrevibacter smithii DSM 2375、Bacteroides coprocola DSM 17136、Clostridium leptum DSM 753、Methanobrevibacter smithii DSM 861、Bacteroides coprophilus DSM 18228、Clostridium methylpentosum DSM 5476、Methanomassiliicoccus luminyensis DSM 25720、Bacteroides dorei DSM 17855、Clostridium saccharolyticum DSM 2544、Methanosphaera stadtmanae DSMZ 3091、Bacteroides dorei HM-29、Clostridium scindens DSM 5676、Mitsuokella multacida DSM 20544、Bacteroides dorei HM-718、Clostridium scindens VPI 12708、Odoribacter splanchnicus DSM 20712、Bacteroides eggerthii DSM 20697、Clostridium sp. ATCC 29733、Olsenella uli DSM 7084、Bacteroides eggerthii HM-210、Clostridium sp. DSM 4029、Oscillibacter sp. HM-1030、Bacteroides finegoldii DSM 17565、Clostridium sp. HM-634、Parabacteroides distasonis ATCC 8503、Bacteroides finegoldii HM-727、Clostridium sp.HM-635、Parabacteroides goldsteinii HM-1050、Bacteroides fragilis HM-20、Clostridium spiroforme DSM 1552、Parabacteroides johnsonii DSM 18315、Bacteroides fragilis HM-709、Clostridium sporogenes ATCC 15579、Parabacteroides johnsonii HM-731、Bacteroides fragilis HM-710、Clostridium sporogenes ATCC 17889、Parabacteroides merdae DSM 19495、Bacteroides intestinalis DSM 17393、Clostridium sporogenes DSM 767、Parabacteroides merdae HM-729、Bacteroides ovatus ATCC 8483、Clostridium. symbiosum HM-309、Parabacteroides merdae HM-730, Bacteroides ovatus HM-222, Clostridium symbiosum HM-319, Parabacteroides sp. HM-77, Bacteroides pectinophilus ATCC 43243, Collinsella aerofaciens ATCC 25986, Peptostreptococcus anaerobius DSM 2949, Bacteroides plebeius DSM 17135, Collinsella stercoris DSM 13279, Prevotella buccae HM-45, Bacteroides rodentium DSM 26882, Coprococcus catus ATCC 27761, Prevotella buccalis DSM 20616, Bacteroides salyersiae HM-725、Coprococcus comes ATCC 27758、Prevotella copri DSM 18205、Bacteroides sp. HM-18、Coprococcus eutactus ATCC 27759、Proteocatella sphenisci DSM 23131、Bacteroides sp. HM-19、Coprococcus eutactus ATCC 51897、Providencia rettgeri ATCC BAA-2525、Bacteroides sp. HM-23、Coprococcus sp. DSM 21649、Roseburia intestinalis DSM 14610、Bacteroides sp. HM-27、Desulfovibrio piger ATCC 29098、Roseburia inulinivorans DSM 16841、Bacteroides sp. HM-28、Dialister pneumosintes ATCC 51894、Ruminococcaceae sp. HM-79、Bacteroides sp. HM-58、Dorea formicigenerans ATCC 27755、Ruminococcus albus ATCC 27210、Bacteroides stercoris DSM 19555、Dorea longicatena DSM 13814、Ruminococcus bromii ATCC 27255、Bacteroides stercoris HM-1036、Eggerthella sp. DSM 11767、Ruminococcus bromii ATCC 51896、Bacteroides thetaiotaomicron ATCC 29148、Eggerthella sp. DSM 11863、Ruminococcus gauvreauii DSM 19829、Bacteroides uniformis ATCC 8492, Eggerthella sp. HM-1099, Ruminococcus gnavus ATCC 29149, Bacteroides vulgatus ATCC 8482, Ethanoligenens harbinense DSM 18485, Ruminococcus gnavus DSM 108212, Bacteroides vulgatus HM-720, Eubacterium eligens ATCC 27750, Ruminococcus gnavus HM-1056, Bacteroides xylanisolvens DSM 18836, Eubacterium rectale ATCC 33656, Ruminococcus lactaris ATCC 29176, Bifidobacterium adolescentis HM-633, Eubacterium siraeum DSM 15702, Ruminococcus lactaris HM-1057, Bifidobacterium angulatum HM-1189, Eubacterium ventriosum ATCC 27560, Ruminococcus torques ATCC 27756, Bifidobacterium ani malis DSM 20104, Faecalibacterium prausnitzii ATCC 27766, Slackia exigua DSM 15923, Bifidobacterium animalis subsp. Lactis DSMZ 10140, Faecalibacterium prausnitzii ATCC 27768, Slackia heliotrinireducens DSM 20476, Bifidobacterium bifidum ATCC 11863, Faecalibacterium prausnitzii DSM 17677, Solobacterium moorei DSM 22971, Bifidobacterium breve DSM 20213, Faecalibacterium prausnitzii HM-473, Streptococcus salivarius subsp. thermophilus ATCC BAA-491, Bifidobacterium catenulatum DSM 16992, Flavonifractor plautii HM-1044, Streptococcus thermophilus ATCC 14485, Bifidobacterium longum infantis ATCC 55813, Flavonifractor plautii HM-303, Subdoligranulum variabile DSM 15176, Bifidobacterium longum subsp. longum HM-845, Granulicatella adiacens ATCC 49175, Turicibacter sanguinis DSM The list may include one or more microbial strains selected from, but not limited to, 14220, Bifidobacterium longum subsp. longum HM-846, Holdemanella biformis DSM 3989, Tyzzerella nexilis DSM 1787, Bifidobacterium longum subsp. longum HM-847, Holdemania filiformis DSM 12042, Veillonella dispar ATCC 17748, Bifidobacterium longum subsp. longum HM-848, Hungatella (formerly Clostridium) hathewayi HM-308, Veillonella sp. HM-49, Bifidobacterium pseudocatenulatum DSM 20438, Hungatella hathewayi DSM 13479, and Veillonella sp. HM-64.

[0165] Conjugated primary bile acids are synthesized from cholesterol in the liver, concentrated and stored in the gallbladder, and secreted into the duodenum to facilitate the solubilization and absorption of dietary lipids. While a large portion of bile acids are reabsorbed and recirculated back to the liver via enterohepatic recirculation, a significant proportion (5%) escapes recirculation and enters the large intestine, where they are metabolized into secondary bile acids by the colonic microorganisms. Through microbial metabolism, the four conjugated primary bile acids produced in the liver—taurochenodeoxycholic acid (TCDCA), glycochenodeoxycholic acid (GCDCA), taurocholic acid (TCA), and glycocholic acid (GCA)—can be converted into over 100 molecules that significantly impact host physiological functions. The unique profile of the molecules produced is determined by the metabolic capacity of the colonic microbial community. As shown below, the first upstream metabolic step in secondary bile acid production is the decoupling of conjugated primary bile acids by microbial bile acid hydrolase (BSH). [ka]

[0166] In some embodiments, the microbial support community may comprise one or more microbial strains having robust and / or very abundant BSH activity, such that decoupling of primary bile acids can occur regardless of differences in host physiological function, diet, multiple active microorganisms present in the microbial consortium, or the existing composition of the conjugated bile acid pool.

[0167] In some embodiments, the supporting microbial communities include Alistipes indistinctus, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bacteroides xylanisolvens, Bifidobacterium angulatum, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum infantis, and Bifidobacterium This may include one or more microbial strains selected from pseudocatenulatum, Blautia obeum, Clostridium hylemonae, Enterococcus faecalis, Hungatella hathewayi, Lactobacillus acidophilus, Methanobrevibacter smithii, Parabacteroides distasonis, Parabacteroides goldsteini, Providencia rettgeri, Roseburia inulinivorans, Ruminococcus bromii, Ruminococcus gnavus, and Turicibacter sanguinis.

[0168] In some embodiments, the disclosure provides a microbial consortium comprising several active microorganisms that shift the bile acid pool from the 7α-dehydroxylation products LCA and DCA by converting CA and CDCA into alternative secondary bile acids. For example, in some embodiments, the microbial consortium disclosed herein comprises microbial strains having robust 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 7β-hydroxysteroid dehydrogenase (7β-HSDH) activity. As shown below, 7α-HSDH produces 7-oxo-CA and 7-oxo-CDCA intermediates, and 7β-HSDH converts CA and CDCA to 7β-CA and ursodeoxycholic acid (UDCA). [ka]

[0169] In some embodiments, the microbial consortium provided herein comprises multiple active microorganisms expressing 7α-HSDH, selected from one or more of Acinetobacter calcoaceticusi, Bacteroides thetaiotaomicron, Bacteroides intestinalis, Bacteroides fragilis, Eggerthella lenta, and Ruminococcus sp. In some embodiments, the microbial consortium provided herein comprises multiple active microorganisms expressing 7β-HSDH, selected from one or both of Ruminococcus torques and Peptostreptococcus productus. Fermentable and synthetic microorganisms

[0170] In some embodiments, the microbial consortium of the present invention further comprises fermentable microorganisms that metabolize a fermentation substrate to produce one or more fermentation products. For example, in some embodiments, the fermentation product is a second metabolite for one or more of a plurality of active microorganisms. In some embodiments, the fermentation product is a metabolite for one or more of supporting microorganisms. In some embodiments, the fermentation substrate is a polysaccharide, and the fermentation product produced is one or more of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H2, and CO2. In some embodiments, the fermentation substrate is an amino acid, and the resulting fermentation product is one or more of the following: acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, floleate, 3-(1H-indole-3-yl)propanoate, 5-aminopentanoate, H2, H2S, and CO2.

[0171] In some embodiments, the microbial consortium of the present invention further includes a synthetic microorganism that catalyzes a synthesis reaction to produce one or more synthetic products by combining one or more metabolites produced by a plurality of active microorganisms and one or more fermentation products produced by a fermentative microorganism. In some embodiments, the fermentation products produced by the fermentative microorganism are a third metabolic substrate for the synthetic microorganism. In some embodiments, one or more synthetic products are a second metabolic substrate for the plurality of active microorganisms. In some embodiments, one or more synthetic products are a fourth metabolic substrate for the fermentative microorganism.

[0172] In some embodiments, synthetic microorganisms catalyze the synthesis of one or more of the following: methane from H2 and CO2, methane from formate and H2, acetate from H2 and CO2, acetate from formate and H2, acetate and sulfides from H2, CO2 and sulfate, propionate and CO2 from succinate, succinate from H2 and fumarate; succinate from formate and fumarate, and butyrate, acetate, H2 and CO2 from lactate.

[0173] In some embodiments, the fermentative microorganism may be, but is not limited to, Bacteroides thetaiotaomicron or Bacteroides vulgatus. In some embodiments, the synthetic microorganism may be, but is not limited to, Methanobrevibacter smithii or Methanomassiliicoccus luminyensis.

[0174] In some embodiments, the fermenting microorganism is selected from Bacteroides thetaiotaomicron strain having a 16S sequence that is at least 80% identical to SEQ ID NO: 20, SEQ ID NO: 76, SEQ ID NO: 139, or SEQ ID NO: 280. In some embodiments, the fermenting microorganism is selected from Bacteroides vulgatus strain having a 16S sequence that is at least 80% identical to SEQ ID NO: 39, SEQ ID NO: 111, SEQ ID NO: 121, SEQ ID NO: 173, SEQ ID NO: 211, SEQ ID NO: 308, SEQ ID NO: 321, or SEQ ID NO: 326. In some embodiments, the synthetic microorganism is selected from Methanobrevibacter smithii strain having a 16S sequence that is at least 80% identical to SEQ ID NO: 292.

[0175] In some embodiments, the fermenting microorganism is selected from Bacteroides thetaiotaomicron strains having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to SEQ ID NO: 20, SEQ ID NO: 76, SEQ ID NO: 139, or SEQ ID NO: 280. In some embodiments, the fermenting microorganism is selected from Bacteroides vulgatus strains having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to SEQ ID NO: 39, SEQ ID NO: 111, SEQ ID NO: 121, SEQ ID NO: 173, SEQ ID NO: 211, SEQ ID NO: 308, SEQ ID NO: 321, or SEQ ID NO: 326. In some embodiments, the synthetic microorganism is selected from Methanobrevibacter smithii strains having a 16S sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 292.

[0176] In some embodiments, the microbial consortium disclosed herein comprises active microorganisms, fermentable microorganisms, and synthetic microorganisms in colony morphology unit (CFU) ratios selected from 1:1:1, 1:2:1, 1:1:2, 2:1:1, 2:1:2, 1:3:1, 1:1:3, 3:1:1, 3:1:3, 2:3:2, 2:2:3, 3:2:2, 3:2:3, 1:5:1, 1:1:5, 5:1:1, 5:1:5, 2:5:2, 2:2:5, 5:2:2, 5:2:5, 3:5:3, 3:3:5, 5:3:3, 5:3:5, 4:5:4, 4:4:5, 5:4:4, and 5:4:5. In some embodiments, the proprietary dosage forms of the microorganism consortium of this disclosure contain active microorganisms, fermentable microorganisms, and synthetic microorganisms in total CFU amounts of approximately one, two, three, four, five, six, seven, eight, nine, or ten orders of magnitude relative to each other. In other embodiments, the proprietary dosage forms of the microorganism consortium of this disclosure contain active microorganisms, fermentable microorganisms, and synthetic microorganisms in total CFU amounts of approximately two orders of magnitude relative to each other. In some embodiments, the proprietary dosage forms of the microorganism consortium of this disclosure contain active microorganisms and fermentable microorganisms in total CFU amounts of approximately one, two, three, four, five, six, seven, eight, nine, or ten orders of magnitude relative to each other. In some embodiments, the proprietary dosage forms of the microorganism consortium of this disclosure contain active microorganisms and synthetic microorganisms in total CFU amounts of one, about two, about three, about four, about five, about six, about seven, about eight, about nine, or about ten orders of magnitude relative to each other. In some embodiments, the proprietary dosage forms of the microorganism consortium of this disclosure contain fermentable microorganisms and synthetic microorganisms in total CFU amounts of one, about two, about three, about four, about five, about six, about seven, about eight, about nine, or about ten orders of magnitude relative to each other. Microbial Consortium Design

[0177] In some embodiments, the microbial consortium disclosed herein is designed to meet one or more of the following criteria: (i) The ability to eliminate or reduce the level of a primary metabolic substrate that causes or contributes to disease in animals; (ii) The ability to metabolize or convert one or more metabolites produced by the metabolism of the first metabolite; (iii) The ability to metabolize one or more nutrients typically found in the human diet; (iv) The ability to perform unique and potentially beneficial biological functions in the gastrointestinal (GI) tract (e.g., bile salt hydrolase activity or butyrate production); (v) The ability to engraft in various biological niches and physical and metabolic compartments of animal GI tubules; (vi) The biomass can be increased by attachment to GI tubes; (vii) The ability to maintain long-term stability within the GI tube of animals; (viii) The ability to increase the flow rate of the precursor of the first metabolite into the biochemical pathway that converts the precursor into a metabolite that is not the first metabolite; (ix) Diversity of constituent microbial species across one or more taxonomic phyla; and (x) Natural proliferation of constituent microbial species in GI tubes of healthy adults.

[0178] In some embodiments, the microbial consortium of the present invention is designed to comprise a plurality of active microorganisms capable of metabolizing a first metabolite that causes or contributes to disease in animals. For example, in some embodiments, the first metabolite can be selected from, but is not limited to, oxalates and bile acids (e.g., litcholic acid (LCA), deoxycholic acid (DCA)). In some embodiments, the microbial consortium is designed to metabolize the first metabolite over a variety of pH ranges found in the GI tube (e.g., pH 4-8). In some embodiments, the microbial consortium is designed to metabolize the first metabolite in the presence of various concentrations of the first metabolite when they are present in different regions of the GI tube.

[0179] For example, when designing active microorganisms to be included in a microbial consortium for the treatment of primary or secondary hyperoxaluria, the ability of candidate microorganisms to metabolize oxalates in a sample can be measured using an in vitro colorimetric assay (e.g., as described in Example 3 below). Microorganisms capable of reducing the concentration of oxalates present in a sample by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, or at least 80% can be included in the microbial consortium disclosed herein.

[0180] In other embodiments, the effectiveness of the designed microbial consortium of the present invention in reducing the concentration of oxalates present in blood, serum, bile, feces, or urine samples when administered to a subject can be measured using in vivo mouse assays. The concentration of oxalates in blood, serum, bile, feces, or urine samples can be measured using liquid chromatography-mass spectrometry (LC-MS) methods, as described in Example 4 below. Microbial consortia capable of reducing blood, serum, bile, feces, or urine oxalate levels by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, or at least 80% compared to levels in untreated controls or pre-administration levels may be candidates for further evaluation for the treatment of primary or secondary hyperoxaluria.

[0181] In some embodiments, the microbial consortium disclosed herein is designed to metabolize one or more metabolites produced by multiple active microorganisms, the one or more metabolites being inhibited by the metabolism of the multiple active microorganisms. In some embodiments, the microbial consortium is designed to maximize the consumption and / or production of a defined set of metabolites using a minimum number of strains. For example, in some embodiments, the microbial consortium is designed to include microorganisms that metabolize formate produced by multiple active microorganisms, the presence of formate inhibiting the metabolism of oxalate by the multiple active microorganisms, for example, in a negative feedback loop. In some embodiments, the microbial consortium is designed to include microorganisms that catalyze the fermentation of polysaccharides to one or more of the following: acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H2, and CO2. In some embodiments, the microbial consortium is designed to catalyze the fermentation of amino acids into one or more of the following: acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, fluoretate, 3-(1H-indole-3-yl)propanoate, 5-aminopentanoate, H2, H2S, and CO2. In some embodiments, the microbial consortium is designed to catalyze the synthesis of one or more of the group consisting of methane from H2 and CO2, methane from formate and H2, acetate from H2 and CO2, acetate from formate and H2, acetate and sulfides from H2, CO2 and sulfate, propionate and CO2 from succinate, and succinate from H2 and fumarate; succinate from formate and fumarate, as well as butyrate, acetate, H2 and CO2 from lactate.In some embodiments, the microbial consortium is designed to catalyze the decoupling of conjugated bile acids for the production of primary bile acids, the conversion of cholic acid (CA) to 7-oxocholic acid, the conversion of 7-oxocholic acid to 7-betacholic acid (7-betaCA), the conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and / or the conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA).

[0182] In some embodiments, the microbial consortium disclosed herein is designed to metabolize one or more metabolites produced by multiple active microorganisms, the one or more metabolites being inhibited by the metabolism of the multiple active microorganisms. In some embodiments, the microbial consortium is designed to maximize the consumption and / or production of a defined set of metabolites using a minimum number of strains. For example, in some embodiments, the microbial consortium is designed to include microorganisms that metabolize formates produced by multiple active microorganisms, the presence of formates inhibiting the metabolism of oxalates by the multiple active microorganisms, for example, in a negative feedback loop. In some embodiments, the microbial consortium is designed to include microorganisms that catalyze the fermentation of polysaccharides into one or more of the following: acetate, propionate, succinate, lactate, butyrate, formates, H2, and CO2. In some embodiments, the microbial consortium is designed to catalyze the fermentation of amino acids into one or more of the following: acetate, propionate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, H2, H2S, and CO2. In other embodiments, the microbial consortium is designed to include microorganisms that catalyze the synthesis of one or more of the following: methane from formate and H2, acetate from H2 and CO2, acetate from formate and H2, acetate and sulfides from H2, CO2 and sulfate, propionate and CO2 from succinate, succinate from H2 and fumarate; succinate from formate and fumarate, and butyrate, acetate, H2 and CO2 from lactate.

[0183] In some embodiments, the microbial consortium is designed to include microorganisms capable of metabolizing one or more nutrients typically found in a wide range of human diets. For example, in some embodiments, the microbial consortium may include oxalates, fructans, inulin, glucuronoxylan, arabinoxylan, glucomannan, β-mannan, dextran, starch, arabinan, xyloglucan, galacturonan, β-glucan, galactomannan, rhamnogalacturonan I, rhamnogalacturonan II, arabinogalactan, mucin O-linked glycans, yeast α-mannan, yeast β-glucan, chitin, alginates, porphyrin, laminarin, carrageenan, agarose, alternan, levan, xanthan gum, galactooligosaccharides, hyaluronan, chondroitin sulfate, dermatan sulfate, heparin sulfate, keratan sulfate, phenylalanine, tyrosine, tryptophan, leucine, and valine. The microbial consortium is designed to include microorganisms capable of metabolizing one or more of the following: isoleucine, glycine, proline, asparagine, glutamine, aspartate, glutamate, cysteine, lysine, arginine, serine, methionine, alanine, arginine, histidine, ornithine, citrulline, carnitine, hydroxyproline, cholic acid, chenodeoxycholic acid, taurochenodeoxycholic acid, glycochenodeoxycholic acid, cholesterol, cinnamic acid, coumaric acid, sinapic acid, ferulic acid, caffeic acid, quinic acid, chlorogenic acid, catechin, epicatechin, gallic acid, pyrogallol, catechol, quercetin, myricetin, campherol, luteolin, apigenin, naringenin, and hesperidin. In some embodiments, the microbial consortium is designed to increase the consumption of dietary carbon and energy sources. In other embodiments, the microbial consortium is designed to enhance the production or consumption of host metabolites, including bile acids, sugars, amino acids, vitamins, short-chain fatty acids, and gases.

[0184] In some embodiments, the microbial consortium is designed to include microorganisms that have potentially beneficial biological functions in the GI tubule. For example, the microbial consortium is designed to include microbial strains with robust and / or very abundant bile salt hydrolase (BSH) activity, such that uncoupling of primary bile acids can occur despite differences in host physiological function, diet, multiple active microorganisms present in the microbial consortium, or existing compositions of the conjugated bile acid pool. In other embodiments, the microbial consortium is designed to include microbial strains capable of producing butyrates from the fermentation of dietary fiber in the GI tubule, contributing to intestinal homeostasis, energy metabolism, anti-inflammatory processes, enhancement of intestinal barrier function, and mucosal immunity.

[0185] In some embodiments, the microbial consortium described herein is designed to colonize various biological niches and physical and metabolic compartments within the GI tubules of animals (e.g., humans).

[0186] As used herein, “engraftment” (and its grammatical variant, e.g., “to engraft”) refers to the ability of a microbial strain or community to establish itself in one or more niches in the intestines of an animal. Operationally, a microbial strain or consortium is “engrafted” if evidence of its establishment can be obtained after administration. In some embodiments, this evidence is obtained by molecular identification of a sample taken from an animal (e.g., matrix-assisted laser desorption / ionization time-of-flight mass spectrometry (MALDI-TOF MS), 16S rRNA sequencing, or genome sequencing). In some embodiments, the sample is a fecal sample. In some embodiments, the sample is a biopsy sample taken from the intestines of an animal (e.g., from a location along the digestive tract of the animal). Engraftment may be transient or persistent. In some embodiments, temporary engraftment means that the microbial strain or community is no longer detectable in the administered animal after approximately 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 6 months, 8 months, 10 months, 1 year, 1.5 years, or 2 years.

[0187] For example, a microbial consortium is designed to colonize one or more niches in the digestive tract, whose composition differs due to several environmental factors, including but not limited to specific physical compartments of the digestive tract, the chemical and biochemical properties of the niche environment (e.g., digestive tract motility, pH), the metabolic substrate composition of the niche environment, and other coexisting microbial species. To analyze the colonization of the designed microbial consortia described herein, an in vivo assay, such as that described in Example 8, can be used, in which a fecal sample from a treated mouse is analyzed for the presence of specific microbial strains constituting the microbial consortium by whole-genome shotgun sequencing of microbial DNA extracted from the fecal pellet and sequence reading data mapped against a comprehensive database of complete sequenced genomes for all defined microbial strains constituting the microbial consortium.

[0188] In some embodiments, the microbial consortium described herein is designed to include microorganisms that, when colonized on the GI tubes of an animal (e.g., a human), support the growth of one or more other microorganisms in the consortium, thereby increasing their biomass. For example, in some embodiments, the microbial consortium is designed to promote the co-culturing potential and / or ecological stability of one or more microbial strains in the consortium.

[0189] In some embodiments, the microbial consortium described herein is designed to contain one or more microorganisms that maintain long-term stability within the GI tubule of an animal (e.g., a human) despite temporary or prolonged changes in the gastrointestinal niche due to dietary changes, the presence or absence of disease, or other physiological or environmental factors. In some embodiments, long-term stability of a community means that the microbial consortium can survive (i.e., maintain its engrafted state) within the GI tubule of an animal after a microbial challenge. In some embodiments, long-term stability may be defined as stability in which at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of the defined microbial strains are detectable by metagenomic analysis, provided that sufficient time is given for the microbial consortium to allow colonization of the microbial challenge strains within the engrafted GI tubule of the animal. For example, in some embodiments, the metagenomic analysis includes whole-genome shotgun sequencing analysis.

[0190] In other embodiments, the long-term stability of a community refers to the characteristics of the microbial strains comprising the consortium that maintain a metabolic phenotype over a period of time or after a microbial challenge. For example, in some embodiments, defined microbial strains comprising the consortium can maintain a metabolic phenotype for at least one week, at least two weeks, at least three weeks, at least four weeks, at least six weeks, at least eight weeks, at least ten weeks, at least twelve weeks, at least four months, at least six months, at least eight months, at least ten months, at least one year, at least one and a half years, or at least two years.

[0191] In some embodiments, long-term stability may be defined as the stability with which defined microbial strains constituting the consortium maintain one or more metabolic phenotypes, such as mucin degradation, polysaccharide fermentation, hydrogen utilization, succinate metabolism, butyrate production, amino acid metabolism, bile acid metabolism, CO2 fixation, formate metabolism, methane production, acetic acid production, hydrogen production, or propionate production, over a period of time or after a microbial challenge.

[0192] In some embodiments, the microbial consortium is designed to include one or more microorganisms that can increase the flow of precursors of the first metabolite into the biochemical pathway that converts the precursors into metabolites that are not the first metabolite. For example, in some embodiments, the microbial consortium may be designed to include microbial strains having robust 7α-HSDH and 7β-HSDH activity that direct precursors of the first metabolites DCA and LCA (CA and CDCA, respectively) into the biochemical pathway that produces the lower 7β-CA and UDCA.

[0193] In some embodiments, the microbial consortium described herein is designed to include representative microbial strains isolated from fecal samples of healthy donors, representing microbial species belonging to a wide variety of taxonomic phyla, including Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, and Euryarchaeota, excluding species known to be associated with pathogens. In some embodiments, microbial consortia with phylogenetic diversity are less susceptible to perturbations in the GI environment and colonize more stably. For example, in some embodiments, the microbial consortium may be designed to include one or more microbial species from Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, or Euryarchaeota.

[0194] In some embodiments, the microbial consortium may be designed to include one or more microbial species from Bacteroidetes and Firmicutes, Bacteroidetes and Actinobacteria, Bacteroidetes and Proteobacteria, Bacteroidetes and Verrucomicrobia, Bacteroidetes and Euryarchaeota, Firmicutes and Actinobacteria, Firmicutes and Proteobacteria, Firmicutes and Verrucomicrobia, Firmicutes and Euryarchaeota, Actinobacteria and Proteobacteria, Actinobacteria and Verrucomicrobia, Actinobacteria and Euryarchaeota, Proteobacteria and Verrucomicrobia, Proteobacteria and Euryarchaeota, or Verrucomicrobia and Euryarchaeota.

[0195] In some embodiments, the microbial consortium includes Bacteroidetes, Firmicutes, and Actinobacteria; Bacteroidetes, Firmicutes, and Proteobacteria; Bacteroidetes, Firmicutes, and Verrucomicrobia; Bacteroidetes, Firmicutes, and Euryarchaeota; Bacteroidetes, Actinobacteria, and Proteobacteria; Bacteroidetes, Actinobacteria, and Verrucomicrobia; Bacteroidetes, Actinobacteria, and Euryarchaeota; Bacteroidetes, Proteobacteria, and Euryarchaeota; Bacteroidetes, Verrucomicrobia, and It may be designed to contain one or more microbial species from Euryarchaeota; Firmicutes, Actinobacteria, and Proteobacteria; Firmicuates, Actinobacteria, and Verrucomicrobia; Firmicuates, Actinobacteria, and Euryarchaeota; Firmicuates, Proteobacteria, and Verrucomicrobia; Firmicuates, Proteobacteria, and Euryarchaeota; Firmicutes, Verrucomicrobia, and Euryarchaeota; Actinobacteria, Proteobacteria, and Verrucomicrobia; Actinobacteria, Proteobacteria, and Euryarchaeota; or one or more microbial species from Proteobacteria, Verrucomicrobia, and Euryarchaeota.

[0196] In some embodiments, the microbial consortium includes Bacteoidetes, Firmicutes, Actinobacteria, and Proteobacteria; Bacteoidetes, Firmicutes, Actinobacteria, and Verrucomicrobia; Bacteoidetes, Firmicutes, Actinobacteria, and Euryarchaeota; Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia; Bacteroidetes, Actinobacteria, Proteobacteria, and Euryarchaeota; Bacteroide Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota; Firmicutes, Actinobacteria, Proteobacteria, and Verrucomicrobia; Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota; or may be designed to contain one or more microbial species from Actinobacteria, Proteobacteria, Verrucomicrobia, and Euryarchaeota.

[0197] In some embodiments, the microbial consortium may be designed to include one or more microbial species from Bacteoidetes, Firmicutes, Actinobacteria, Proteobacteria, and Verrucomicrobia; Bacteoidetes, Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota; Bacteoidetes, Firmicutes, Actinobacteria, Verrucomicrobia, and Euryarchaeota; Bacteoidetes, Firmicutes, Proteobacteria, Verrucomicrobia, and Eurarchaeota; or one or more microbial species from Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, and Eurarchaeota.

[0198] In some embodiments, the microbial consortium may be designed to include one or more microbial species from Bacteoidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, and Euryarchaeota.

[0199] For example, in some embodiments, the microbial consortium can be designed to include one or more Bacteroidetes strains listed in Table 4. In some embodiments, the microbial consortium can be designed to include a Bacteroidetes strain having a 16S sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the Bacteroidetes microorganisms listed in Table 4. In some embodiments, the microbial consortium can be designed to include a Bacteroidetes strain having a 16S sequence that is at least 80% identical to any one of the Bacteroidetes microorganisms listed in Table 4.

[0200] In some embodiments, the microbial consortium can be designed to include one or more Firmicutes strains listed in Table 4. In some embodiments, the microbial consortium can be designed to include a Firmicutes strain having a 16S sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the Firmicutes microorganisms listed in Table 4. In some embodiments, the microbial consortium can be designed to include a Firmicutes strain having a 16S sequence that is at least 80% identical to any one of the Firmicutes microorganisms listed in Table 4.

[0201] In some embodiments, the microbial consortium can be designed to include one or more Actinobacteria strains listed in Table 4. In some embodiments, the microbial consortium can be designed to include an Actinobacteria strain having a 16S sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the Actinobacteria microorganisms listed in Table 4. In some embodiments, the microbial consortium can be designed to include an Actinobacteria strain having a 16S sequence that is at least 80% identical to any one of the Actinobacteria microorganisms listed in Table 4.

[0202] In some embodiments, the microbial consortium can be designed to include one or more Proteobacteria strains listed in Table 4. In some embodiments, the microbial consortium can be designed to include a Proteobacteria strain having a 16S sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the Proteobacteria microorganisms listed in Table 4. In some embodiments, the microbial consortium can be designed to include a Proteobacteria strain having a 16S sequence that is at least 80% identical to any one of the Proteobacteria microorganisms listed in Table 4.

[0203] In some embodiments, the microbial consortium may be designed to include one or more Verrucomicrobia strains listed in Table 4. In some embodiments, the microbial consortium may be designed to include Verrucomicrobia strains having a 16S sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any of the Verrucomicrobia microorganisms listed in Table 4. In some embodiments, the microbial consortium may be designed to include Verrucomicrobia strains having a 16S sequence that is at least 80% identical to any of the Verrucomicrobia microorganisms listed in Table 4.

[0204] In some embodiments, the microbial consortium may be designed to include Methonobrevibacter smithii. In some embodiments, the microbial consortium may be designed to include a Methonobrevibacter smithii strain containing a 16S sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 292. In some embodiments, the microbial consortium may be designed to include a Methonobrevibacter smithii strain containing a 16S sequence that is at least 80% identical to SEQ ID NO: 292.

[0205] In some embodiments, the microbial consortium is designed so that when administered to a subject, multiple active microorganisms and their supporting communities have one or more synergistic effects. For example, in some embodiments, administration of a microbial consortium containing multiple active microorganisms in combination with supporting communities results in improved metabolism for a first metabolic substrate compared to the metabolism achieved by administering either the multiple active microorganisms or the supporting communities alone. For example, in some embodiments, administration of a microbial consortium results in improved oxalate metabolism in a subject (measured, for example, by urinary oxalate levels) compared to a subject administered either the multiple active microorganisms or the supporting communities alone. In other embodiments, administration of a microbial consortium results in enhanced conversion of primary bile acids (e.g., DCA and / or LCA) in a subject compared to a subject administered either the multiple active microorganisms or the supporting communities alone. In some embodiments, a microbial composition containing multiple active microorganisms in combination with a microbial support community results in improved engraftment to the GI than achieved by administering either the multiple active microorganisms or the microbial support community alone. In some embodiments, a microbial composition containing multiple active microorganisms in combination with a microbial support community results in a greater biomass in the GI tube than achieved by administering either the multiple active microorganisms or the microbial support community alone. In some embodiments, a microbial composition containing multiple active microorganisms in combination with a microbial support community results in improved long-term stability than achieved by administering either the multiple active microorganisms or the microbial support community alone. In some embodiments, a microbial composition containing multiple active microorganisms in combination with a microbial support community results in improved clinical efficacy in treating diseases than achieved by administering either the multiple active microorganisms or the microbial support community alone.

[0206] In some embodiments, the microbial consortium contains at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 4, each containing 20-300, 20-250, 20-200, 20-190, 20-180, 20-170, 20-160, 20-150, 20-140, 20-130, 20-120, 20-110, 20-100, 20-90, 20-80, 20- 70, 20-60, 20-50, 50-300, 50-250, 50-200, 50-190, 50-180, 50-170, 50-160, 50-150, 50-140, 50-130, 50-120, 50-110, 50-100, 50-90, 50-80, 50-70, 50-60, 10 Designed to contain microbial strains of 0-300, 100-250, 100-200, 100-190, 100-180, 100-170, 100-160, 100-150, 100-140, 100-130, 100-120, 100-110, 70-80, 80-90, or 150-160.

[0207] In some embodiments, the microbial consortium contains at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 22, with each containing 20-160, 30-160, 40-160, 50-160, 60-160, 70-160, 80-160, 90-160, 100-160, 110-160, 120-160, 130-160, 140-160, 150-160, and 20-1 40, 30-140, 40-140, 50-140, 60-140, 70-140, 80-140, 90-140, 100-140, 110-140, 120-140, 130-140, 20-120, 30-120, 40-120, 50-120, 60-120, 70-120, 80-120, Designed to contain 90-120, 100-120, 110-120, 20-100, 30-100, 40-100, 50-100, 60-100, 70-100, 80-100, 90-100, 20-80, 30-80, 40-80, 50-80, 60-80, or 70-80 microbial strains.

[0208] In some embodiments, the microbial consortium is designed to include 20-104, 40-104, 60-104, 80-104, 100-104, 20-80, 40-80, 60-80, 20-60, or 40-60 microbial strains, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 23.

[0209] In some embodiments, the microbial consortium is designed to include 20-104, 40-104, 60-104, 80-104, 100-104, 20-80, 40-80, 60-80, 20-60, or 40-60 microbial strains, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 24.

[0210] In some embodiments, the microbial consortium contains at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 20, specifically 20-158, 30-158, 40-158, 50-158, 60-158, 70-158, 80-158, 90-158, 100-158, 110-158, 120-158, 130-158, 140-158, 150-158, and 20-1 40, 30-140, 40-140, 50-140, 60-140, 70-140, 80-140, 90-140, 100-140, 110-140, 120-140, 130-140, 20-120, 30-120, 40-120, 50-120, 60-120, 70-120, 80-120, Designed to contain 90-120, 100-120, 110-120, 20-100, 30-100, 40-100, 50-100, 60-100, 70-100, 80-100, 90-100, 20-80, 30-80, 40-80, 50-80, 60-80, or 70-80 microbial strains.

[0211] In some embodiments, the microbial consortium contains at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 16, such as 20-152, 30-152, 40-152, 50-152, 60-152, 70-152, 80-152, 90-152, 100-152, 110-152, 120-152, 130-152, 140-152, 150-152, and 20-1 40, 30-140, 40-140, 50-140, 60-140, 70-140, 80-140, 90-140, 100-140, 110-140, 120-140, 130-140, 20-120, 30-120, 40-120, 50-120, 60-120, 70-120, 80-120, Designed to contain 90-120, 100-120, 110-120, 20-100, 30-100, 40-100, 50-100, 60-100, 70-100, 80-100, 90-100, 20-80, 30-80, 40-80, 50-80, 60-80, or 70-80 microbial strains.

[0212] In some embodiments, the microbial consortium is designed to include 20-88, 40-88, 60-88, 80-88, 20-80, 40-80, 60-80, or 40-60 microbial strains, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 17.

[0213] In some embodiments, the microbial consortium is designed to include 20-89, 40-89, 60-89, 80-89, 20-80, 40-80, 60-80, or 40-60 microbial strains, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 18.

[0214] In some embodiments, the microbial consortium is designed to include 20-75, 40-75, 60-75, 80-75, 20-60, or 40-60 microbial strains, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 19.

[0215] In some embodiments, the microbial consortium includes Actinobacteria of 2-51, 5-51, 10-51, 20-51, 30-51, or 40-51, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 4; 10-102, 20-102, 30-102, 40-102, 50-102, 60-102, 70-102, 80-102, 90-102, 10-50, 20-50, 30-5 Designed to include 0 or 40-50 Bacteroidetes; 1 or 2 Euryacrchaeota; 20-197, 40-197, 60-197, 80-197, 100-197, 120-197, 140-197, 160-197, 180-197, 20-150, 40-150, 60-150, 80-150, 100-150, 120-150, 140-150, 20-100, 40-100, 60-100, or 80-100 Firmicutes; 2-24, 8-24, 12-24, 18-24, or 20-24 Proteobacteria; and 1 Verrucomicrobia.

[0216] In some embodiments, the microbial consortium comprises 2-20, 5-20, 10-20, or 15-20 Actinob, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 16. Designed to include: Acteria; 2-48, 10-48, 20-48, 30-48, 40-48 Bacteroidetes; 2-76, 10-76, 20-76, 30-76, 40-76, 50-76, 60-76, 70-76, 2-50, 10-50, 20-50, 30-50, 40-50 Firmicutes; 2-7 Proteobacteria; and 1 Verrucomicrobia.

[0217] In some embodiments, the microbial consortium is designed to include 2-22, 10-22, or 20-22 Actinobacteria; 2-27, 10-27, or 20-27 Bacteroidetes; 2-29, 10-29, or 20-29 Firmicutes; 1-9 Proteobacteria; and one Verrucomicrobia, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 17.

[0218] In some embodiments, the microbial consortium is designed to include 2-18 or 10-18 Actinobacteria; 2-27, 10-27, or 20-27 Bacteroidetes; 2-38, 10-38, 20-38, 30-38 Firmicutes; and 2-6 Proteobacteria, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 18.

[0219] In some embodiments, the microbial consortium is designed to include 2–7 Actinobacteria; 2–20 or 10–20 Bacteroidetes; 2–38, 10–38, 20–38, or 30–38 Firmicutes; 2–8 Proteobacteria; and one Verrucomicrobia, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 19.

[0220] In some embodiments, the microbial consortium comprises 2 to 20 or 10 to 20 Actinobacteria, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 20; 2 to 42 Designed to include 10-42, 20-42, 30-42, or 40-42 Bacteroidetes; 2-84, 10-84, 20-84, 30-84, 40-84, 50-84, 60-84, 70-84, 80-84, 2-50, 10-50, 20-50, 30-50, or 40-50 Firmicutes; 2-11 Proteobacteria; and 1 Verrucomicrobia.

[0221] In some embodiments, the microbial consortium is designed to include 2 - 20, or 10 - 20 Actinobacteria; 2 - 44, 10 - 44, 20 - 44, 30 - 44 or 40 - 44 Bacteroidetes; 1 or 2 Euryarcheota; 2 - 83, 10 - 83, 20 - 83, 30 - 83, 40 - 83, 50 - 83, 60 - 83, 70 - 83, 80 - 83, 2 - 50, 10 - 50, 20 - 50, 30 - 50, or 40 - 50 Firmicutes; 2 - 10 Proteobacteria; and 1 Verrucomicrobia, each having a 16S sequence that is at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the microorganisms listed in Table 22.

[0222] In some embodiments, the microbial consortium is designed to include 2 - 15, or 10 - 15 Actinobacteria; 2 - 25, 10 - 25, or 20 - 25 Bacteroidetes; 2 - 55, 10 - 55, 20 - 55, 30 - 55, 40 - 55, 50 - 55, 2 - 25, 10 - 25, or 20 - 25 Firmicutes; 2 - 8 Proteobacteria; and 1 Verrucomicrobia, each having a 16S sequence that is at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the microorganisms listed in Table 23.

[0223] In some embodiments, the microbial consortium is designed to include 2–11 Actinobacteria; 2–28, 10–28, or 20–28 Bacteroidetes; 1 Euryarchaeota; 2–56, 10–56, 20–56, 30–56, 40–56, 50–56, 2–25, 10–25, or 20–25 Firmicutes; 2–7 Proteobacteria; and 1 Verrucomicrobia, each containing at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical 16S sequences to any one of the microorganisms listed in Table 24. Isolation and propagation of microbial strains

[0224] Active and supporting microbial strains can be obtained from human donor fecal samples or purchased from the United States Cell Culture and Cell Lineage Preservation Center (ATCC; www.atcc.org), the Leibniz Society DSMZ (www.dsmz.de), or BEI Resources (www.beiresources.org). Microbial strains purchased from depositaries can be cultured according to the depositary's instructions for use, and microbial strains derived from human donors can be cultured according to the culture conditions listed in Table 3 below.

[0225] Fecal donors can be selected based on multiple criteria, including medical history questionnaires, physical examinations, and blood and stool tests to assess the absence of pathogens. Once fecal samples are collected from donors, serially diluted aliquots of the fecal samples can be prepared, and these aliquots can be plated onto various microbial culture media suitable for the growth of anaerobic organisms. The fecal samples can then be cultured in an anaerobic chamber (5% CO2, 5% H2, 90% N2) to isolate microbial strains. Specific enrichment techniques can be performed on species with specific metabolic capabilities, such as consumption of oxalates or bile acids, or tolerance to them. To enrich strains with oxalate metabolic capabilities, serially diluted aliquots of fecal samples can be plated onto agar growth media supplemented with various concentrations of potassium oxalate (20 mM, 40 mM, 80 mM, 160 mM, or 200 mM). To enrich species capable of metabolizing bile acids, serially diluted fecal samples can be plated onto growth medium supplemented with 2% bile. Archaea can be isolated by diluting fecal samples and plating them onto culture medium containing a mixture of antibiotics lethal to both Gram-positive and Gram-negative bacteria. Microbial strains can be identified by either 16S rRNA gene sequencing or proteomic fingerprinting using high-throughput matrix-assisted laser desorption / ionization time-of-flight mass spectrometry (MALDI-TOF MS).

[0226] In some embodiments, the method for producing a microbial consortium described herein includes the step of culturing each of several active microorganisms and supporting microorganisms individually, and then combining the microorganisms to form a consortium. In other embodiments, the method for producing a microbial consortium described herein includes the step of culturing all of the several active microorganisms and supporting microorganisms together. In yet another embodiment, the method for producing a microbial consortium includes the step of culturing one or more microbial strains individually, co-culturing two or more microbial strains having suitable culture and growth conditions, and then combining the individually cultured microbial strains with the defined co-culturned microbial strains to form a microbial consortium. In yet another embodiment, the method for producing a microbial consortium includes the step of culturing one or more microbial strains individually, co-culturing two or more microbial strains having suitable culture and growth conditions, and then combining the individually cultured microbial strains with the defined co-culturned microbial strains to form a microbial consortium. Pharmaceutical composition

[0227] This disclosure also provides pharmaceutical compositions containing an effective amount of the microbial consortium described herein. The compositions can be formulated for use in various delivery systems. One or more physiologically acceptable buffers or carriers may also be included in the composition for a suitable formulation. Suitable formulations for use in this disclosure are described in Remington's Pharmaceutical Sciences, Mack Publishing Company, Philadelphia, Pa., 17th ed., 1985. It is found there. For a brief overview of methods for drug delivery, see, for example, Langer (Science 249:1527-1533, 1990).

[0228] In some embodiments, the microbial cells of the present invention are recovered by microfiltration and centrifugation. In some embodiments, microfiltration is performed using a membrane containing a non-reactive polymer. For example, in some embodiments, the membrane comprises polyvinylidene fluoride, polysulfone, or nitrocellulose. In some embodiments, the membrane for microfiltration has a pore size of approximately 0.2 to 0.45 μm. In some embodiments, the cells are centrifuged at a force of approximately 1000 to 30000, 5000 to 30000, 10000 to 30000, 15000 to 30000, 20000 to 30000, 25000 to 30000, 1000 to 25000, 5000 to 25000, 10000 to 25000, 15000 to 25000, 20000 to 25000, 1000 to 20000, 5000 to 20000, 10000 to 20000, 15000 to 20000, 1000 to 15000, 5000 to 15000, 10000 to 15000, 1000 to 10000, 5000 to 10000, 1000 to 5000 g. In some embodiments, the cells are approximately 1×10 6 ~1×10 12 、1×10 7 ~1×10 12 、1×10 8 ~1×10 12 、1×10 9 ~1×10 12 、1×10 10 ~1×10 12 、1×10 11 ~1×10 12 、1×10 6 ~1×10 11 、1×10 7 ~1×10 11 、1×10 8 ~1×10 11 、1×10 9 ~1×10 11 、1×10 10 ~1×10 11 、1×10 6 ~1×10 10 、1×10 7 ~1×10 10 、1×10 8 ~1×10 10、 ~1×10 9 ~1×1010 , 1 x 10 6 ~1 × 10 9 , 1 x 10 7 ~1 × 10 9 , 1 x 10 8 ~1 × 10 9 , 1 x 10 6 ~1 × 10 8 , 1 x 10 7 ~1 × 10 8 , 1 x 10 6 ~1 × 10 7 It is concentrated in CFU.

[0229] In some embodiments, the microbial cells of the present invention are frozen. In some embodiments, the microbial cells of the present invention are mixed with one or more cryopreservatives (CPAs) before freezing. In some embodiments, the ratio of cells to CPA is approximately 25:1, 10:1, 5:1, 4:1, 3:1, 2:1, 1:1, 1:2, 1:3, 1:4, 1:5, 1:10, or 1:25. In some embodiments, the CPA comprises one or more of glycerol, maltodextrin, sucrose, inulin, trehalose, and alginates. In some embodiments, the CPA further comprises one or more antioxidants. In some embodiments, the antioxidants are selected from the list of cysteine, ascorbic acid, and riboflavin.

[0230] In some embodiments, the microbial cells of the present invention are freeze-dried. In some embodiments, the freeze-dried cells are used to prepare the oral dose of the present invention. In some embodiments, primary drying is performed at approximately below -20°C. In some embodiments, primary drying is followed by secondary drying at a higher temperature, for example, above 0°C, above 5°C, or above 10°C.

[0231] In some embodiments, the pharmaceutical compositions disclosed herein may comprise the microbial consortium of the present invention and one or more agents, the agents being, but not limited to, carbohydrates (e.g., glucose, sucrose, galactose, mannose, ribose, arabinose, xylose, fructose, maltose, cellobiose, lactose, deoxyribose, hexose); lipids (e.g., lauric acid (12:0), myristic acid (14:0), palmitic acid (16:0), palmitic acid Leic acid (16:1), margaric acid (17:0), heptadecenoic acid (17:1), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2), linolenic acid (18:3), octadecatetraenoic acid (18:4), arachidonic acid (20:0), eicosenoic acid (20:1), eicosadienoic acid (20:2), eicosatetraenoic acid (20:4), eicosapentaenoic acid (20:5) (EPA), docosanic acid (22:0), docosenoic acid (22:1), docosapentaenoic acid (22:5), docosa Hexaenoic acid (22:6) (DHA), and tetracosanoic acid (24:0); inorganic substances (e.g., chloride, sodium, calcium, iron, chromium, copper, iodine, zinc, magnesium, manganese, molybdenum, phosphorus, potassium, and selenium); vitamins (e.g., vitamin C, vitamin A, vitamin E, vitamin B12, vitamin K, riboflavin, niacin, vitamin D, vitamin B6, folic acid, pyridoxine, thiamine, pantothenic acid, and biotin); buffers (e.g., sodium citrate, magnesium carbonate, magnesium bicarbonate, calcium carbonate, and calcium bicarbonate); preservatives (e.g., alpha-tocopherol, ascorbate, parabens, chlorobutanol, and phenol); binders (e.g., starch, alpha-starch, gelatin, polyvinylpyrrolidone, cellulose, methylcellulose, sodium carboxymethylcellulose, ethylcellulose, polyacrylamide, polyvinyloxazolidone, polyvinyl alcohol, C 12 ~C 18 fatty acid alcohols, Polyethylene glycol, polyols, sugars, oligosaccharides); lubricants (e.g., magnesium stearate, calcium stearate, zinc stearate, hydrogenated vegetable oil, Sterotex, polyoxyethylene monostearate, talc, polyethylene glycol, sodium benzoate, sodium lauryl sulfate, magnesium lauryl sulfate, and diesel fuel); dispersants (e.g., starch, alginic acid, polyvinylpyrrolidone, guar gum, kaolin, bentonite, refined wood cellulose, sodium starch glycolate, The following are selected from the group consisting of isoamorphous silicates and microcrystalline cellulose; disintegrants (e.g., corn starch, potato starch, its alpha and modified starches, sweeteners, clays, e.g., bentonite, microcrystalline cellulose, alginates, sodium starch glycolate, gums, e.g., agar, guar, locust bean, karaya, pectin, tragacanth, sodium bicarbonate in combination with citric acid, and sodium bicarbonate in combination with tartaric acid); flavorings; sweeteners; and colorants. In some embodiments, additional nutrients, e.g., oxalates or formates, are added to support robust recovery of a particular strain from the capsule.

[0232] In certain embodiments, the microbial consortium of the present invention is administered orally as a lyophilized powder, capsule, tablet, lozenge, granule, gel, or liquid. In some embodiments, the microbial consortium of the present invention is administered as a tablet or pill, which may be compressed, compressed multiple times, laminated multiple times, and / or coated. For example, in some embodiments, the lyophilized powder is filled into capsules of sizes "0", "00", or "000" to accommodate various strengths. In some embodiments, the tablets or pills include an enteric coating. Therapeutic applications

[0233] The present invention provides a microbial consortium capable of colonizing one or more niches in the digestive tract, where it can metabolize a first metabolic substrate that causes or contributes to disease in animals. In some embodiments, the animal is a mouse. In some embodiments, the animal is a germ-free mouse. In some embodiments, the animal is a mouse colonized with a human microbiome. In some embodiments, the animal is a human.

[0234] In some embodiments of the present invention, when administered to animals, the animals are pre-treated with one or more antibiotics prior to administration of the microbial consortium. In some embodiments, the one or more antibiotics are selected from ampicillin, enrofloxacin, clarithromycin, and metronidazole. In some embodiments, the animals are treated with a polyethylene glycol enteric pre-treatment procedure.

[0235] In some embodiments, when administered to animals, the microbial consortium of the present invention significantly reduces the concentration of a first metabolite present in blood, serum, bile, feces, or urine compared to samples collected before treatment from the same animals or from corresponding control animals that have not received the microbial consortium. For example, in some embodiments, when administered to animals consuming a high-oxalate diet, the microbial consortium of the present invention significantly reduces the concentration of oxalates present in blood, serum, bile, feces, or urine samples compared to samples collected before treatment from the same animals or from corresponding control animals that have not received the microbial consortium. As used herein, “high-oxalate diet” refers to a diet that induces a hyperoxaluria phenotype in animals. For example, in some embodiments, animals may be kept on a high-oxalate diet for 7 days to 1 month. In some embodiments, animals may be kept on a high-oxalate diet for 7 days, 14 days, 21 days, or 1 month. In some embodiments, the high-oxalate diet may have a calcium-to-oxalate molar ratio of less than 2.0. For example, in some embodiments, the high-oxalate diet may have a calcium-to-oxalate molar ratio of about 0.1 to about 0.8. In some embodiments, animals may be maintained on a nutritionally complete, grain-based diet rich in complex polysaccharides and may be freely provided with drinking water supplemented with about 0.5% to 1% oxalate. In some embodiments, control animals may be maintained on a diet as shown in Table 1 or on a high-oxalate diet as shown in Table 2. [Table 1] [Table 2]

[0236] In some embodiments, the microbial consortium of the present invention is administered to animals consuming a diet supplemented with one or more bile acids. In some embodiments, the diet is supplemented with one or more of TCDCA, GCDCA, TCA, GCA, CA, CDCA, LCA, or DCA. For example, in some embodiments, animals may be maintained on a diet supplemented with one or more bile acids for 7 days to 1 month. In some embodiments, animals may be maintained on a diet supplemented with bile acids for 7 days, 14 days, 21 days, or 1 month.

[0237] In some embodiments, the microbial consortium of the present invention is used to treat subjects who have or are at risk of developing a metabolic disease or condition. For example, in some embodiments, the metabolic disease is primary hyperoxaluria. In some embodiments, the metabolic disease is secondary hyperoxaluria. In some embodiments, the metabolic disease is secondary hyperoxaluria associated with bowel resection surgery or IBD. In some embodiments, multiple microbial consortia of the present invention, when administered to a subject, significantly reduce the concentration of oxalates present in blood, serum, bile, feces, or urine samples by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, or at least 80% compared to an untreated subject or pre-administration concentration.

[0238] In some embodiments, the microbial consortium of the present invention significantly alters the profile and / or concentration of bile acids present in animals. For example, in some embodiments, the microbial consortium of the present invention significantly alters the profiles and concentrations of Tβ-MCA, Tα-MCA, TUDCA, THDCA, TCA, 7β-CA, 7-oxo-CA, TCDCA, Tω-MCA, TDCA, α-MCA, β-MCA, ω-MCA, Muro-CA, d4-CA, CA, TLCA, UDCA, HDCA, CDCA, DCA, and LCA in animals.

[0239] In some embodiments, the highly complex defined enterobacteria community of the present invention can be used to treat animals having cholestatic diseases, such as primary sclerosing cholangitis, primary biliary cholangitis, progressive familial intrahepatic cholestasis, or non-alcoholic steatohepatitis. For example, in some embodiments, the animal may be a mammal, and more particularly a human.

[0240] In some embodiments, the microbial consortium of the present invention can be administered via the intestinal route. For example, in some embodiments, the microbial consortium is administered orally, rectally (e.g., by enema, suppository, or colonoscopy), or orally or via a nasal tube.

[0241] In some embodiments, the microbial consortium of the present invention can be administered to specific locations along the digestive tract. For example, in some embodiments, the microbial consortium can be administered to one or more locations in the digestive tract, including the mouth, esophagus, stomach, small intestine (duodenum, jejunum, ileum), large intestine (cecum, ascending colon, transverse colon, descending colon), or rectum. In some embodiments, the microbial consortium can be administered to all regions of the digestive tract. Dosage

[0242] In some embodiments, the microbial consortium of the present invention comprises at least 1 × 10 6 Colony-forming units (CFU) or larger, at least 2 × 10⁻¹⁶ units. 6 CFU or higher, at least 3x10 6 CFU or higher, at least 4x10 6 CFU or higher, at least 5x10 6 CFU or higher, at least 6x10 6 CFU or higher, at least 7x10 6 CFU or higher, at least 8x10 6 CFU or higher, at least 9x10 6 CFU or higher, at least 1 x 10⁻⁶ 7CFU or higher, at least 2 x 10 7 CFU or higher, at least 3x10 7 CFU or higher, at least 4x10 7 CFU or higher, at least 5x10 7 CFU or higher, at least 6x10 7 FU or higher, at least 7x10 7 CFU or higher, at least 8x10 7 CFU or higher, at least 9x10 7 CFU or higher, 1x10 8 CFU or higher, at least 2 x 10 8 CFU or higher, at least 3x10 8 CFU or higher, at least 4x10 8 CFU or higher, at least 5x10 8 CFU or higher, at least 6x10 8 CFU or higher, at least 7x10 8 CFU or higher, at least 8x10 8 CFU or higher, at least 9x10 8 CFU or higher, 1x10 9 CFU or higher, at least 2 x 10 9 CFU or higher, at least 3x10 9 CFU or higher, at least 4x10 9 CFU or higher, at least 5x10 9 CFU or higher, at least 6x10 9 CFU or higher, at least 7x10 9 CFU or higher, at least 8x10 9 CFU or higher, at least 9x10 9 CFU or higher, 1x10 10 CFU or higher, at least 2 x 10 10CFU or more than that, at least 3×10 10 CFU or more than that, at least 4×10 10 CFU or more than that, at least 5×10 10 CFU or more than that, at least 6×10 10 CFU or more than that, at least 7×10 10 CFU or more than that, at least 8×10 10 CFU or more than that, at least 9×10 10 CFU or more than that, 1×10 11 CFU or more than that, at least 2×10 11 CFU or more than that, at least 3×10 11 CFU or more than that, at least 4×10 11 CFU or more than that, at least 5×10 11 CFU or more than that, at least 6×10 11 CFU or more than that, at least 7×10 11 CFU or more than that, at least 8×10 11 CFU or more than that, at least 9×10 11 CFU or more than that, 1×10 12 CFU or more than that, at least 2×10 12 CFU or more than that, at least 3×10 12 CFU or more than that, at least 4×10 12 CFU or more than that, at least 5×10 12 CFU or more than that, at least 6×10 12 CFU or more than that, at least 7×10 12 CF or more than that, at least 8×10 12 CFU or more than that, or at least 9×10 12 It is administered in a dosage form having a total amount of a microbial consortium of CFU or more than that.

[0243] In some embodiments, the microbial consortium of the present invention includes 0.1 ng to 500 mg, 0.5 ng to 500 mg, 1 ng to 500 mg, 5 ng to 500 mg, 10 ng to 500 mg, 50 ng to 500 mg, 100 ng to 500 mg, 500 ng to 500 mg, 1 μg to 500 mg, 5 μg to 500 mg, 10 μg to 500 mg, 500 μg to 500 mg, 1 mg to 500 mg, 5 mg to 500 mg, 10 mg to 500 mg, 50 mg to 500 mg, and 100 mg to 500 mg. 500mg, 0.1ng~100mg, 0.5ng~100mg, 1ng~100mg, 5ng~100mg, 10ng~100mg, 50ng~100mg, 100ng~100mg, 500ng~500mg, 1μg~100mg, 5μg~100mg , 10μg~100mg, 50μg~100mg, 100μg~100mg, 500μg~100mg, 1mg~500mg, 5mg~100mg, 10mg~100mg, 50mg~100mg, 0.1ng~50mg, 0.5ng~50mg, 1ng~ 50mg, 5ng~50mg, 10ng~50mg, 50ng~50mg, 100ng~50mg, 500ng~500mg, 1μg~50mg, 5μg~50mg, 10μg~50mg, 50μg~50mg, 100μg~50mg, 500μg~50m g, 1mg~500mg, 5mg~50mg, 10mg~50mg, 0.1ng~10mg, 0.5ng~10mg, 1ng~10mg, 5ng~10mg, 10ng~10mg, 50ng~10mg, 100ng~10mg, 500ng~500mg, 1 μg~10mg, 5μg~10mg, 10μg~10mg, 50μg~10mg, 100μg~10mg, 500μg~10mg, 1mg~500mg, 5mg~10mg, 0.1ng~5mg, 0.5ng~5mg, 1ng~5mg, 5ng~5mg, 1 0ng~5mg, 50ng~5mg, 100ng~5mg, 500ng~500mg, 1μg~5mg, 5μg~5mg, 10μg~5mg, 50μg~5mg, 100μg~5mg, 500μg~5mg, 1mg~500mg, 0.1ng~1mg, 0.5ng~1mg、1ng~1mg、5ng~1mg、10ng~1mg、50ng~1mg、100ng~1mg、500ng~500mg、1μg~1mg、5μg~1mg、10μg~1mg、50μg~1mg、100μg~1mg、500μg~1mg、0.1ng~500μg、0.5ng~500μg、1ng~500μg、5ng~500μg、10ng~500μg、50ng~500μg、100ng~500μg、500ng~500μg、1μg~500μg、5μg~500μg、10μg~500μg、50μg~500μg、100μg~500μg、0.1ng~100μg、0.5ng~100μg、1ng~100μg、5ng~100μg、10ng~100μg、50ng~100μg、100ng~100μg、500ng~100μg、1μg~100μg、5μg~100μg、10μg~100μg、50μg~100μg、0.1ng~50μg、0.5ng~50μg、1ng~50μg、5ng~50μg、10ng~50μg、50ng~50μg、100ng~50μg、500ng~50μg、1μg~50μg、5μg~50μg、10μg~50μg、0.1ng~10μg、0.5ng~10μg、1ng~10μg、5ng~10μg、10ng~10μg、50ng~10μg、100ng~10μg、500ng~10μg、1μg~10μg、5μg~10μg、0.1ng~5μg、0.5ng~5μg、1ng~5μg、5ng~5μg、10ng~5μg、50ng~5μg、100ng~5μg、500ng~5μg、1μg~5μg、0.1ng~1μg、0.5ng~1μg、1ng~1μg、5ng~1μg、10ng~1μg、50ng~1μg、100ng~1μg、500ng~1μg、0.1ng~500ng、0.5ng~500ng、1ng~500ng、5ng~500ng、10ng~500ng、50ng~500ng、100ng~500ng、0.1ng~100ng、0.5ng~100ng、1ng~100ng、5ng~100ng、10ng~100ng、50ng~100ng、0.1ng~50ng、0.5ng~50ng、1ng~50ng、5ng~50ng、10ng~50ng、0.1ng~10ng、0.5ng~10ng、1ng~10ng、5ng~10ng、0.The drug is administered in dosage forms containing a total dry weight of the microbial consortium in the following concentrations: 1 ng to 5 ng, 0.5 ng to 5 ng, 1 ng to 5 ng, 0.1 ng to 1 ng, 0.1 ng to 1 ng, or 0.1 ng to 0.5 ng.

[0244] In other embodiments, the microbial consortium of the present invention is administered at doses of 0.1 ng to 500 mg per day, 0.5 ng to 500 mg per day, 1 ng to 500 mg per day, 5 ng to 500 mg per day, 10 ng to 500 mg per day, 50 ng to 500 mg per day, 1 μg to 500 mg per day, 5 μg to 500 mg per day, 10 μg to 500 mg per day, 50 μg to 500 mg per day, 100 μg to 500 mg per day, 500 μg to 500 mg per day, 1 mg to 500 mg per day, and 5 mg to 500 mg per day. mg, 10mg~500mg per day, 50mg~500mg per day, 100mg~500mg per day, 0.1ng~100mg per day, 0.5ng~100mg per day, 1ng~100mg per day, 5ng~100mg per day, 10ng~100mg per day, 50ng~ per day 100mg, 100ng~100mg per day, 500ng~500mg per day, 1μg~100mg per day, 5μg~100mg per day, 10μg~100mg per day, 50μg~100mg per day, 100μg~100mg per day, 500μg~100mg per day, 1m per day g-500mg, 5mg-100mg per day, 10mg-100mg per day, 50mg-100mg per day, 0.1ng-50mg per day, 0.5ng-50mg per day, 1ng-50mg per day, 5ng-50mg per day, 10ng-50mg per day, 50ng-50mg per day, 100ng-50mg per day, 500ng-500mg per day, 1μg-50mg per day, 5μg-50mg per day, 10μg-50mg per day, 50μg-50mg per day, 100μg-50mg per day, 500μg-50mg per day, 1mg-500mg per day 5mg-50mg, 10mg-50mg per day, 0.1ng-10mg per day, 0.5ng-10mg per day, 1ng-10mg per day, 5ng-10mg per day, 10ng-10mg per day, 50ng-10mg per day, 100ng-10mg per day, 500ng-500mg per day, 1μg-10mg per day, 5μg-10mg per day, 10μg-10mg per day, 50μg-10mg per day, 100μg-10mg per day, 500μg-10mg per day, 1mg-500mg per day, 5mg-10mg per day, 0.1ng-5mg per day, 0.5ng~5mg, 1ng~5mg per day, 5ng~5mg per day, 10ng~5mg per day, 50ng~5mg per day, 100ng~5mg per day, 500ng~500mg per day, 1μg~5mg per day, 5μg~5mg per day, 10μg~5mg per day, 50μg~5mg per day, 100μ per day g~5mg, 500μg~5mg per day, 1mg~500mg per day, 0.1ng~1mg per day, 0.5ng~1mg per day, 1ng~1mg per day, 5ng~1mg per day, 10ng~1mg per day, 50ng~1mg per day, 100ng~1mg per day, 500ng~500mg per day, per day 1μg~1mg, 5μg~1mg daily, 10μg~1mg daily, 50μg~1mg daily, 100μg~1mg daily, 500μg~1mg daily, 0.1ng~500μg daily, 0.5ng~500μg daily, 1ng~500μg daily, 5ng~500μg daily, 10ng~500μg daily, 50ng~500μg daily, 100ng~500μg daily, 500ng~500μg daily, 1μg~500μg daily, 5μg~500μg daily, 10μg~500μg daily, 50μg~500μg daily, 100μg~500μg daily, 0.1ng~100μg daily, 1 0.5ng~100μg per day, 1ng~100μg per day, 5ng~100μg per day, 10ng~100μg per day, 50ng~100μg per day, 100ng~100μg per day, 500ng~100μg per day, 1μg~100μg per day, 5μg~100μg per day, 10μg~100μg per day, 50μg~100μg per day, 0.1ng~50μg per day, 0.5ng~50μg per day, 1ng~50μg per day, 5ng~50μg per day, 10ng~50μg per day, 50ng~50μg per day, 100ng~50μg per day, 500ng~50μg per day, 1μg~50μg per day g, 5μg~50μg per day, 10μg~50μg per day, 0.1ng~10μg per day, 0.5ng~10μg per day, 1ng~10μg per day, 5ng~10μg per day, 10ng~10μg per day, 50ng~10μg per day, 100ng~10μg per day, 500ng~10μg per day, 1μg~10μg per day, 5μg~10μg per day, 0.1ng~5μg per day, 0.5ng~5μg per day, 1ng~5μg per day, 5ng~5μg per day, 10ng~5μg per day, 50ng~5μg per day, 100ng~5μg per day, 500ng~5μg per day, 1μg~5μg per day, 0.1 ng to 1 μg, 0.5 ng to 1 μg per day, 1 ng to 1 μg per day, 5 ng to 1 μg per day, 10 ng to 1 μg per day, 50 ng to 1 μg per day, 100 ng to 1 μg per day, 500 ng to 1 μg per day, 0.1 ng to 500 ng per day, 0.5 ng to 500 ng per day, 1 ng to 500 ng per day, 5 ng to 500 ng per day, 10 ng to 500 ng per day, 100 ng to 500 ng per day, 0.1 ng to 100 ng per day, 0.5 ng to 100 ng per day, 1 ng to 100 ng per day, 5 ng to 500 ng per day It is consumed at rates of 100ng, 10ng-100ng per day, 50ng-100ng per day, 0.1ng-50ng per day, 0.5ng-50ng per day, 1ng-50ng per day, 5ng-50ng per day, 10ng-50ng per day, 0.1ng-10ng per day, 0.5ng-10ng per day, 1ng-10ng per day, 5ng-10ng per day, 0.1ng-5ng per day, 0.5ng-5ng per day, 1ng-5ng per day, 0.1ng-1ng per day, 0.1ng-1ng per day, or 0.1ng-0.5ng per day.

[0245] In some embodiments, the microbial consortium of the present invention is administered for a period of at least 1 day to 1 week, 1 week to 1 month, 1 month to 3 months, 3 months to 6 months, 6 months to 1 year, or longer than 1 year. For example, in some embodiments, the microbial consortium of the present invention is administered for a period of at least 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, or 1 year.

[0246] In some embodiments, the microbial consortium of the present invention can be administered as a single dose or in multiple doses. For example, in some embodiments, the microbial consortium of the present invention is administered once daily for 2, 3, 4, 5, 6 days, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, or 1 year. In some embodiments, the microbial consortium of the present invention is administered multiple times a day. For example, in some embodiments, the microbial consortium of the present invention is administered twice, three, four, or five times a day. In some embodiments, the microbial consortium of the present invention is administered intermittently. For example, in some embodiments, the microbial consortium of the present invention is administered once a week, once a month, or whenever the subject needs it. Combination therapy

[0247] In some embodiments, the microbial consortium of the present invention can be administered in combination with other agents. For example, in some embodiments, the microbial consortium of the present invention can be administered together with an antimicrobial agent, antifungal agent, antiviral agent, antiparasitic agent, or prebiotic. In some embodiments, the microbial consortium of the present invention can be administered after the administration of an antimicrobial agent, antifungal agent, antiviral agent, antiparasitic agent, or prebiotic. In some embodiments, administration may be sequential over a period of several hours or several days, or it may be simultaneous.

[0248] For example, in some embodiments, the microbial consortium includes fluoroquinolone antibiotics (ciprofloxacin, levaquin, phloxin, techin, avelox, and norflox); cephalosporin antibiotics (cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cephamandol, cefoxitin, cefprodil, and ceftoviprole); and penicillin antibiotics (amoxicillin, ampicillin). It may be administered together with, or before, one or more antimicrobial agents selected from penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin; tetracycline antibiotics (tetracycline, minocycline, oxytetracycline, and doxycycline); and carbapenem antibiotics (ertapenem, doripenem, imipenem / cilastatin, and meropenem).

[0249] For example, in some embodiments, the microbial consortium includes abacavir, acyclovir, adefovir, amprenavir, atazanavir, cidofovir, darunavir, delavirdin, didanosine, docosanol, efavirenz, elvitegravir, emtricitabine, enfuvirtide, etravirine, famciclovir, foscamet, homivirsen, ganciclovir, indinavir, idoxuridine, lamibudici , lopinavir, maraviroc, MK-2048, nelfinavir, nevirapine, penciclovir, raltegravir, rilpivirine, ritonavir, saquinavir, stabudine, tenofovir, trifluridine, valacyclovir, valganciclovir, vidarabine, ivacitabine, amantadine, oseltamivir, rimantadine, tipranavir, za It can be administered with one or more antiviral agents selected from lucitabine, zanamivir, and zidovudine.

[0250] In some embodiments, the microbial consortium includes miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxiconazole, sertaconazole, sulconazole, and thioconazole; triazole antifungal agents, e.g., fluconazole, itraconazole, isabconazole, rabconazole, posaconazole, voriconazole, terconazole, and albaconazole; thiazole antifungal agents, e.g. It can be administered with one or more antifungal agents selected from abafungin; allylamine antifungal agents, e.g., terbinafine, naftifine, and butenafine; as well as echinocandin antifungal agents, e.g., anidurafungin, caspofungin, and micafungin; polygodial; benzoic acid; cyclopirox; tolnaphthate; undecylenic acid; flucytosine or 5-fluorocytosine; griseofulvin; and haloprozin.

[0251] In some embodiments, the microbial consortium may be administered with one or more anti-inflammatory and / or immunosuppressant agents selected from cyclophosphamide, mycophenolate mofetil, corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, cyclosporine A, mercaptopurine, azathioprine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, sodium cromoglycate, anti-leukotrienes, anticholinergics, monoclonal anti-IgE, immunomodulatory peptides, immunomodulatory small molecules, immunomodulatory cytokines, immunomodulatory antibodies, and vaccines.

[0252] In some embodiments, the microbial consortium of the present invention can be administered with one or more prebiotics selected from, but not limited to, amino acids, biotin, fructooligosaccharides, galactooligosaccharides, inulin, lactose, mannan-oligosaccharides, oligofructose-fortified inulin, oligofructose, oligodextrose, tagatose, trans-galactooligosaccharides, and xylooligosaccharides. [Examples]

[0253] The disclosure described above will be more readily understood by referring to the following examples. These examples are included solely for the purpose of illustrating certain aspects and embodiments of the disclosure and are not intended to limit the scope of the disclosure in any way. (Example 1) Sources and identification of active and supporting microbial strains

[0254] The active and supporting microbial strains were derived from human donor fecal samples or purchased from one of the following three depositary institutions: the United States Cell Culture Lineage Preservation Center (ATCC; www.atcc.org), the Leibniz Society DSMZ (www.dsmz.de), or BEI Resources (www.beiresources.org).

[0255] The microbial strains purchased from the depositary institution were cultured according to the depositary institution's instructions for use. Isolation of active and supporting microbial strains derived from donors

[0256] Fecal donors were selected based on multiple criteria, including a medical history questionnaire, physical examination, and blood and stool tests to assess the absence of pathogens. Fecal samples from donors who did not meet the inclusion criteria based on any of the above assessments were discarded from the isolation facility.

[0257] Donors provided fecal samples sealed in plastic containers. Upon collection, the fecal samples were immediately transferred to an anaerobic chamber (5% CO2, 5% H2, 90% N2) within 15 minutes of collection.

[0258] After transferring to an anaerobic chamber, fresh fecal samples were labeled, weighed, evaluated for abnormalities (presence of urine, toilet paper, etc.), and scored according to the Bristol Stool Scale. Fecal samples weighing less than 45g or not conforming to Bristol Stool Scale types 2, 3, 4, or 5 were rejected. Fecal samples that met the acceptance criteria were processed and portioned. 45g of fecal sample was transferred to a sterile container for specific pathogen testing. The remaining sample was mixed with a cryopreservative, homogenized, and portioned into cryovials (approximately 2g of sample per vial; 6 vials per fecal sample). These vials were transferred from the anaerobic chamber to a -80°C freezer for storage using dry ice until shipment.

[0259] Serially diluted aliquots of fecal samples were prepared, and microbial strains were isolated by plating these aliquots onto various microbial culture media suitable for the growth of anaerobic organisms. All cultures were grown under anaerobic conditions throughout the culture period. Various enteromicrobial species were isolated using approximately 20 different media / culture conditions. Specific enrichment techniques were performed on species with specific metabolic capabilities, such as consumption of oxalates or bile acids, or tolerance to them. To enrich strains with oxalate metabolism capabilities, serially diluted aliquots of fecal samples were plated onto agar growth media supplemented with various concentrations of potassium oxalate (20 mM, 40 mM, 80 mM, 160 mM, or 200 mM). To enrich species capable of metabolizing bile acids, serially diluted aliquots of fecal samples were plated onto growth media supplemented with 2% bile. To isolate archaea, diluted fecal samples were plated onto a culture medium containing a mixture of antibiotics lethal to both Gram-positive and Gram-negative bacteria. This archaeal isolation plate was co-incubated in a small sealed container with another plate containing a heterogeneous population of microorganisms derived from the fecal sample, which included hydrogen-producing microorganisms, thereby obtaining hydrogen (through diffusion within the small container) to enable archaeal growth on the archaeal isolation plate.

[0260] Single colonies were collected from isolation or enrichment plates for further isolation (second passaging) on ​​appropriate microbial culture agar plates. After incubation at 37°C, once uniformly separated colony morphologies were obtained by plating the single colonies, the cultures were further investigated for strain identification. Preliminary strain identification was performed either by 16S rRNA gene sequencing or by generating and analyzing proteomic fingerprints using high-throughput matrix-assisted laser desorption / ionization time-of-flight mass spectrometry (MALDI-TOF MS). If multiple colony morphologies were obtained by plating the single colonies, each unique colony morphology was collected for further isolation on appropriate culture agar plates until a uniform colony morphology was obtained (third or subsequent passaging). Single culture identity was confirmed by 16S rRNA gene sequencing.

[0261] Isolated colonies of the target species, purified into monocultures, and novel strains of unknown species were inoculated into culture tubes containing appropriate broth medium and incubated at 37°C under anaerobic conditions. For most strains, sufficient growth was visualized during this first broth subculturing, as indicated by turbidity. However, some strains required more than one subculturing to achieve sufficient growth. Sterile glycerol solution was added to the microbial cultures to achieve a final glycerol concentration of 25%, after which the cultures were mixed and divided into cryovials. The cryovials were removed from the anaerobic gas chamber and immediately transferred to -80°C.

[0262] After freezing for at least 10 hours, one vial of each purified and frozen isolate was retrieved from the freezer, thawed under anaerobic conditions, and then plated onto an agar plate containing appropriate growth medium. The plates were incubated at 37°C under anaerobic conditions. Growth on the plates was observed to confirm recovery and uniform morphology for each purified isolate. Subsequently, individual colonies of the isolates were analyzed by 16S rRNA gene sequencing to confirm the identity and colony purity of each frozen isolate against the National Center for Biotechnology Information (NCBI) 16S rRNA gene database.

[0263] Table 3 reports a list of donor-derived isolates and summaries of their corresponding isolation and growth / banking media. Table 4 reports additional identification information for the isolates.

[0264] Candidate active strains were identified using in vitro activity-based assays, bioinformatics screening to identify strains with the genetic ability to metabolize oxalates, and identification of target species with known oxalate metabolic activity based on scientific literature. Active oxalate metabolizing strains obtained from depositaries ("commercial strains") include those listed in Table 5. Supporting commercial strains include those listed in Table 6. The strains in Tables 5 and 6 are identified by their genus / species and depositary catalog number. "ATCC" strains were obtained from ATCC, "DSM" strains from the Liebniz Institute DSMZ, and "HM" strains from BEI Resources. MALDI-TOF MS

[0265] MALDI-TOF mass spectrometry was used for preliminary identification of bacterial strains (genera and / or species) using a BD Bruker MALDI Biotyper. Briefly, an α-cyano-4-hydroxycinnamic acid (HCCA) matrix was prepared in Bruker standard solvent (50% acetonitrile, 47.5% water, and 2.5% trifluoroacetic acid). Sample bacterial colony smears were placed on disposable MALDI BioTyper Biotarget plates, the HCCA matrix was overlaid, and the plates were allowed to dry. For strains requiring longer extraction times, 70% formic acid was added to the sample smear before adding the HCCA matrix. Bruker Bacterial Testing Standards (BTS) were also placed on the Biotarget for quality control analysis. The Biotarget was then mounted on the Biotyper MALDI-TOF machine, and the samples were analyzed. The machine was configured to perform quality control analysis on BTS quality control samples first, and to interrupt the process if the BTS quality control analysis failed. Next, the spectra generated for the test samples were compared with a database of reference proteomics spectra containing strains belonging to species previously characterized by proteomics fingerprinting. DNA extraction

[0266] DNA was extracted from fecal samples using the Qiagen DNeasy Power Soil Kit (Qiagen, Germantown, MD) according to the manufacturer's instructions. Alternative methods for extracting DNA from fecal samples are well known and routinely practiced in the art (e.g., described in Sambrook and Russell, Molecular Cloning: A Laboratory Manual, 3rd ed., 2001). Whole-genome shotgun sequencing

[0267] DNA sample sequencing is performed using the TruSeq Nano DNA Library. The procedure was performed using the Preparation Kit (Illumina, San Diego, CA, US) and the NextSeq Platform (Illumina, San Diego, CA, US). In short, sequencing libraries were prepared from DNA extracted from each sample. DNA was mechanically fragmented using an ultrasonic disruptor. The fragmented DNA was enriched by end repair and size selection, 3' end adenylation, adapter ligation, and according to the TruSeq Nano DNA Library Preparation Kit manual (Illumina, San Diego, CA, US). Samples were sequenced to generate more than 50,000,000 Ard-end reads of 150, 250, or 300 bp length. 16S rRNA gene sequencing and species identification

[0268] Microbial species identification was performed by full-length Sanger sequencing of 16S rRNA genes using 27F and 1492 primers (PMID 18296538). Species were identified by a bidirectional best BLAST search against a database of selected 16S rRNA gene sequences of the type species. To further refine species identification, 16S rRNA gene sequences were inserted into the phylogenetic tree of selected 16S rRNA gene sequences of the type species. If the sequence formed a monophyletic cluster with a known species, the strain was assigned to that species. Otherwise, the strain was assigned to a novel species. Where necessary, isolates were further characterized by whole-genome sequencing. Genome assemblies were inserted into the phylogenetic tree of selected genomes of the type species. If the sequence formed a monophyletic cluster with a known species, the strain was assigned to that species. Otherwise, the strain was assigned to a novel species. [Table 3-1] [Table 3-2] [Table 3-3] Table 3-4 Table 3-5 Table 3-6 Table 3-7 Table 3-8 Table 3-9 Table 3-10 Table 3-11 Table 3-12 Table 3-13 Table 3-14 Table 3-15 Table 3-16 Table 3-17 Table 3-18 Table 3-19 Table 3-20 Table 3-21 Table 3-22 Table 3-23 Table 3-24 Table 3-25 Table 3-26 Table 3-27 Table 3-28 Table 3-29 Table 3-30 Table 3-31 Table 3-32 Table 3-33 Table 3-34 Table 3-35 Table 3-36 Table 3-37 Table 3-38 Table 3-39 Table 3-40 Table 3-41 Table 3-42 Table 3-43 Table 3-44 Table 4-1 Table 4-2 Table 4-3 Table 4-4 Table 4-5 Table 4-6 Table 4-7 Table 4-8 Table 4-9 Table 4-10 Table 4-11 Table 4-12 Table 4-13 Table 4-14 Table 4-15 Table 4-16 Table 4-17 Table 4-18 Table 4-19 Table 4-20 Table 4-21 Table 5 Table 6-1 Table 6-2 Table 6-3 Table 6-4 Table 6-5 (Example 2) Susceptibility of commercially available microbial strains to oxalate concentrations

[0269] To determine the effect of oxalate on the growth of commercially available microbial strains, cultures were grown to saturation in their respective bank media (e.g., Mega Media or Chopped Meat Media) and then diluted back into the same bank media containing 0.5% or 0.125% oxalate, or without oxalate. Figure 1 shows the % inhibition of microbial strain growth in the presence of 0.5% oxalate (black bars) or 0.125% oxalate (white bars). % inhibition was calculated by determining the ratio of the optical density (OD) of the microbial strain with background subtracted in the presence of oxalate to the OD of the same microbial strain grown in the absence of oxalate. (Example 3) In vitro oxalate metabolism by commercially available microbial strains

[0270] A 48-well deep-well plate was filled with 2.5 mL of commercially available microbial medium per strain per condition. Potassium oxalate was added to achieve a final oxalate concentration of 7.5 mM or 750 μM. 50 μl of each microbial strain from the bank medium was added to the appropriate well and mixed by grinding. 1 mL of each sample was transferred to the appropriate well of a 96-well collection plate containing 25 μl of 6N HCl and mixed by grinding. The collection plate was lidded and incubated under anaerobic conditions at 37°C for 0, 24, or 72 hours.

[0271] The oxalate metabolic activity of microbial strains was measured using a commercially available colorimetric enzyme kit (Sigma Aldrich Oxalate Assay Kit, catalog number MAK315) according to the manufacturer's instructions for use.

[0272] In short, an acidified microbial suspension was centrifuged at >10,000 × g for 1 minute to settle intact cells and cell debris. 10 μl of the sample supernatant was transferred to each of three separate wells of a multiwell plate designated as “sample blank,” “sample,” or “internal standard.” 10 μl of dH2O was added to the sample blank and sample wells, and 10 μl of oxalate standard material was added to the internal standard well. Blank reagents were prepared for all sample blank wells by mixing 155 μl of reagent B and 1 μl of horseradish peroxidase ("HRP") enzyme per sample blank well. 157 μl of working reagent (155 μl of reagent B, 1 μl of oxalate oxidase enzyme, and 1 μl of HRP) was prepared for each sample and internal standard well. 150 μl of blank reagent was added to each sample blank well, and 150 μl of working reagent was added to each sample and internal standard well. The solutions were mixed and incubated at room temperature for 10 minutes. After incubation, the optical density at 595 nm was measured for each sample well using a BioTek Epoch 2 plate reader. The sample and internal standard values ​​were compared with the measured OD of the sample blank wells. 595 The measured OD of the sample and internal standard wells 595 The correction was made by subtracting from the corrected OD. The percentage of oxalates remaining in each sample after 24 or 72 hours of incubation was used. 595 The value was determined by dividing it by the sample well at the initial time point (i.e., t=0 hours).

[0273] Figure 2 shows the percentage of oxalate remaining in microbial strain cultures in Mega Media (Figure 2A) or Chopped Meat Media (Figure 2B) plated with 7.5 mM oxalate (black bar graph) or 750 μM oxalate (white bar graph) after 72 hours of incubation under anaerobic conditions at 37°C. In vitro oxalate metabolic activity of microbial strains cultured at different pH levels

[0274] To determine the effect of pH on oxalate metabolism, the above in vitro oxalate metabolism assay was performed at an oxalate concentration of 7.5 mM in culture medium at pH 7.2 or in culture medium adjusted to pH 4.5 with NaOH.

[0275] Figure 3 shows the percentage of oxalate remaining in microbial strain cultures in Mega Media (Figure 3A) or Chopped Meat Media (Figure 3B) plated with 7.5 mM oxalate at pH 4.5 (black bar graph) or pH 7.2 (white bar graph) after 72 hours of incubation under anaerobic conditions at 37°C. Microbial consortium's in vitro oxalate metabolic activity

[0276] To determine the oxalate metabolic activity of the microbial consortium, an in vitro oxalate metabolism assay was performed at an oxalate concentration of 7.5 mM.

[0277] Figure 4 shows the absorbance (595 nm) of cultures containing only O. formigenes, only active microbial strains, only supporting microbial strains, or a complete microbial consortium (i.e., both active and supporting microbial strains) in Mega Media (Figure 4A) or Chopped Meat Media (Figure 4B) at the time of oxalate addition (t=0, black bar graph) or after 72 hours (white bar graph). (Example 4) Analysis of oxalates by liquid chromatography-tandem mass spectrometry (LC-MS / MS)

[0278] To quantify the oxalate level in the incubation medium, aliquots of the medium were transferred to a polypropylene tube containing 60 μl of 6N HCl / ml medium, mixed with a vortex mixer, flash-frozen, and stored at -70°C. On the day of analysis, the sample was thawed, mixed with a vortex mixer, and then mixed with 50 μl of medium or medium diluted with 0.1% formic acid, and 20 μl of internal standard (1 mM in 0.1% formic acid). 13The sample was transferred to a polypropylene tube containing C2-oxalate while mixing, and then mixed using a vortex mixer. A 500 μl aliquot of 2% formic acid was added and mixed using a vortex mixer. The entire sample was passed through a prepared Strata-X-AW solid-phase extraction plate (Phenomenex, 10 mg, 8E-S038-AGB), washed, and then eluted with 5% ammonium hydroxide in methanol. The eluate was then dried under nitrogen gas, reconstituted in 0.1% formic acid, and placed in an API 6500 autosampler. 5 μl of the eluate was injected into a 2.1 × 50 mM Waters XBridge HILIC 3.5 μm particle size column. The LC-MS / MS parameters were as shown in Table 7.

[0279] To quantify oxalate levels in urine, urine samples were collected, immediately flash-frozen, and stored at -70°C. On the day of analysis, the samples were thawed, mixed in a vortex mixer, and then mixed with 50 μl of urine or urine diluted with 0.1% formic acid in 20 μl of an internal standard (1 mM in 0.1% formic acid). 13 C2-oxalate + 5mM 2 The sample was transferred to a polypropylene tube containing H3-creatinine while mixing, and then mixed using a vortex mixer. A 500 μl aliquot of 2% formic acid was added and mixed using a vortex mixer. The entire sample was passed through a prepared Strata-X-AW solid-phase extraction plate (Phenomenex, 10 mg, 8E-S038-AGB), washed, and then eluted with 5% ammonium hydroxide in methanol. The eluate was then dried under nitrogen gas, reconstituted in 0.1% formic acid, and placed in an API 6500 autosampler. 5 μl was injected into a 2.1 × 50 mM Waters XBridge HILIC 3.5 μm particle size column. LC-MS / MS parameters were as shown in Table 7. [Table 7] (Example 5) In vivo oxalate metabolism in Balb / c male mice treated with a microbial consortium containing commercially available microbial strains.

[0280] This example describes a test in which a microbial consortium containing commercially available microbial strains tests the ability to degrade oxalates in vivo in Balb / c male mice.

[0281] To determine the in vivo oxalate degradation activity of the microbial consortia described herein, 30 gnotobiotic (n=3 per condition) Balb / c male mice were weighed on day 0, and the mice were colonized by oral force-administration with either multiple active microorganisms only, support communities only, O. formigenes only, or the complete microbial consortium (active organisms and support). Multiple active microorganisms and microbial support communities contained strains marked with "X" in the vertical column of Table 8. Colonized mice were fed either a defined low-complexity diet supplemented with an excess amount of oxalate to induce hyperoxaluria (see Table 2 above), or a nutritionally equivalent control diet lacking oxalate (see Table 1 above).

[0282] After a two-week period, the mice were sacrificed, and a variety of samples were collected, including their final urine, feces, serum, kidneys, liver, gallbladder, cecum, and spleen. [Table 8-1] [Table 8-2] [Table 8-3] [Table 8-4] [Table 8-5] [Table 8-6] [Table 8-7] [Table 8-8] [Table 8-9] [Table 8-10] [Table 8-11]

[0283] Figures 5A and 5B show the percentage body weight gain and food consumption of non-committed mice and mice that received one of the following by forced oral administration: O. formigenes alone, active microorganisms alone, supporting microorganisms alone, or a complete microbial consortium (active organism and support), respectively.

[0284] Table 9 shows the incidence of diarrhea in non-committed mice and mice that received forced oral administration of any of the following: O. formigenes alone, active microorganisms alone, supporting microorganisms alone, or the complete microbial consortium (active organism and support). Mice treated with the complete microbial consortium were observed to have normal fecal solids and a reduced incidence of diarrhea. [Table 9]

[0285] Table 10 shows the incidence of fatty liver in non-committed mice and mice that received forced oral administration of any of the following: O. formigenes alone, active microorganisms alone, supporting microorganisms alone, or a complete microbial consortium (active organism and support). [Table 10] Urinary oxalate concentration

[0286] To evaluate the effect of the microbial consortium described herein on steady-state levels of urinary oxalates that correlate well with human urolithiasis, the last urine was collected from all test groups. Each mouse was placed at the bottom of a standard petri dish and placed in a CO2 chamber, and CO2 was administered for 90 seconds according to the approved IACUC protocol until the mouse stopped moving and tended to lie on the bottom of the chamber. The lid of the CO2 chamber was opened and the anesthetized mouse was placed on its side in the petri dish. The lid of the CO2 chamber was changed, the last urine was collected in the petri dish and transferred to a sterile microcentrifuge tube. The urine samples were processed and prepared for solid-phase extraction, and then analyzed by LC / MS as described in Example 4 above.

[0287] As shown in Table 11 and Figures 6A-B, mice fed a control diet without oxalate supplementation predictably showed lower levels of urinary oxalate (1.2 mM in non-committed controls) compared to mice fed a diet containing an excess amount of oxalate (11.9 mM in non-committed controls), demonstrating that hyperoxaluria can be induced in gnotobiotic mice by supplementing the diet with oxalate.

[0288] Regardless of diet, the lowest levels of urinary oxalates were observed in mice colonized with a complete microbial consortium (active organism and support); mean oxalate levels in consortium-colonized mice fed an oxalate-free (control) diet were approximately 50% lower than those observed in non-colonized mice, and in animals fed a high-oxalate diet, steady-state urinary oxalate levels were approximately 66% lower in consortium-colonized mice compared to non-colonized controls (4.5 mM vs. 11.9 mM).

[0289] Mice treated with a complete microbial consortium showed superior results in terms of urinary oxalate concentration compared to mice treated with only multiple active microorganisms or microbial support communities, as well as mice treated with only O. formigenes. Mice colonized with only O. formigenes or only multiple active microorganisms and supplemented with oxalate-supplemented diets showed urinary oxalate concentrations that were not significantly different from those observed in non-colonized mice. Furthermore, mice colonized with only microbial support communities showed significantly higher urinary oxalate levels than non-colonized controls (16.7 mM and 11.9 mM, respectively). Colonization with only multiple active microorganisms or only support communities did not reduce urinary oxalate levels, but colonization with a complete consortium resulted in a synergistic reduction in urinary oxalate concentration. [Table 11] Serum liver enzyme assay

[0290] Mouse serum samples were analyzed by Charles River Laboratories against a standard panel of serum liver enzymes. Figures 7A, 7B, 7C, 7D, 7E, 7F, 7G, and 7H show serum levels or function of alanine transaminase, aspartate transaminase, albumin, alanine phosphatase, albumin / globulin ratio, total bilirubin, gamma-glutamyltransferase, and prothrombin time in gnotobiotic Balb / c mice treated by forced oral administration of Oxalobacter formigenes only (O. formigenes), active strain only (active), support strain only (support), both active and support strains (active and support), or saline vehicle control (saline), respectively, while fed a normal (non-bold) or high-oxalic acid (bold) diet. Renal function assay

[0291] Mouse serum samples were analyzed by Charles River Laboratories for a standard panel of serum renal metabolites / electrolytes. Figures 8A, 8B, 8C, 8D, 8E, 8F, 8G, and 8H show serum levels of urea, creatinine, phosphorus, calcium, chloride, sodium, potassium, and globulin in gnotobiotic Balb / c mice treated by forced oral administration of Oxalobacter formigenes only (O. formigenes), active strain only (active), support strain only (support), both active and support strains (active and support), or saline vehicle control (saline), respectively, while fed a normal (non-bold) or high-oxalic acid (bold) diet. Triglyceride, cholesterol, glucose, and creatine kinase assays

[0292] Mouse serum samples were analyzed by Charles River Laboratories for a standard panel of triglycerides, cholesterol, glucose, and creatine kinases. Figures 9A, 9B, 9C, and 9D show serum triglyceride, cholesterol, glucose, and creatine kinase levels in gnotobiotic Balb / c mice fed a normal (non-bold) or high-oxalic acid (bold) diet and treated by forced oral administration of Oxalobacter formigenes only (O. formigenes), active strain only (active), support strain only (support), both active and support strains (active + support), or saline vehicle control, as described above. (Example 6) In vivo oxalate metabolism in C57 / B6 female mice treated with a microbial consortium containing commercially available microbial strains.

[0293] This example describes a test in which a microbial consortium containing commercially available microbial strains tests the ability to degrade oxalates in vivo in C57 / B6 female mice.

[0294] To test whether the in vivo activity of the microbial consortia described herein is observed in different sexes and strains of test mice, female C57 / B6 mice (n=3 per condition) were orally colonized with one of the following: multiple active microorganisms only, support communities only, support communities plus O. formigenes only, multiple active microorganisms lacking support communities plus O. formigenes, a complete microbial consortium (active organisms and support), or fecal samples from human donors found to be positive for O. formigenes DNA. The multiple active microorganisms and support communities contained strains marked with "X" in the vertical column of Table 8. Colonized mice were fed a defined low-complexity diet supplemented with an excess amount of oxalate to induce hyperoxaluria (see Table 2 above) or a nutritionally equivalent control diet lacking oxalate (see Table 1 above). After a period of two weeks, the mice were sacrificed, and urine, feces, serum, and tissue samples were collected for analysis. Urinary oxalate concentration

[0295] Urine samples were collected last from all groups, processed for solid-phase extraction, and then analyzed for oxalate concentration by LC-MS as described in Example 4. The absolute oxalate concentration detected in each urine feed was normalized based on the ratio of oxalate to creatinine.

[0296] As shown in Table 12, urinary oxalate levels were reduced in mice colonized with a complete microbial consortium. Partial reductions were also observed in mice colonized with only the support community, the support community plus multiple active microorganisms lacking O. formigenes, and multiple active microorganisms alone. [Table 12] (Example 7) In vivo oxalate metabolism in C57 / B6 female mice treated with the microbiological consortium's cryopreservation solution.

[0297] To test whether the microbial consortia described herein retain in vivo activity after freezing, individual live microbial cultures of commercially available strains were pooled in approximately equal proportions to form support communities only, support communities plus multiple active microorganisms lacking O. formigenes, and O. formigenes communities containing two commercially available strains of O. formigenes. These were frozen as aliquots in 30% glycerol in the vapor phase of a liquid nitrogen dewar for one month and then administered to mice. The multiple active microorganisms and support communities contained strains marked with "X" in the vertical column of the notation in Table 8.

[0298] Female C57 / B6 gnotobiote mice (n=3 per condition) were colonized by oral force-administration with either only active microorganisms (including O. formigenes), only support communities, or a complete microbial consortium (active organisms and support). Hyperoxaluria was induced in colonized mice by providing them with free access to drinking water sweetened with sucralose and containing 0.875% oxalate. Control mice were provided with drinking water sweetened with sucralose but without oxalate. All mice were maintained on standard autoclavable mousebreeder diet (LabDiet®, St. Louis, MO). After a period of two weeks, the mice were sacrificed, and a variety of samples, including urine, feces, serum, and kidneys, were collected. Urinary oxalate concentration

[0299] Similar to Example 6, urine was collected last from all groups, processed for solid-phase extraction, and then analyzed for oxalate concentration by LC / MS. The absolute oxalate concentration detected in each urine sample was normalized based on the ratio of oxalate to creatinine.

[0300] As shown in Table 13, mice provided with drinking water containing 0.875% oxalate showed significantly elevated urinary oxalate levels compared to mice given control water (e.g., approximately a four-fold increase in both mice administered with only multiple active microorganisms and mice administered with only support communities). Consistent with Examples 5 and 6, mice colonized with a complete microbial consortium had significantly lower urinary oxalate levels compared to mice administered with only multiple active microorganisms or only support communities. Furthermore, compared to Examples 5 and 6, the complete microbial consortium still showed significant oxalate metabolic activity in mice maintained on significantly different standard feed formulations. [Table 13] (Example 8) In vivo engraftment of oxalate-metabolizing microbial strains

[0301] Fecal samples from treated mice described in Example 5 were analyzed for the presence of oxalate-metabolizing microbial strains by whole-genome shotgun sequencing of microbial DNA extracted from the fecal solids. DNA extraction and whole-genome shotgun sequencing from the fecal samples were performed using the method already described in Example 1. The sequence reading data was mapped to a comprehensive database of fully sequenced genomes of all defined microbial strains, including those of the microbial consortium. The results of this experiment are summarized in Figures 10A-F.

[0302] Table 14 shows the detection of engrafted oxalate-metabolizing microbial strains in the treated mice described in Example 5. Microbial strains were counted as "detected" if their relative abundance was >0.1% of the total sequence reading data. [Table 14]

[0303] Table 15 shows the detection of engrafted support microbial strains in the treated mice described in Example 5. A microbial strain was counted as "detected" if its relative abundance was >0.1% of the total sequence reading data. [Table 15] (Example 9) In vitro oxalate metabolism by donor-derived strains

[0304] To determine the in vitro oxalate metabolic activity of three donor-derived O. formigenes strains, the strains were grown in YFCAC basic medium at pH 7.0, 6.0, or 5.0 in the presence of 80 mM oxalate. The strains were incubated at 37°C for 72 hours, and at the end of the protocol, the amount of oxalate in the medium was quantified by LC-MS as described in Example 4. For all three strains, the amount of oxalate remaining in the culture medium after 72 hours was below the detection limit when assayed at pH 7.0 or 6.0. Oxalate degradation was not detected in any of the three strains when incubated at pH 5.0.

[0305] To determine the oxalate metabolic activity of additional donor-derived microbial strains, the strains were grown under anaerobic conditions in YCFAC basic medium at pH 7.0, 6.0, or 5.0 in the presence of 2 mM oxalate. The strains were incubated at 37°C for 120 hours, and at the end of the protocol, the amount of oxalate in the medium was quantified by LC / MS as described in Example 4. Donor-derived strains of O. formigenes were included as a positive control. Results are reported as the percentage of oxalate remaining in the medium at the end of the assay compared to the starting concentration (Figure 11). As expected, the amount of oxalate remaining during culture of donor-derived O. formigenes was below the detection limit when assayed at pH 6 or pH 7, but no oxalate degradation was detected at pH 5. In contrast, none of the other donor-derived isolates tested were found to reduce oxalate by more than 11% at any of the pH levels tested. (Example 10) Growth of donor-derived O. formigenes strains at different pH and oxalate concentrations.

[0306] Three O. formigenes strains isolated from donor fecal samples were assayed for their growth ability at different pH levels (5.0, 6.0, or 7.0) and different oxalate concentrations (0 mM, 2 mM, 40 mM, 80 mM, 120 mM, and 160 mM). The strains were grown under anaerobic conditions in appropriate bank medium, and the turbidity of the cultures was recorded at 24, 48, 72, and 144 hours. The results of this assay are reported in Figures 12A–12C. One O. formigenes strain (FBI00067) was observed to grow well at lower pH levels; another strain (FBI00133) was observed to be more tolerant at higher oxalate concentrations. (Example 11) Design of support communities including donor-derived strains

[0307] Microbial support communities were designed using donor-derived strains. Five candidate communities were designed according to different design principles.

[0308] The support communities for candidate consortium I were designed to incorporate all isolated species present in more than 50% of a pair of healthy donor fecal samples. The communities further included donor-derived strains represented in the proof-of-concept consortium of commercially available strains, or (if no matching species was isolated) strains of the most closely related species within that genus. The final consortium (active organism and support) contained a total of 152 strains and 70 species, as listed in Table 16.

[0309] Supporting communities for candidate consortia II and III were designed to maximize the consumption and / or proportion of defined sets of metabolites using a minimum number of strains. In both cases, the target metabolites were identified by a literature review and by bioinformatics annotation of healthy microbiomes. Next, the genomes of donor strains were analyzed bioinformatics to identify strains capable of producing or consuming the target metabolites. A literature review was also performed to identify donor strains belonging to species known to consume and / or produce each target metabolite. Donor strains were scored for their ability to produce or consume the metabolites, and communities were designed to maximize coverage of the desired metabolites by a minimum number of species. Supporting communities for candidate consortia II were designed to enhance the consumption of 51 dietary carbon and energy sources. Supporting communities for candidate consortia III were designed to enhance the production or consumption of host-present metabolites, including bile acids, sugars, amino acids, vitamins, SCFAs, and gases. The strains included in Candidate Consortium II are listed in Table 17, and the strains included in Candidate Consortium III are listed in Table 18.

[0310] The support communities for Candidate Consortium IV were constructed using strains isolated solely from fecal samples of two healthy donors. Originating multiple support strains from one or a few donors may offer advantages in enhancing co-culturing and / or ecological stability. Both of the selected specific donors had fecal samples found to be capable of reducing urinary oxalates in vivo and potentially enhancing the use of the communities in embodiments of the present invention designed to degrade oxalates. The strains included in Candidate Consortium IV are listed in Table 19.

[0311] The supporting communities for candidate consortium V were designed to include all strains isolated from healthy donor fecal samples, excluding species known to be associated with disease development. This diverse community incorporated species from all five major phyla (Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, and Verrucomicrobia), including normal enterosymbiotic bacteria. The final consortium contained a total of 103 species and 158 strains, which are listed in Table 20. [Table 16-1] [Table 16-2] [Table 16-3] [Table 16-4] [Table 16-5] [Table 16-6] [Table 16-7] [Table 16-8] Table 16-9 Table 16-10 Table 17-1 Table 17-2 Table 17-3 Table 17-4 Table 17-5 Table 17-6 Table 18-1 Table 18-2 Table 18-3 Table 18-4 Table 18-5 Table 19-1 Table 19-2 Table 19-3 Table 19-4 [Table 19-5] [Table 20-1] [Table 20-2] [Table 20-3] [Table 20-4] [Table 20-5] [Table 20-6] [Table 20-7] [Table 20-8] [Table 20-9] (Example 12) In vivo oxalate reduction by candidate consortiums in germ-free mouse models fed low-complexity diets.

[0312] As described in Example 1, a consortium of five candidate oxalate-eliminating microorganisms, including active and supporting microorganisms isolated from human fecal samples, were tested in vivo for their ability to control oxalate levels in germ-free mice fed a limited-component, low-complexity diet supplemented with oxalates (see Table 1).

[0313] One week prior to colonization, sterile C57Bl / 6NTac mice (n=4 per condition) were fed purified feed rich in casein and monosaccharides supplemented with oxalates to induce hyperoxaluria (see Table 2). One week later, candidate consortia (I-V) described in Example 11 were introduced into the mice by oral force-administration. One group of mice was colonized with PBS alone as a negative control. Another group of mice was colonized with a previously characterized microbial consortium containing a microbial strain obtained from the depositary, which had already been shown to reduce oxalate levels in vivo, as a positive control (see Examples 6 and 7; see Table 8). Urine and fecal samples were collected weekly for the following two weeks, with day 14 post-colonization being the endpoint. The final urine (collected immediately after euthanasia) was processed by solid-phase extraction, and oxalate levels were quantified by LC / MS as described in Example 4.

[0314] The mean urinary oxalate concentrations in each test group at the test endpoint are reported in Figure 13. Mice colonized with a proof-of-concept group (+) containing a commercially available O. formigenes strain showed a mean reduction of 53% in urinary oxalate compared to non-colonized negative controls (-). Five unique candidate groups (I-V), each containing three internal isolates of O. formigenes, were found to reduce urinary oxalate by 32-70%, demonstrating efficacy comparable to the positive control group. The reduction in urinary oxalate for all tested groups was statistically significant compared to the negative controls. (Example 13) In vivo oxalate reduction in germ-free mice fed a highly complex diet by a candidate consortium.

[0315] The five candidate oxalate-eliminating microbial consortiums described in Example 10 were further tested for their ability to control oxalate levels in vivo in germ-free mice fed a nutritionally complete complex diet.

[0316] One week prior to colonization, sterile C57Bl / 6NTac mice (n=4 per condition) were fed a complex grain-based diet and given free access to drinking water supplemented with 0.875% oxalate to induce hyperoxaluria. One week later, the mice were colonized with the treatment population by oral force-dose. One group of mice was colonized with PBS alone as a negative control. Another group of mice was colonized with a previously characterized microbial consortium containing a microbial strain obtained from the depositary, which had been shown to reduce oxalate levels in vivo, as a positive control (see Examples 6 and 7; see Table 8). Urine and fecal samples were collected weekly for the following two weeks, with day 8 post-colonization being the test endpoint. The final urine (collected immediately after euthanasia) was processed by solid-phase extraction, and oxalate levels were quantified by LC / MS as described in Example 4.

[0317] Figure 14 shows the mean urinary oxalate concentrations for each test group at the test endpoint. Mice colonized with a positive control group containing a commercially available O. formigenes (+) strain showed a mean reduction of 54% in urinary oxalate compared to non-colonized negative controls (-). Five unique candidate groups (I-V), each containing three internal isolates of O. formigenes, were found to reduce urinary oxalate by 49-75%, demonstrating efficacy comparable to the positive control group. The reduction in urinary oxalate for all tested groups was statistically significant compared to the negative controls. (Example 14) In vivo oxalate reduction in humanized gnotobiotic mice by a candidate consortium

[0318] The five candidate oxalate-eliminating microbial consortiums described in Example 11 were further tested for their ability to control oxalate levels in vivo in humanized re-established mice fed a nutritionally complete complex diet.

[0319] Sterile C57Bl / 6NTac mice (n=4 per condition) were humanized by introducing previously characterized human donor fecal samples lacking O. formigenes and failing to recognizably degrade urinary oxalates. One week after colonization, the humanized mice were fed a complex grain-based diet supplemented with oxalates to induce hyperoxaluria. One week later, the mice were freely given an antibiotic cocktail containing ampicillin (1 mg / ml) and enrofloxacin (0.575 mg / ml) in drinking water for 7 days, after which the antibiotic treatment was discontinued, and the treatment groups (I-V) were introduced via oral force-administration. One group of mice was colonized with PBS alone as a negative control. Another group of mice was colonized with a previously characterized microbial consortium containing a microbial strain obtained from the depositary, which had been shown to reduce oxalate levels in vivo, as a positive control (see Examples 6 and 7; see Table 8). The last group of mice was immobilized with a set of strains ("presumably oxalate degraders") containing three donor strains of O. formigenes, in addition to other donor strains expected to possess oxalate degradation activity. This set of strains is listed in Table 21. [Table 21-1] [Table 21-2]

[0320] Samples were collected weekly from mice for two weeks after re-establishment to determine the composition of the microbiome and urinary oxalate levels. The test endpoint was 14 days after establishment of the experimental colony. The mean urinary oxalate concentration for each test group at the test endpoint is shown in Figure 15. Re-establishment with a proof-of-concept colony (+) containing a commercially available O. formigenes strain resulted in a mean 52% reduction in urinary oxalate compared to a quasi-treatment negative control (-). Five unique candidate colonies (I-V), each containing three donor-derived strains of O. formigenes, were found to reduce urinary oxalate by 22-65%, demonstrating efficacy comparable to the positive control colony. The reduction in urinary oxalate for all tested colonies was statistically significant for all but one colony (IV), and no significant differences were observed among the remaining established colonies. In particular, re-establishing only a group of presumed oxalate-degrading microorganisms did not result in a reduction of urinary oxalates, demonstrating the enhancing effect of combining multiple active oxalate-degrading microorganisms with a rationally designed support community.

[0321] Mouse fecal samples were analyzed by metagenomic sequencing to determine the composition of the microbiome. Briefly, genomic DNA was extracted from mouse fecal solids and sequenced using short-read (Illumina) sequencing. Individual reads were classified against a comprehensive reference database containing genomes from species across the entire Tree of Life. All classified reads were summed, normalized by genome size, and relative abundance estimates were obtained. The results of this analysis are summarized in Figure 16. Re-establishment by one of the candidate microbial consortia (I-V) resulted in enhanced diversity of microbiome species compared to both the proof-of-concept consortium and the putative oxalate degrader collection. (Example 15) Effect of candidate support communities on in vivo engraftment of O. formigenes

[0322] The five candidate oxalate-eliminating microbial consortiums described in Example 10 were further tested for their ability to support the engraftment of the active oxalate-degrading microorganism O. formigenes into germ-free mice.

[0323] Sterile C57Bl / 6NTac mice (n=4 per condition) were colonized with candidate microbial consortia (I-V) via oral force-administration. One group of mice was colonized with only the supporting microbial community as a negative control. At the end of the experiment, fecal samples were analyzed via metagenomic sequencing to measure the relative and absolute abundance of O. formigenes in the microbiome. Briefly, genomic DNA was extracted from mouse fecal solids and sequenced using short-read (Illumina) sequencing. Individual reads were classified against a comprehensive reference database containing genomes from species across the entire Tree of Life. All classified reads were summed and normalized by genome size to obtain estimates of relative abundance. Estimates of absolute abundance were obtained by injecting a known amount of heterologous cells into the fecal samples prior to DNA extraction and sequencing.

[0324] The results of this study are reported in Figure 17. O. formigenes was detected in all mice colonized with one of the five candidate consortia, and treatment with candidate V resulted in the highest levels of O. formigenes in the fecal samples. (Example 16) Production of exemplary therapeutic oxalate degradation consortia

[0325] This embodiment describes the production of an exemplary microbial consortium intended for use in human subjects. In one embodiment of the present invention, the exemplary consortium consists of strains listed in Table 22, including three active oxalate-degrading strains of donor-derived O. formigenes. In another embodiment of the present invention, the exemplary consortium consists of strains listed in Table 23. In another embodiment of the present invention, the exemplary consortium consists of strains listed in Table 24. All strains included in the exemplary consortium meet at least one of five criteria: a. The ability to eliminate oxalates in vitro has been experimentally confirmed. b. Belonging to a species known to metabolize formate, a major byproduct and a potent inhibitor of oxalate metabolism in the intestinal tract. c. Belonging to a species known to contribute to the metabolism of one or more nutrients typically found in the human diet. d. Belonging to a species known to perform unique and potentially beneficial biological functions in the GI tubule (e.g., bile salt hydrolase activity or butyrate production). e. Belonging to a species found in the GI ducts of one or more healthy human adults.

[0326] The final drug product consists of up to seven active pharmaceutical ingredients (APIs), each containing at least one characterized bacterial strain. Some APIs are pure cultures, while others are derived from mixed culture fermentation of anaerobic and facultative aerobic bacteria. The culture conditions for the APIs are determined by those skilled in the art.

[0327] Cells are collected and microfiltration is performed using a membrane with a pore size of 0.2-0.45 μm made of a non-reactive polymer, such as polyvinylidene fluoride, polysulfone, and / or nitrocellulose; and a combination of centrifugation (10,000-20,000 g centrifugal force) to obtain 1 × 10⁶ cells. 6 ~1 × 10 12 The biomass was concentrated to a final CFU concentration of CFU / ml. The concentrated biomass was mixed with sterile cryoprotectant (CPA) in a volume ratio of 10:1 to 1:10.

[0328] CPA consists of cryoprotective agents / carbohydrates / bulks / nutrients, such as glycerol (0-250 g / l), maltodextrin (0-100 g / l), sucrose (0-100 g / l), inulin (0-40 g / l), trehalose (0-50 g / l), and / or alginate (0-10 g / l). In addition, antioxidants, such as cysteine ​​(0.25-0.50 g / l), ascorbic acid (0-5 g / l), and / or riboflavin (0-0.01 g / l), are added to CPA. Specific concentrations are determined by those skilled in the art.

[0329] Finally, additional nutrients, such as oxalates (0-100 mM) or formates (0-100 mM), are added to support the robust reactivation of a particular strain from the capsule, with the specific concentration determined by those skilled in the art.

[0330] Cells are cryopreserved in CPA or a combination of CPA, or lyophilized, to prepare various solid oral drug formulations (e.g., enteric-coated capsules or enteric-coated tablets). The formulated cells are lyophilized to produce a stable product. Primary drying is performed below the disintegration temperature of the selected formulation (typically below -20°C), followed by secondary drying at a higher temperature (5°C or higher). The lyophilized powder is filled into capsules of sizes "0" to "000" to provide varying strengths. To prepare tablets, the lyophilized powder is added to a binder (e.g., sucrose or starch) and compressed into tablets. The tablets are enterically coated to protect the drug product from the low pH environment of the stomach.

[0331] The composition of a drug product is defined by the relative abundance of various intended strains. The relative abundance of microbial strains in the active pharmaceutical ingredient (API) or drug product is determined as follows: Whole bacterial genomic DNA is extracted from precipitated aliquots (e.g., 1 ml) of the API / drug product, quantified, normalized by concentration, and prepared into an indexed library for whole-genome shotgun sequencing on an Illumina sequencer (e.g., NovaSeq). After quality trimming, short paired-end Illumina read data (PE-150) are classified using a taxonomically structured database constructed from the genomic sequences of strains in a custom bioinformatics pipeline and the drug product. The taxonomically structured database links fixed-length (k-mer) genomic nucleotide sequences to the least common ancestor(s) (phylogenetic, species, phylum) containing the same k-mer in the database. 150-base pair sequencing read data are classified by obtaining a taxa for all k-mers in the read data and by assigning a classification based on the least common ancestor. Sequences that do not contain kmers are discarded from the database. Read data that are not classified at the strain level are distributed to the strain level using Bayes' theorem to estimate the true strain-level abundance. The relative abundance of a strain is calculated as the percentage of read data classified as that strain, divided by the genome size. The absolute abundance is calculated by dividing the total number of bacterial cells in the drug product (quantified by the Beckman-Coulter Counter) by the percentage relative abundance.

[0332] Those skilled in the art can determine useful ratios of active and supporting microorganisms constituting an exemplary consortium and will ensure that the relative abundance of supporting microbial strains is at least sufficient to enable the function and stable colonization of multiple active microorganisms. [Table 22-1] [Table 22-2] Table 22-3 Table 22-4 Table 22-5 Table 22-6 Table 22-7 Table 22-8 Table 22-9 Table 23-1 Table 23-2 Table 23-3 Table 23-4 Table 23-5 Table 23-6 Table 24-1 Table 24-2 Table 24-3 Table 24-4 [Table 24-5] [Table 24-6] (Example 17) In vivo oxalate reduction by the Therapeutic Microbial Consortium in healthy humans treated with a high-oxalate / low-calcium diet.

[0333] This study evaluates the ability of a rationally designed consortium of oxalate-degrading microorganisms to reduce urinary oxalate levels in vivo in human subjects.

[0334] Approximately 64 healthy subjects will be enrolled in the trial. Six days prior to administration of the consortium, subjects will be given a high-oxalate / low-calcium (HOLC) diet to induce a temporary hyperoxaluria state similar to that seen in intestinal hyperoxaluria (Langman et al., 2016, "A A double-blind, placebo-controlled, randomized phase 1 crossover study with ALLN-177, an orally administered oxalate degrading enzyme, (Am J Nephrol. 44(2):150-8). When administered to healthy subjects for 7 days, this diet resulted in urinary oxalate degrading enzyme levels. It has been previously shown that increasing the dose from 27.2 ± 9.5 mg / day at screening to 80.8 ± 24.1 mg / day is appropriate. This is well above the generally acceptable upper limit of the normal range (40 mg / day) and is clearly within the range widely observed in intestinal hyperoxaluria.

[0335] Some subjects are further pre-treated with a range of broad-spectrum antibiotics (a combination of metronidazole and clarithromycin) to pre-remove bacteria from the intestinal tract and to promote the subsequent colonization of heterologous communities. This combination is selected based on complementary coverage of Gram-positive and Gram-negative bacteria, broad coverage of obligate anaerobes (the dominant microbial population in the GI tube), broad coverage of facultative anaerobes including Enterobacteria (i.e., pathogenic human commensal bacteria), and the relatively favorable safety and tolerability profiles of the constituent drugs. The goal of antibiotic pre-treatment is to reduce the existing gastrointestinal bacterial load, in an attempt to suppress colonization resistance, a microorganism-mediated phenomenon that can limit the colonization of strains in the consortium.

[0336] On day 6 of HOLC diet administration and (if necessary) antibiotic pretreatment, some subjects are further given polyethylene glycol (PEG) intestinal pretreatment, an approach commonly used in fecal transplantation and well known to those skilled in the art. This treatment is designed to remove residual antibiotics from the gastrointestinal tract and further reduce the residual bacterial load from the host.

[0337] Six days after administration of the HOLC diet, subjects are administered a therapeutic microbial consortium. The duration of treatment with either the consortium or placebo is 10 days. Urinary oxalate excretion is used as a biomarker for treatment efficacy and is monitored by LC-MS as described in Example 4. Fecal samples are collected at all stages of the trial (including one month post-treatment) and used to monitor the composition of the microbiome by metagenomic sequencing. This facilitates monitoring the level and persistence of engraftment of the consortium strains.

[0338] Approximately 64 healthy individuals will be randomly assigned in a 1:1:1:1 ratio to one of the following five regimens: a. Pre-treatment with antibiotics followed by PEG intestinal pre-treatment, and then treatment by the consortium. b. Treatment by the consortium after antibiotic pretreatment. c. Treatment with antibiotic placebo followed by PEG bowel preparation, and then treatment by consortium. d. Placebo treatment following antibiotic pretreatment.

[0339] Participants will be confined for two periods, separated by approximately 20-day drug-free intervals. The first confinement period is approximately 18 days and includes a 10-day course of therapeutic consortium or placebo, following antibiotic / antibiotic-placebo pretreatment, followed by either PEG-assisted bowel preparation or no bowel preparation. The second confinement period is approximately 6 days. The sample size for this study was selected to identify approximately 20% change in urinary oxalate levels between cohorts. This study will enable the evaluation of the therapeutic consortium's ability to reduce urinary oxalate levels in human subjects. This study will further evaluate the efficacy of the described pretreatment methods (antibiotic pretreatment and PEG pretreatment). (Example 18) In vivo oxalate reduction in human patients with intestinal hyperoxaluria by a therapeutic microbiome consortium.

[0340] Enteric hyperoxaluria is characterized by increased renal oxalate excretion (>40 mg / day), recurrent kidney stones, renal calcium deposition (nephrocalcemia), and, in severe cases, excessive absorption or consumption of dietary oxalates leading to progressive renal impairment and end-stage renal failure (Liu and Nazzal, 2019, "Enteric hyperoxaluria: role of microbiota and "Antibiotics," Curr Opin Nephrol Hypertens. 28(4):352-359; Ermer et al., 2016; "Oxalate, inflammasome, and progression of kidney disease," Curr Opin Nephrol Hypertens. 25(4):363-71). Roux-en-Y gastric bypass (RYGB) surgery is a common comorbidity associated with intestinal hyperoxaluria (approximately 60% of RYGB patients). This study evaluates the ability of an oxalate-degrading microbial consortium to reduce urinary oxalate levels in vivo in a cohort of up to approximately 16 Roux-en-Y gastric bypass (RYGB) patients with intestinal hyperoxaluria.

[0341] A cohort of up to approximately 16 participants will receive antibiotic pretreatment, PEG intestinal pretreatment, and 10 days of treatment with the therapeutic microbiome consortium, as described in Example 17. Urine and fecal samples will be collected at different stages of treatment to monitor urinary oxalate levels and engraftment of the consortium strain, as described in Example 17. Fecal samples will be collected again at 30, 60, and 90 days to assess long-term engraftment of the consortium strain by metagenomic sequencing. This study will demonstrate the consortium's ability to reduce urinary oxalate levels in RYGB patients. (Example 19) Screening of strains for in vitro bile acid compound metabolic activity

[0342] In vitro metabolic screening is necessary to clearly characterize the ability of microbial strains to degrade bile acid compounds. Strains are screened against a panel of bile acid compounds, and structural transformations of bile acids are evaluated as described. Briefly, a single microbial culture is collected overnight by anaerobic centrifugation and resuspended in fresh, pre-reduced growth medium (e.g., Mega Medium) supplemented with 100 μM bile acids (e.g., TCA, TCDCA, GCA, GCDCA, CA, CDCA, 3oxoCA, 7oxoCA, 12oxoCA, UDCA, DCA, LCA, 3oxoLCA), and incubated at 37°C for 24 hours. Cultures are collected for bile acid analysis at 0, 6, and 24 hours after bile acid addition. For bile acid analysis, 2 ml of culture is collected and immediately acidified with 50 μl of 6N HCl to halt all metabolic activity and protonate the bile acids to make them soluble in organic solvents. The acidified culture is extracted for bile acids and analyzed by LC-MS (UPLC-QTOF or ULC-QQQ).

[0343] A preliminary screening of commercially available strains using TCA as a feeder molecule was performed using this protocol, and the results are illustrated in Figure 18. (Example 20) Screening of strains for resistance to bile acids

[0344] To determine the effect of bile acid presence on microbial strain growth, microbial cultures are grown to saturation in their respective bank media (e.g., Mega Media or Chopped Meat Media) and then diluted back into the same bank media containing varying concentrations of bile acid. Percentage growth inhibition is calculated by determining the ratio of the absorbance (OD) of the microbial strain grown in the presence of bile acid (with background subtraction) to the OD of the same microbial strain grown in the absence of bile acid. (Example 21) Mouse chemically induced primary sclerosing cholangitis model and microbiome-induced shifts in bile acid composition

[0345] This embodiment describes the establishment of a mouse chemically induced primary sclerosing cholangitis (PSC) model and demonstrates that alterations to the microbiome can change the composition of the bile acid pool and affect disease severity.

[0346] On day 0 of the experiment, sterile 7-9 week old female C57B / 6N mice were weighed, and one of two rationally designed microbial consortia was orally administered to the mice for colonization. One cohort of mice was colonized with a complete microbial consortium containing multiple microorganisms, including species with 7α-dehydroxylation activity and species with bile salt hydrolase (BSH) activity. A second cohort of mice was colonized with a partial microbial consortium, which was identical in composition to the complete consortium except for the lack of species with 7α-dehydroxylation activity. A control cohort of mice was treated with sterile saline.

[0347] Mice are fed a standard research diet for two weeks to stabilize their microbiome. Starting on day 14 and continuing for another 14 days, the standard diet is supplemented with an equimolar concentration of 1% (weight / weight) hepatotoxic secondary bile acid LCA, or conjugated bile acid GCDCA or primary bile acid CDCA to induce PSCs. GCDCA can be metabolized to CDCA by a microbial population with BSH activity, and CDCA can be metabolized to LCA by a microbial population with 7α-dehydroxylation activity.

[0348] On days 0, 7, 14, 21, and 28, mice are monitored for indicators of chemically induced PSC (e.g., weight loss, reduced food consumption, elevated liver enzyme levels), and fecal samples are collected. Fecal samples are analyzed by LC / MS to determine the composition of the bile acid pool, and metagenomic sequencing is used to monitor the engraftment of microbial strains. Mice are euthanized on or before day 28, and final samples are collected to allow screening for additional PSC indicators (e.g., changes in GI physiology, cecal bile acid composition).

[0349] Mice fed a diet supplemented with hepatotoxic LCA are expected to have elevated fecal LCA levels and exhibit signs of PSC, thereby establishing a mouse disease model. Mice colonized with a complete set of microorganisms and fed a diet supplemented with GCDCA or CDCA are similarly expected to have elevated LCA content, as upstream substrates can be metabolized to LCA by the colonized microorganisms. Mice inoculated with a partial set of microorganisms and fed a diet supplemented with conjugated bile acids are expected to lack LCA in their bile acid pool, as the colonized microbial population lacks the activity necessary to metabolize upstream substrates to LCA. Therefore, these mice are expected to exhibit less severe signs of PSC. Taken together, these results demonstrate that alterations to the microbiome can promote shifts in the bile acid pool in animals and influence disease severity. (Example 22) In a mouse PSC model treated by a microbial consortium, hepatotoxic bile acids were reduced in Human reduction

[0350] This embodiment evaluates the ability of a bile acid metabolic microbial consortium, comprising multiple active microorganisms and supporting communities of these microorganisms, to alter the bile acid pool and influence disease severity in animals. The microbial consortium comprises multiple active microorganisms and supporting communities of these microorganisms, wherein the multiple active microorganisms include strains experimentally confirmed to possess 3α-HSDH and / or 3β-HSDH activity, and the supporting communities of these microorganisms include strains experimentally confirmed to possess 7α-HSDH activity, 7β-HSDH activity, and / or bile acid hydrolase activity.

[0351] To test the in vivo activity of the bile acid-metabolizing microbial consortia described herein, sterile C57B / 6N female mice are weighed on day 0, and the mice are colonized by oral force-administration with either a subset of active microorganisms only, a support community only, or a complete microbial consortium (active organisms and support). The mice are fed a standard research diet for two weeks, during which time the microorganisms are stabilized. Starting on day 14 and continuing for 14 days, the standard diet is supplemented with 1% (weight / weight) hepatotoxic secondary bile acid LCA to induce PSCs. Body weight, diet weight, and fecal bile acid composition are monitored over the two-week period. After the two-week period, the mice are sacrificed, and diverse final samples, including cecum, feces, and serum, are collected.

[0352] Mice treated with a complete microbial consortium (active organism and support) are expected to have reduced hepatotoxic LCA levels compared to untreated controls (no microbial implantation) and exhibit less severe signs of PSC. Mice treated with only the active microorganisms are also expected to have lower LCA levels compared to untreated mice, but lower than mice treated with the complete consortium. Mice implanted with only the support community are not expected to have substantially lower LCA levels than untreated mice. Taken together, these results demonstrate the ability of bile acid-metabolizing microbial consortia to alter the bile acid pool in animals and subsequently alleviate PSC symptoms. In certain embodiments, for example, the following items are provided: (Item 1) A consortium of microorganisms for administration to animals, It contains multiple active microorganisms and an effective amount of microbial support communities. The plurality of active microorganisms metabolize the first metabolite to produce one or more metabolites, and the first metabolite is the cause or contributing factor of a disease in animals. The aforementioned supporting community of microorganisms includes between 1 and 300 microbial strains. The following four conditions apply to the aforementioned supporting communities of microorganisms: 1) The supporting community of microorganisms metabolizes one or more metabolites produced by the plurality of active microorganisms, and the one or more metabolites inhibit the metabolism of the first metabolic substrate by one or more of the plurality of active microorganisms. 2) Conditions that increase the flow rate of the precursor of the first metabolic substrate into the biochemical pathway that converts the precursor into metabolites other than the first metabolic substrate, 3) Conditions under which the support community of microorganisms, when administered to an animal, improve one or more of the properties of the multiple active microorganisms selected from the group consisting of a) colonization in the gastrointestinal tract, b) biomass, c) metabolism of the first metabolic substrate, and d) long-term stability, compared to the administration of the multiple active microorganisms in the absence of the support community of microorganisms, and 4) The microbial support community ferments polysaccharides into one or more of the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H2 and CO2; ferments amino acids into one or more of the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, floleate, 3-(1H-indole-3-yl)propanoate, 5-aminopentanoate, H2, H2S and CO2; methane from H2 and CO2; methane from formate and H2; acetate from H2 and CO2. Conditions for catalyzing one or more reactions selected from the group consisting of acetate from formate and H2, acetate and sulfide from H2, CO2 and sulfate, propionate and CO2 from succinate, succinate from H2 and fumarate, succinate from formate and fumarate, and succinate from lactate, succinate, acetate, H2 and CO2, decoupling of conjugated bile acids to produce primary bile acids, conversion of cholic acid (CA) to 7-oxocholic acid, conversion of 7-oxocholic acid to 7-betacholic acid (7-betaCA), conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA). A microbial consortium that satisfies at least one of the following conditions. (Item 2) The aforementioned supporting community of microorganisms 1) Metabolizing one or more metabolites produced by the plurality of active microorganisms, which inhibit the metabolism of the first metabolic substrate by one or more of the plurality of active microorganisms, 2) Increase the flow rate of the precursor of the first metabolic substrate into the biochemical pathway that converts the precursor into a metabolite that is not the first metabolic substrate. The microbial consortium described in item 1. (Item 3) The aforementioned supporting community of microorganisms 1) Metabolizing one or more metabolites produced by the plurality of active microorganisms, which inhibit the metabolism of the first metabolic substrate by one or more of the plurality of active microorganisms, 2) When administered to the animal, improves one or more of the properties of the multiple active microorganisms selected from the group consisting of a) colonization in the gastrointestinal tract, b) biomass, c) metabolism of the first metabolic substrate, and d) long-term stability, compared to the administration of the multiple active microorganisms in the absence of the supporting community of the microorganisms. The microbial consortium described in item 1. (Item 4) The aforementioned supporting community of microorganisms 1) Metabolizing one or more metabolites produced by the plurality of active microorganisms, which inhibit the metabolism of the first metabolic substrate by one or more of the plurality of active microorganisms, 2) Fermentation of polysaccharides into one or more of the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H2 and CO2; fermentation of amino acids into one or more of the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, floleate, 3-(1H-indole-3-yl)propanoate, 5-aminopentanoate, H2, H2S and CO2; methane from H2 and CO2, formate and methane from H2, acetate from H2 and CO2, formate The synthesis of one or more of the group consisting of acetate from H2, acetate and sulfide from H2, CO2 and sulfate, propionate and CO2 from succinate, succinate from H2 and fumarate, the synthesis of succinate from formate and fumarate, and butyrate from lactate, acetate, H2 and CO2, the decoupling of conjugated bile acids to produce primary bile acids, the conversion of cholic acid (CA) to 7-oxocholic acid, the conversion of 7-oxocholic acid to 7-betacholic acid (7-betaCA), the conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and the conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA), The microbial consortium described in item 1. (Item 5) The aforementioned supporting community of microorganisms 1) Increase the flow rate of the precursor of the first metabolite into the biochemical pathway that converts the precursor into a metabolite that is not the first metabolite. 2) When administered to the animal, improves one or more of the properties of the multiple active microorganisms selected from the group consisting of a) colonization in the gastrointestinal tract, b) biomass, c) metabolism of the first metabolic substrate, and d) long-term stability, compared to the administration of the multiple active microorganisms in the absence of the supporting community of the microorganisms. The microbial consortium described in item 1. (Item 6) The aforementioned supporting community of microorganisms 1) Increase the flow rate of the precursor of the first metabolite into the biochemical pathway that converts the precursor into a metabolite that is not the first metabolite. 2) Fermentation of polysaccharides into one or more of the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H2 and CO2; fermentation of amino acids into one or more of the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, floleate, 3-(1H-indole-3-yl)propanoate, 5-aminopentanoate, H2, H2S and CO2; methane from H2 and CO2, formate and methane from H2, acetate from H2 and CO2, formate The synthesis of one or more of the group consisting of acetate from H2, acetate and sulfide from H2, CO2 and sulfate, propionate and CO2 from succinate, succinate from H2 and fumarate, the synthesis of succinate from formate and fumarate, and butyrate from lactate, acetate, H2 and CO2, the decoupling of conjugated bile acids to produce primary bile acids, the conversion of cholic acid (CA) to 7-oxocholic acid, the conversion of 7-oxocholic acid to 7-betacholic acid (7-betaCA), the conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and the conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA), The microbial consortium described in item 1. (Item 7) The aforementioned supporting community of microorganisms 1) When administered to the animal, it improves one or more properties of the multiple active microorganisms selected from the group consisting of a) colonization in the gastrointestinal tract, b) biomass, c) metabolism of the first metabolic substrate, and d) long-term stability, compared to the administration of the multiple active microorganisms in the absence of the supporting community of the microorganisms. 2) Fermentation of polysaccharides into one or more of the group consisting of acetate, acetoin, 2-oxoglutarate, propionate, 1,3-propanediol, succinate, ethanol, lactate, butyrate, 2,3-butanediol, acetone, butanol, formate, H2 and CO2; fermentation of amino acids into one or more of the group consisting of acetate, propionate, butanoate, butyrate, isobutyrate, 2-methylbutyrate, isovalerate, isocaproate, 3-phenylpropanoate, floleate, 3-(1H-indole-3-yl)propanoate, 5-aminopentanoate, H2, H2S and CO2; methane from H2 and CO2, formate and methane from H2, acetate from H2 and CO2, formate The synthesis of one or more of the group consisting of acetate from H2, acetate and sulfide from H2, CO2 and sulfate, propionate and CO2 from succinate, succinate from H2 and fumarate, succinate from formate and fumarate, and butyrate from lactate, acetate, H2 and CO2, the decoupling of conjugated bile acids to produce primary bile acids, the conversion of cholic acid (CA) to 7-oxocholic acid, the conversion of 7-oxocholic acid to 7-betacholic acid (7-betaCA), the conversion of chenodeoxycholic acid (CDCA) to 7-oxochenodeoxycholic acid, and the conversion of 7-oxochenodeoxycholic acid to ursodeoxycholic acid (UDCA), The microbial consortium described in item 1. (Item 8) The aforementioned supporting community of microorganisms 1) Metabolizing one or more metabolites produced by the plurality of active microorganisms, which inhibit the metabolism of the first metabolic substrate by one or more of the plurality of active microorganisms, 2) Increase the flow rate of the precursor of the first metabolic substrate into the biochemical pathway that converts the precursor into a metabolite that is not the first metabolic substrate. 3) When administered to animals, improves one or more of the properties of the multiple active microorganisms selected from the group consisting of a) colonization in the gastrointestinal tract, b) biomass, c) metabolism of the first metabolic substrate, and d) long-term stability, compared to the administration of the multiple active microorganisms in the absence of the supporting community of the microorganisms. The microbial consortium described in item 1. (Item 9) The aforementioned supporting community of microorganisms 1) Increase the flow rate of the precursor of the first metabolite into the biochemical pathway that converts the precursor into a metabolite that is not the first metabolite. 2) When administered to animals, compared to the administration of the multiple active microorganisms in the absence of the supporting community of the microorganisms, improves one or more of the properties of the multiple active microorganisms selected from the group consisting of a) engraftment in the gastrointestinal tract, b) biomass, c) metabolism of the first metabolic substrate, and d) long-term stability, 3) Fermentation of polysaccharides into one or more of the group consisting of acetate, acetoin, 2-oxoglut...

Claims

[Claim 1] The invention described in the present specification.

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