Methods for treating lipid and cholesterol metabolism associated diseases and conditions

Abstract

Methods and uses of compositions (e.g. comprising one or more microbial strains, one or more components (e.g. microbial components), one or more metabolites (e.g. microbial metabolites), or any combination thereof) for prevention, reduction of risk, treatment, and / or improvement of metabolism (e.g. lipid and cholesterol metabolism) associated diseases, disorders, and conditions are disclosed.

Description

METHODS AND USES OF MICROBIOME COMPOSITIONS, COMPONENTS, OR METABOLITES FOR TREATING LIPID AND CHOLESTEROL METABOLISMASSOCIATED DISEASES, DISORDERS, AND CONDITIONSCROSS REFERENCE TO RELATED APPLICATIONS

[0001] The present application claims priority to United States Provisional Patent Application No. 63 / 581,550 filed September 8, 2023, the entire contents of which are hereby incorporated by reference in their entirety.BACKGROUND

[0002] Many diseases, disorders, or conditions including, but not limited to, lipid- induced metabolic syndrome, cerebral infarction / stroke, myocardial infarction / heart attack, Type II diabetes / diabetes mellitus, glucose intolerance, alcoholism, metabolic syndrome, kidney disease, cardiorenal syndrome, vascular diseases (e.g., hypertension, peripheral arterial disease), Alzheimer’s disease, asthma (e.g., due to abdominal obesity or central / truncal obesity), atherosclerosis, hypothyroidism, liver disease, LDL- hypercholesterolemia, hypertriglyceridemia, mixed hyperlipoproteinemia, coronary heart disease, stroke, peripheral arterial disease, high blood pressure, hyperlipidemia, steatosis, non-alcoholic steatohepatitis (NASH), fatty -liver disease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), liver fibrosis, cirrhosis, or hepatocellular carcinoma are suspected to be associated with improper metabolism (e.g. improper lipid metabolism or improper cholesterol metabolism). Currently, there are no effective treatments to improve and / or treat the overall health and well-being of subjects (e.g. patients), regain and maintain their proper metabolism levels, and by extension improve and / or treat metabolism associated diseases, disorders, and conditions (e.g. including any diseases associated with lipid and / or cholesterol metabolism), and finding new drugs or treatment methods is a priority.SUMMARY

[0003] The present disclosure provides an insight that compositions (e.g. microbiome compositions) and methods as described herein may be used to treat diseases,disorders, or conditions (e.g. metabolism (e.g. lipid and cholesterol metabolism) associated diseases, disorders, and conditions) in a subject (e.g. a mammal (e.g. human, mice, etc.)). Furthermore, the present disclosure identifies that compositions (e.g. microbiome compositions) and methods as described herein may be used to treat and / or improve the metabolic health of a subject (e.g. prevent, improve, and / or repair metabolism associated cell damage or organ damage), and improve overall functionality and health of a subject. Moreover, the present disclosure appreciates that compositions (e.g. microbiome compositions) and methods as described herein may be used to treat and / or improve the health and overall functionality of any organs, tissues, and / or other internal parts of a subject. Among other things, the present disclosure describes technologies that can be used to treat, prevent, and / or reduce the risk of a disease, disorder, or condition (e.g. metabolism (e.g. lipid and cholesterol metabolism) associated diseases, disorders, and conditions). In some embodiments, the present disclosure describes compositions and methods to evaluate the effects of administering such compositions (e.g. microbiome compositions as described herein) to a subject and / or to identify or characterize effects and / or modulation of levels of metabolites or a metabolome in a subject upon administration of such compositions. In some embodiments, the metabolites that may be modulated may be associated with certain diseases, disorders, or conditions. In some embodiments, such technologies can be useful to discern metabolite-level differences in a particular subject (e.g., patient) or population (e.g. before and after administration of disclosed compositions). Accordingly, the present disclosure also provides technologies that can be useful to identify and / or assess the nature and effect of disclosed compositions in specific subjects (e.g., patients) and / or populations and thus provide subject-specific information on how to treat a disease, disorder, or condition (e.g. metabolism (e.g. lipid and cholesterol metabolism) associated diseases, disorders, and conditions) in an individual subject or individual population. For example, in some embodiments, technologies provided herein can be useful to identify subject-specific compositions, based on the metabolome in subject-specific samples, and treat and / or prevent a disease, disorder, or condition (e.g. metabolism (e.g. lipid and cholesterol metabolism) associated diseases, disorders, and conditions) by administering disclosed compositions (e.g. subject-specific compositions) (e.g. to modulate subject's metabolome). Thus, technologies described herein may be useful as therapeutics and tools for reducing the risk of certain diseases, disorders, or conditions (e.g. metabolism associated (e.g. lipid and cholesterolmetabolism) diseases, disorders, and conditions), and for treating and / or preventing such diseases, disorders, or conditions.

[0004] The present disclosure appreciates the insight that compositions described herein (e.g. microbiome compositions) directly influence metabolic activity and therefore influence the functioning of organs, organ systems, and overall health of a subject. Prior technologies have been limited to treating only a part of such systems, e.g., dysfunctions associated with a particular organ. The present disclosure recognizes that such technologies, while beneficial, are triaging only a portion of the overall issues. The present disclosure, therefore, provides compositions and methods directed to improving function and overall health (e.g., metabolic health) of cells, tissues, organs, organ systems, one or more connected organs, and / or a subject.

[0005] Among other things, the present disclosure provides a method of treating or preventing a metabolism-associated disease, disorder, or condition (e.g. lipid and cholesterol metabolism). In some embodiments, a method comprises administering to a subject a composition comprising one or more microbial strains or microbial components. In some embodiments, a method comprises administering to a subject a composition comprising one or more microbial metabolites. In some embodiments, a method comprises administering to a subject a composition comprising (i) one or more microbial strains or microbial components, or (ii) one or more microbial metabolites.

[0006] In some embodiments, a metabolism-associated disease, disorder, or condition is or comprises one or more of body weight gain, lipid accumulation in liver, accumulation of visceral fat, elevated blood triglyceride levels, hypercholesterolemia, inflammation, and / or high blood-cholesterol levels (e.g. Low Density Lipoprotein (LDL) levels). In some embodiments, a subject has been diagnosed with or is at high risk of a lipid disease, disorder, or condition. In some embodiments, a lipid disease, disorder, or condition is or comprises one or more of body weight gain, lipid accumulation in liver, accumulation of visceral fat, elevated blood triglyceride levels, hypercholesterolemia, inflammation, and / or high blood-cholesterol levels (e.g. Low Density Lipoprotein (LDL) levels).

[0007] In some embodiments, a subject has been diagnosed with or is at high risk of a metabolic disease, disorder, or condition. In some embodiments, a subject has been diagnosed with or is at high risk of lipid-induced metabolic syndrome, cerebral infarction / stroke, myocardial infarction / heart attack, Type II diabetes / diabetes mellitus,glucose intolerance, alcoholism, metabolic syndrome, kidney disease, cardiorenal syndrome, vascular diseases (e.g., hypertension, peripheral arterial disease), Alzheimer’s disease, asthma (e.g., due to abdominal obesity or central / truncal obesity), atherosclerosis, hypothyroidism, liver disease, LDL-hypercholesterolemia, hypertriglyceridemia, mixed hyperlipoproteinemia, coronary heart disease, stroke, peripheral arterial disease, high blood pressure, hyperlipidemia, steatosis, non-alcoholic steatohepatitis (NASH), fatty-liver disease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), liver fibrosis, cirrhosis, or hepatocellular carcinoma.

[0008] In some embodiments, a subject is animal. In some embodiments, a subject is a mammal, e.g., a mammal that experiences or is susceptible to a disease, disorder, or condition as described herein. In some embodiments, an animal is a vertebrate, e.g., a mammal, such as a non-human primate, (particularly a higher primate), a sheep, a dog, a rodent (e.g. a mouse or rat), a guinea pig, a goat, a pig, a cat, a rabbit, or a cow. In some embodiments, an animal is a non-mammal animal, such as a chicken, an amphibian, a reptile, or an invertebrate. In some embodiments, a subject is a human.

[0009] In some embodiments, a subject is suffering from or susceptible to one or more metabolism-associated disease, disorder, or condition as described herein. In some embodiments, a subject displays one or more symptoms of one or more metabolism- associated disease, disorder, or condition as described herein. In some embodiments, a subject has been diagnosed with one or more metabolism-associated disease, disorder, or condition as described herein. In some embodiments, the subject is receiving or has received certain therapy to diagnose and / or to treat one or more metabolism-associated disease, disorder, or condition.

[0010] In some embodiments, one or more microbial strains are from a mammalian microbiome. In some embodiments, one or more microbial strains are from a human microbiome. In some embodiments, a human microbiome is the microbiome of the subject. In some embodiments, a human microbiome is administered to maintain or modulate the microbiome of the subject.

[0011] In some embodiments, one or more microbial components or microbial metabolites are selected from Appendix 1, Appendix 3, or Appendix 4. In some embodiments, metabolites can be from one or more microbial strains. In some embodiments, metabolites can be from a source that is not a microbial strain, e.g.,synthetically generated. In some embodiments, one or more microbial metabolites is or comprises a bile acid, Cholesterol, chenodeoxycholic acid, 16α-chenodeoxycholic acid (CDCA), oxysterols, taurochenodeoxycholic acid, cholic acid, lithocholic acid, ursodeoxycholic acid, triglycerides, very-low density lipoprotein (VLDL), VLDL-TG, cholesterol, eicosanoids, arachidonic acid, docosahexaenoic acid, eicosapentaenoic acid, trimethylamines (TMA), trimethylamine-N-oxide (TMAO), endogenous ethanol, acetone, acetaldehyde, butyrate, choline, or any combination thereof. In some embodiments, one or more microbial metabolites is or comprises Tauroursodeoxycholic acid, taurocholic acid, long-chain acyl-CoA dehydrogenase (LCAD), deoxycholic acid (DCA), lithocholic acid (LCA), taurochenodeoxycholic acid, ursodeoxycholic acid, 7α-hydroxycholesterol, chenodeoxycholic acid, 27-hydroxycholesterol, 7α-hydroxy-4-cholestene-3-one, or any combination thereof. In some embodiments, one or more microbial components or microbial metabolites is Butyrylcamitine, Theobromine, p-Hydroxyphenylpyruvic acid, Propionic acid, Picolinic acid, 2-Hydroxy-4methylvaleric acid, N6-Acetylysine, Urocanic acid, N5-Ethylglutamine, Trigonelline, Stachydrine, Ectoine, 5-Hydroxylysine, Arginine (arg), Cholic acid, 2-(4-Hydroxyphenyl)propionic acid, N-Acetyltryptophan, Hydroxyproline, Argininosuccinic acid, Glutamic acid (Glu), Sarcosine, 5- Methoxyindoleacetic acid, Indole-3-lactic acid, Isovalerylalanine, N-Acetylleucine, 1- Methylhistidine, N-Acetylephenylalanine, Proline (Pro), or any combination thereof. In some embodiments, one or more microbial components or microbial metabolites is 4- Hydroxyphenylpyruvic, Ectoine, Gramine, N-Acetyl-L-phenylalanine, Nepsilon-Acetyl-L- lysine, Stachydrine, Trigonelline, 3-Ureidopropionic acid, Theobromine, Hippuric acid, Imidazolepropionic acid, NG-Methyl-L-arginine, trans-Urocanic Acid, N-Acetyl-L-leucine, Sarcosine, Isobutyrylcarnitine, b-Hydroxyisovaleric acid, L-Theanine / N5-Ethylglutamine, 5- Hydroxylysine, Phenaceturic acid, betaine, hydroxyproline, Picolinic acid, 2-Aminoadipic acid, Glycerophosphocholine, carnitine, Glycerol 3-phosphate, Argininosuccinic acid, creatine, Terephthalic acid, Homocitrulline, Mucic acid, Homocysteinesulfinic acid, Trimethyllysine, Spermidine, Glyoxylic acid, XA0013 C6H6O4S, 3-Indoxylsulfuric acid, Nicotinamide, N-Formylglycine, Ureidoglycolate, N-Methylproline, Glucaric acid, Butyrylcarnitine, Methionine sulfoxide, Carboxymethyllysine, Glycolic acid, Phenaceturic acid, Diethanolamine, Phosphorylcholine, Guanidinosuccinic acid, N-Acetylhistidine, Glyceric acid, S-Methylmethionine, Cysteine glutathione disulfide, Kynurenine, N- Acetylphenylalanine, Threonic acid, Malic acid, 7,8-Dihydrobiopterin, Homovanillic acid,Taurocholic acid, 5 Methoxyindoleacetic acid, butyrate, b-Hydroxyisovaleric acid, 2- Oxoglutaric acid, N-Acetyltryptophan, Thiaproline, Hypotaurine, Cholic acid, Acetoacetic acid, Ethanolamine, Guanidoacetic acid, S-Sulfocysteine, Myristic acid C14:0 XA0027, or any combination thereof.

[0012] In some embodiments, one or more microbial strains are or comprise Gluconacetobacter sp., Terrisporobacter sp., Coprococcus sp., Lactobacillus sp., Clostridium sp., Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus sp., Acidaminococcus sp., or a combination thereof. In some embodiments, one or more microbial strains are or comprise Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, one or more microbial strains are or comprise Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Clostridium butyricum, Paenibacillus barengoltzii, Veillonella atypica, Bifidobacterium breve, Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, one or more microbial strains are or comprise Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., Bifidobacterium sp., or a combination thereof. In some embodiments, one or more microbial strains are or comprise Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, Bifidobacterium breve, or a combination thereof. In some embodiments, one or more microbial strains is or comprises Bacillus subtilis.

[0013] In some embodiments, a composition comprises two or more microbial strains. In some embodiments, a composition comprises five or more microbial strains. In some embodiments, a composition comprises ten or more microbial strains.

[0014] In some embodiments, a composition is administered topically, orally, subcutaneously, intravenously, intramuscularly, intracerebrally, intrathecally, rectally, opthalmically, intravitreally, or suprachoroidally. In some embodiments, a composition is administered orally. In some embodiments, a composition is administered intravenously.

[0015] In some embodiments, a composition is formulated as a syrup, a liquid, a tablet, a troche, a gummy, a capsule, a powder, a gel, a film, an injection, or an eye drop.

[0016] In some embodiments, each microbial strain of the one or more microbial strains is present in the composition at a concentration from 101to 1015CFU. In some embodiments, each microbial strain of the one or more microbial strains is present in the composition at a concentration of at least 106CFU. In some embodiments, each microbial strain of one or more microbial strains in a composition comprises 101colony forming units (CFUs) to 1020CFU. In some embodiments, each microbial strain of one or more microbial strains in a composition comprises 101colony forming units (CFUs) to 1015CFU. In some embodiments, each microbial strain of one or more microbial strains in a composition comprises 106CFU to 1015CFUs. In some embodiments, each microbial strain of one or more microbial strains in a composition comprises about 101CFU to 1015CFU, or about 102CFU to 1014CFU, or about 103CFU to 1013CFU, or about 104CFU to 1013CFU, or about 105CFU to 1012CFU, or about 106CFU to 1011CFU, or about 107CFU to 1010CFU, or about 108CFU to 109CFU, or about 105CFU to 1010CFU, or about 108CFU to 1012CFU. In some embodiments, each microbial strain of one or more microbial strains in a composition comprises at least about 101, 5 x 101, 102, 5 x 102, 103, 5 x 103, 104, 5 x 104, 105, 5 x 105, 106, 5 x 106, 107, 5 x 107, 108, 5 x 108, 109, 5 x 109, 1010, 5 x 1010, 1011, 5 x 1011, 1012, or more CFUs. In some embodiments, each of one or more microbial strains in a composition comprises at most about 1015, 5 x 1014, 1014, 5 x 1013, 1013, 5 x 1012, 1012, 5 x 1011, 1011, 5 x 1010, 1010, 5 x 109, 109, 5 x 108, 108, or less CFUs. In some embodiments, each microbial strain of one or more microbial strains in a composition comprises same number of CFUs. In some embodiments, some microbial strains of one or more microbial strains in a composition comprises a different number of CFUs.

[0017] The present disclosure provides, among other things, a composition for use in treating a metabolic disease, disorder, or condition comprising one or more microbial strains or microbial components. In some embodiments, a composition, as described herein, is for use in treating a metabolic disease, disorder, or condition comprises one or more microbial metabolites (e.g. derived from sources other than microbial strains (e.g. synthetically derived), derived from one or more microbial strains).

[0018] The present disclosure provides a composition comprising one or more microbial strains selected from Gluconacetobacter sp., Terrisporobacter sp., Coprococcus sp., Lactobacillus sp., Clostridium sp., Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus sp., Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises one or more microbial strains selected from Gluconacetobacterhansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises one or more microbial strains selected from Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Clostridium butyricum, Paenibacillus barengoltzii, Veillonella atypica, Bifidobacterium breve, Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises one or more microbial strains selected from Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., Bifidobacterium sp., or a combination thereof. In some embodiments, a composition comprises one or more microbial strains selected from Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, Bifidobacterium breve, or a combination thereof.

[0019] In some embodiments, a composition comprises a microbial strain. In some embodiments, a microbial strain is Bacillus subtilis.

[0020] In some embodiments, a composition comprises at least two microbial strains selected from a group consisting of Gluconacetobacter sp., Terrisporobacter sp., Coprococcus sp., Lactobacillus sp., Clostridium sp., Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus sp., Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises at least two microbial strains selected from a group consisting of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises at least two microbial strains selected from Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Clostridium butyricum, Paenibacillus barengoltzii, Veillonella atypica, Bifidobacterium breve, Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises at least two microbial strains selected from Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., Bifidobacterium sp., or a combination thereof. In some embodiments, a composition comprises at least two microbial strains selected from a group consisting of Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus,Lactobacillus plantarum, Veillonella atypica, Bifidobacterium breve, or a combination thereof.

[0021] In some embodiments, a composition comprises at least five microbial strains selected from a group consisting of Gluconacetobacter sp., Terrisporobacter sp., Coprococcus sp., Lactobacillus sp., Clostridium sp., Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus sp., Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises at least five microbial strains selected from a group consisting of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises at least five microbial strains selected from Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Clostridium butyricum, Paenibacillus barengoltzii, Veillonella atypica, Bifidobacterium breve, Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises at least five microbial strains selected from Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., Bifidobacterium sp., or a combination thereof. In some embodiments, a composition comprises at least five microbial strains selected from a group consisting of Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, Bifidobacterium breve, or a combination thereof.

[0022] In some embodiments, a composition comprises or consists of Gluconacetobacter sp., Terrisporobacter sp., Coprococcus sp., Lactobacillus sp., Clostridium sp., Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus sp., Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises or consists of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises or consists of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Clostridium butyricum, Paenibacillus barengoltzii, Veillonella atypica, Bifidobacterium breve, Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises or consists of Gluconacetobacter hanseni,Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., Bifidobacterium sp., or a combination thereof. In some embodiments, a composition comprises or consists of Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, Bifidobacterium breve, or a combination thereof.

[0023] In some embodiments, a composition as described herein comprises at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten microbial strains (e.g. microbial strains as disclosed herein). In some embodiments, a composition as described herein comprises at most one, at most two, at most three, at most four, at most five, at most six, at most seven, at most eight, at most nine, or at most ten microbial strains (e.g. microbial strains as disclosed herein). In some embodiments, a composition as described herein comprises one, two, three, four, five, six, seven, eight, nine, ten, or more microbial strains (e.g. microbial strains as disclosed herein).

[0024] In some embodiments, a composition as described herein comprises at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten microbial components (e.g. microbial components as disclosed herein). In some embodiments, a composition as described herein comprises at most one, at most two, at most three, at most four, at most five, at most six, at most seven, at most eight, at most nine, or at most ten microbial components (e.g. microbial components as disclosed herein). In some embodiments, a composition as described herein comprises one, two, three, four, five, six, seven, eight, nine, ten, or more microbial components (e.g. microbial components as disclosed herein).

[0025] In some embodiments, a composition, as described herein, comprises one or more microbial metabolites (e.g. derived from sources other than microbial strains (e.g. synthetically derived), derived from one or more microbial strains), wherein the composition is for treating an metabolism-associated disease, disorder, or condition.

[0026] In some embodiments, a composition as described herein comprises at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten microbial metabolites (e.g. microbial metabolites as disclosed herein). In some embodiments, a composition as described herein comprises at most one, at most two, at most three, at most four, at most five, at most six, at most seven, atmost eight, at most nine, or at most ten microbial metabolites (e.g. microbial metabolites as disclosed herein). In some embodiments, a composition as described herein comprises one, two, three, four, five, six, seven, eight, nine, ten, or more microbial metabolites (e.g. microbial metabolites as disclosed herein).

[0027] In some embodiments, composition is for topical, oral, subcutaneous, intravenous, intramuscular, intracerebral, intrathecal, rectal, opthalmical, intravitreal, or suprachoroidal administration. In some embodiments, a composition is for oral administration. In some embodiments, a composition is for intravenous administration.

[0028] The present disclosure provides, among other things, a composition for use in modulating one or more microbial metabolites in a subject. In some embodiments, a composition is for use in modulating one or more features in a subject. In some embodiments, one or more features is or comprises: (i) level of cell viability; (ii) level or activity of a nucleic acid or protein, or form thereof; (iii) body weight gain; (iv) lipid accumulation in liver; (v) accumulation of visceral fat; (vi) elevated blood triglyceride levels; (vii) blood-cholesterol levels; (viii) oxidative stress; (ix) hypercholesterolemia; or (x) inflammation.

[0029] In some embodiments, a composition is for use in characterizing ability of one more microbial strains to modulate one or more microbial metabolites in a subject.

[0030] The present disclosure provides that a use of a composition as described herein is for treating or ameliorating a disease, disorder, or condition in a subject, wherein the disease, disorder, or condition is a metabolic disease, disorder, or condition associated with one or more microbial metabolites. In some embodiments, a use of a composition as described herein is for treating or ameliorating lipid-induced metabolic syndrome, cerebral infarction / stroke, myocardial infarction / heart attack, Type II diabetes / diabetes mellitus, glucose intolerance, alcoholism, metabolic syndrome, kidney disease, cardiorenal syndrome, vascular diseases (e.g., hypertension, peripheral arterial disease), Alzheimer’s disease, asthma (e.g., due to abdominal obesity or central / truncal obesity), atherosclerosis, hypothyroidism, liver disease, LDL-hypercholesterolemia, hypertriglyceridemia, mixed hyperlipoproteinemia, coronary heart disease, stroke, peripheral arterial disease, high blood pressure, hyperlipidemia, steatosis, non-alcoholic steatohepatitis (NASH), fatty-liver disease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), liver fibrosis, cirrhosis, or hepatocellular carcinoma. In some embodiments, a useof a composition as described herein is for treating or ameliorating fatty-liver disease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), steatosis, non-alcoholic steatohepatitis (NASH), liver fibrosis, cirrhosis, or hepatocellular carcinoma.

[0031] The present disclosure provides a method of screening a microbial strain, comprising contacting the microbial strain to a culture comprising liver cells or liver cell lines that model a metabolic disease, disorder, or condition, and determining whether the microbial strain altered a feature of the culture, wherein the feature is associated with the metabolic disease, disorder, or condition.

[0032] In some embodiments, a step of determining comprises comparing a feature before and after performance of the step of contacting. In some embodiments, a step of determining comprises comparing a feature after the step of contacting with a comparable reference.

[0033] In some embodiments, a comparable reference is a historical reference. In some embodiments, a comparable reference is a negative control reference. In some embodiments, a comparable reference is a positive control reference.

[0034] In some embodiments, a feature is a level of cell viability. In some embodiments, a feature is level or activity of a nucleic acid or protein, or form thereof. In some embodiments, a feature is or comprises weight gain. In some embodiments, a feature is or comprises lipid accumulation in liver cells. In some embodiments, a feature is or comprises accumulation of visceral fat. In some embodiments, a feature is or comprises triglyceride levels. In some embodiments, a feature is or comprises cholesterol levels. In some embodiments, a feature is or comprises inflammation.

[0035] In some embodiments, a microbial strain may alter one or more features of a culture. In some embodiments, one or more features is associated with the metabolic disease, disorder, or condition. In some embodiments, one or more features is or comprises (i) level of cell viability; (ii) level or activity of a nucleic acid or protein, or form thereof; (iii) body weight gain; (iv) lipid accumulation in liver; (v) accumulation of visceral fat; (vi) elevated blood triglyceride levels; (vii) blood-cholesterol levels; (viii) oxidative stress; (ix) hypercholesterolemia; or (x) inflammation.

[0036] The present disclosure provides a method comprising administering to a subject a composition comprising one or more microbial strains or microbial components.In some embodiments, the present disclosure provides a method comprising administering to a subject a composition comprising one or more microbial metabolites. In some embodiments, microbial metabolites can be from one or more microbial strains. In some embodiments, microbial metabolites can be from a source that is not a microbial strain, e.g., synthetically generated.

[0037] In some embodiments, a microbial strain or the microbial metabolite may alter a feature of the subject. In some embodiments, a microbial strain, a microbial component, or a microbial metabolite may alter one or more features of the subject. In some embodiments, a feature is a level of cell viability. In some embodiments, a feature is level or activity of a nucleic acid or protein, or form thereof. In some embodiments, a feature is or comprises body weight gain. In some embodiments, a feature is or comprises lipid accumulation in liver. In some embodiments, a feature is or comprises accumulation of visceral fat. In some embodiments, a feature is or comprises triglyceride levels. In some embodiments, a feature is or comprises cholesterol levels. In some embodiments, a feature is or comprises inflammation.

[0038] In some embodiments, a feature is associated with a metabolism-associated disease, disorder, or condition.

[0039] The present disclosure provides a method of characterizing a microbial strain, comprising adding the microbial strain to a culture comprising liver cells or liver cell lines that model a metabolic disease, disorder, or condition, and determining whether the microbial strain affects levels of one or more features of the liver cells or liver cell lines, wherein the one or more features are associated with the metabolic disease, disorder, or condition.

[0040] The present disclosure provides a method of manufacturing a pharmaceutical treatment comprising characterizing one or more microbial strains, microbial components, or microbial metabolites comprising the steps of adding the one or more microbial strains to a culture comprising liver cells or liver cell lines that model a metabolic disease, disorder, or condition, and determining whether the one or more microbial strains affect levels of one or more features of the liver cells or liver cell lines, wherein the one or more features are associated with the metabolic disease, disorder, or condition.

[0041] The present disclosure provides a method of manufacturing a pharmaceutical treatment comprising adding one or more microbial strains or microbial components, to asyrup, a liquid, a tablet, a troche, a gummy, a capsule, a powder, a gel, a film, an injection, or an eye drop. The present disclosure provides a method of manufacturing a pharmaceutical treatment comprising adding one or more microbial metabolites, to a syrup, a liquid, a tablet, a troche, a gummy, a capsule, a powder, a gel, a film, an injection, or an eye drop.

[0042] The present disclosure provides a method of assessing a microbial strain for ability to affect one or more features of a culture, comprising adding the microbial strain to the culture comprising liver cells or liver cell lines that model a metabolic disease, disorder, or condition, and determining whether the microbial strain affects levels of one or more features of the liver cells or liver cell lines, wherein the one or more features are associated with the metabolic disease, disorder, or condition.

[0043] In some embodiments, a method further comprises before adding the microbial strain to the culture, determining levels of one or more features of the liver cells or liver cell lines in the culture, after adding the microbial strain to the culture, determining the levels of the same one or more features of the liver cells or liver cell lines in the culture, and comparing the levels of one or more features determined before adding the microbial strain with the levels of one or more features determined after adding the microbial strain.

[0044] In some embodiments, one or more features includes: (i) level of cell viability; (ii) level or activity of a nucleic acid or protein, or form thereof; (iii) body weight gain; (iv) lipid accumulation in liver; (v) accumulation of visceral fat; (vi) elevated blood triglyceride levels; (vii) blood-cholesterol levels; (viii) oxidative stress; (ix) hypercholesterolemia; (x) inflammation; or (xi) a combination thereof.

[0045] The present disclosure provides that a composition as described herein is for use in treating or preventing a metabolic disease, disorder, or condition, comprising one or more microbial strains or microbial components. The present disclosure further provides that a composition as described herein is for use in treating or preventing a metabolic disease, disorder, or condition, comprising one or more microbial metabolites. In some embodiments, one or more microbial components or microbial metabolites of a one or more microbial strains are selected from Appendix 1, Appendix 3, or Appendix 4.

[0046] In some embodiments, a composition as described herein is for use in treating or preventing a metabolism-associated disease, disorder, or condition.

[0047] The present disclosure provides an injection comprising a composition of as described herein.

[0048] The present disclosure provides a food supplement comprising a composition as described herein.

[0049] The present disclosure provides a kit comprising a composition as described herein, for example, for use in treating or preventing a metabolic disease, disorder, or condition.. In some embodiments, a kit comprises a monitoring device. In some embodiments, a monitoring device is a cholesterol monitor.

[0050] These, and other aspects encompassed by the present disclosure, are described in more detail below and in the claims. DEFINITIONS

[0051] The scope of the present invention is defined by the claims appended hereto and is not limited by certain embodiments described herein. Those skilled in the art, reading the present specification, will be aware of various modifications that may be equivalent to such described embodiments, or otherwise within the scope of the claims. In general, terms used herein are in accordance with their understood meaning in the art, unless clearly indicated otherwise. Explicit definitions of certain terms are provided below; meanings of these and other terms in particular instances throughout this specification will be clear to those skilled in the art from context.

[0052] Use of ordinal terms such as “first,” “second,” “third,” etc., in the claims to modify a claim element does not by itself connote any priority, precedence, or order of one claim element over another or the temporal order in which acts of a method are performed, but are used merely as labels to distinguish one claim element having a certain name from another element having a same name (but for use of the ordinal term) to distinguish the claim elements.

[0053] The articles “a” and “an,” as used herein, should be understood to include the plural referents unless clearly indicated to the contrary. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context. In some embodiments, exactly one member of a group is present in, employed in, or otherwise relevant to a given product or process. In some embodiments, more than one, orall group members are present in, employed in, or otherwise relevant to a given product or process. It is to be understood that the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, descriptive terms, etc., from one or more of the listed claims is introduced into another claim dependent on the same base claim (or, as relevant, any other claim) unless otherwise indicated or unless it would be evident to one of ordinary skill in the art that a contradiction or inconsistency would arise. Where elements are presented as lists (e.g., in Markush group or similar format), it is to be understood that each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It should be understood that, in general, where embodiments or aspects are referred to as “comprising” particular elements, features, etc., certain embodiments or aspects “consist,” or “consist essentially of,” such elements, features, etc. For purposes of simplicity, those embodiments have not in every case been specifically set forth in so many words herein. It should also be understood that any embodiment or aspect can be explicitly excluded from the claims, regardless of whether the specific exclusion is recited in the specification.

[0054] Administration: As used herein, the term “administration” typically refers to the administration of a composition to a subject or system to achieve delivery of an agent to the subject or system. In some embodiments, the agent is, or is included in, the composition; in some embodiments, the agent is generated through metabolism of the composition or one or more components thereof. Those of ordinary skill in the art will be aware of a variety of routes that may, in appropriate circumstances, be utilized for administration to a subject, for example a human. For example, in some embodiments, administration may be ocular, oral, parenteral, topical, etc. In some particular embodiments, administration may be bronchial (e.g., by bronchial instillation), buccal, dermal (which may be or comprise, for example, one or more of topical to the dermis, intradermal, interdermal, transdermal, etc.), enteral, intra-arterial, intradermal, intragastric, intramedullary, intramuscular, intranasal, intraperitoneal, intrathecal, intravenous, intraventricular, within a specific organ (e. g. intrahepatic), mucosal, nasal, oral, rectal, subcutaneous, sublingual, topical, tracheal (e.g., by intratracheal instillation), vaginal, vitreal, etc. In many embodiments provided by the present disclosure, administration is oral administration. In some embodiments, administration may involve only a single dose. In some embodiments, administration may involve application of a fixed number of doses. In some embodiments, administration may involve dosing that is intermittent (e.g., a plurality of doses separated intime) and / or periodic (e.g., individual doses separated by a common period of time) dosing. In some embodiments, administration may involve continuous dosing (e.g., perfusion) for at least a selected period of time. Administration of cells can be by any appropriate route that results in delivery to a desired location in a subject where at least a portion of the delivered cells or components of the cells remain viable. A period of viability of cells after administration to a subject can be as short as a few hours, e.g., twenty-four hours, to a few days, to as long as several years, i.e., long-term engraftment. In some embodiments, administration comprises delivery of a bacterial extract or preparation comprising one or more bacterial metabolites and / or byproducts but lacking fully viable bacterial cells.

[0055] Analog: As used herein, the term “analog” refers to a substance that shares one or more particular structural features, elements, components, or moieties with a reference substance. Typically, an “analog” shows significant structural similarity with the reference substance, for example sharing a core or consensus structure, but also differs in certain discrete ways. In some embodiments, an analog is a substance that can be generated from the reference substance, e.g., by chemical manipulation of the reference substance. In some embodiments, an analog is a substance that can be generated through performance of a synthetic process substantially similar to (e.g., sharing a plurality of steps with) one that generates the reference substance. In some embodiments, an analog is or can be generated through performance of a synthetic process different from that used to generate the reference substance.

[0056] Approximately: As applied to one or more values of interest, includes to a value that is similar to a stated reference value. In certain embodiments, the term “approximately” or “about” refers to a range of values that fall within r10% (greater than or less than) of the stated reference value unless otherwise stated or otherwise evident from the context (except where such number would exceed 100% of a possible value).

[0057] Comparable: As used herein, the term “comparable” refers to two or more agents, entities, situations, sets of conditions, subjects, etc., that may not be identical to one another but that are sufficiently similar to permit comparison therebetween so that one skilled in the art will appreciate that conclusions may reasonably be drawn based on differences or similarities observed. In some embodiments, comparable sets of conditions, circumstances, individuals, or populations are characterized by a plurality of substantially identical features and one or a small number of varied features. Those of ordinary skill in theart will understand, in context, what degree of identity is required in any given circumstance for two or more such agents, entities, situations, sets of conditions, etc. to be considered comparable. For example, those of ordinary skill in the art will appreciate that sets of circumstances, individuals, or populations are comparable to one another when characterized by a sufficient number and type of substantially identical features to warrant a reasonable conclusion that differences in results obtained or phenomena observed under or with different sets of circumstances, individuals, or populations are caused by or indicative of the variation in those features that are varied.

[0058] Conservative: As used herein, refers to instances when describing a conservative amino acid substitution, including a substitution of an amino acid residue by another amino acid residue having a side chain R group with similar chemical properties (e.g., charge or hydrophobicity). In general, a conservative amino acid substitution will not substantially change the functional properties of interest of a protein, for example, the ability of a receptor to bind to a ligand. Examples of groups of amino acids that have side chains with similar chemical properties include: aliphatic side chains such as glycine (Gly, G), alanine (Ala, A), valine (Val, V), leucine (Leu, L), and isoleucine (Ile, I); aliphatic-hydroxyl side chains such as serine (Ser, S) and threonine (Thr, T); amide-containing side chains such as asparagine (Asn, N) and glutamine (Gln, Q); aromatic side chains such as phenylalanine (Phe, F), tyrosine (Tyr, Y), and tryptophan (Trp, W); basic side chains such as lysine (Lys, K), arginine (Arg, R), and histidine (His, H); acidic side chains such as aspartic acid (Asp, D) and glutamic acid (Glu, E); and sulfur-containing side chains such as cysteine (Cys, C) and methionine (Met, M). Conservative amino acids substitution groups include, for example, valine / leucine / isoleucine (Val / Leu / Ile, V / L / I), phenylalanine / tyrosine (Phe / Tyr, F / Y), lysine / arginine (Lys / Arg, K / R), alanine / valine (Ala / Val, A / V), glutamate / aspartate (Glu / Asp, E / D), and asparagine / glutamine (Asn / Gln, N / Q). In some embodiments, a conservative amino acid substitution can be a substitution of any native residue in a protein with alanine, as used in, for example, alanine scanning mutagenesis. In some embodiments, a conservative substitution is made that has a positive value in the PAM250 log-likelihood matrix disclosed in Gonnet, G.H. et al., 1992, Science 256:1443-1445, which is incorporated herein by reference in its entirety. In some embodiments, a substitution is a moderately conservative substitution wherein the substitution has a nonnegative value in the PAM250 log-likelihood matrix.

[0059] Control: As used herein, refers to the art-understood meaning of a “control” being a standard against which results are compared. Typically, controls are used to augment integrity in experiments by isolating variables in order to make a conclusion about such variables. In some embodiments, a control is a reaction or assay that is performed simultaneously with a test reaction or assay to provide a comparator. A “control” also includes a “control animal.” A “control animal” may have a modification as described herein, a modification that is different as described herein, or no modification (i.e., a wild- type animal). In one experiment, a "test" (i.e., a variable being tested) is applied. In a second experiment, the “control,” the variable being tested is not applied. In some embodiments, a control is a historical control (i.e., of a test or assay performed previously, or an amount or result that is previously known). In some embodiments, a control is or comprises a printed or otherwise saved record. A control may be a positive control or a negative control.

[0060] Determining, measuring, evaluating, assessing, assaying and analyzing: Determining, measuring, evaluating, assessing, assaying and analyzing are used interchangeably herein to refer to any form of measurement, and include determining if an element is present or not. These terms include both quantitative and / or qualitative determinations. Assaying may be relative or absolute. “Assaying for the presence of” can be determining the amount of something present and / or determining whether or not it is present or absent.

[0061] Dosage form: Those skilled in the art will appreciate that the term “dosage form” may be used to refer to a physically discrete unit of an agent (e.g., a therapeutic agent) for administration to a subject. Typically, each such unit contains a predetermined quantity of agent. In some embodiments, such quantity is a unit dosage amount (or a whole fraction thereof) appropriate for administration in accordance with a dosing regimen that has been determined to correlate with a desired or beneficial outcome when administered to a relevant population (i.e., with a therapeutic dosing regimen). Those of ordinary skill in the art appreciate that the total amount of a therapeutic composition or agent administered to aparticular subject is determined by one or more attending physicians and may involve administration of multiple dosage forms.

[0062] Dosing regimen: Those skilled in the art will appreciate that the term “dosing regimen” may be used to refer to a set of unit doses (typically more than one) that are administered individually to a subject, typically separated by periods of time. In some embodiments, a given agent has a recommended dosing regimen, which may involve one or more doses. In some embodiments, a dosing regimen comprises a plurality of doses each of which is separated in time from other doses. In some embodiments, individual doses are separated from one another by a time period of the same length; in some embodiments, a dosing regimen comprises a plurality of doses and at least two different time periods separating individual doses. In some embodiments, all doses within a dosing regimen are of the same unit dose amount. In some embodiments, different doses within a dosing regimen are of different amounts. In some embodiments, a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount different from the first dose amount. In some embodiments, a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount same as the first dose amount. In some embodiments, a dosing regimen is correlated with a desired or beneficial outcome when administered across a relevant population.

[0063] Engineered: In general, the term “engineered” refers to the aspect of having been manipulated by the hand of man. For example, a cell or organism is considered to be “engineered” if it has been manipulated so that its genetic information is altered (e.g., new genetic material not previously present has been introduced, for example by transformation, mating, somatic hybridization, transfection, transduction, or other mechanism, or previously present genetic material is altered or removed, for example by substitution or deletion mutation, or by mating protocols). As is common practice and is understood by those in the art, progeny of an engineered polynucleotide or cell are typically still referred to as “engineered” even though the actual manipulation was performed on a prior entity.

[0064] Excipient: As used herein, refers to an inactive (e.g., non-therapeutic) agent that may be included in a pharmaceutical composition, for example to provide or contribute to a desired consistency or stabilizing effect. In some embodiments, suitable pharmaceutical excipients may include, for example, starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like.

[0065] Functional: As used herein, a functional” biological molecule is a biological molecule in a form in which it exhibits a property and / or activity by which it is characterized. A biological molecule may have two functions (i.e., bifunctional) or many functions (i.e., multifunctional).

[0066] Gene: As used herein, refers to a DNA sequence in a chromosome that codes for a product (e.g., an RNA product and / or a polypeptide product). In some embodiments, a gene includes coding sequence (i.e., sequence that encodes a particular product). In some embodiments, a gene includes non-coding sequence. In some particular embodiments, a gene may include both coding (e.g., exonic) and non-coding (e.g., intronic) sequence. In some embodiments, a gene may include one or more regulatory sequences (e.g., promoters, enhancers, etc.) and / or intron sequences that, for example, may control or impact one or more aspects of gene expression (e.g., cell-type-specific expression, inducible expression, etc.). For the purpose of clarity, we note that, as used in the present disclosure, the term “gene” generally refers to a portion of a nucleic acid that encodes a polypeptide or fragment thereof; the term may optionally encompass regulatory sequences, as will be clear from context to those of ordinary skill in the art. This definition is not intended to exclude application of the term “gene” to non-protein-coding expression units but rather to clarify that, in most cases, the term as used in this document refers to a polypeptide-coding nucleic acid.

[0067] Improve, increase, enhance, inhibit or reduce: As used herein, the terms “improve,” “increase,” “enhance,” “inhibit,” “reduce,” or grammatical equivalents thereof, indicate values that are relative to a baseline or other reference measurement. In some embodiments, a value is statistically significantly difference that a baseline or other reference measurement. In some embodiments, an appropriate reference measurement may be or comprise a measurement in a particular system (e.g., in a single individual) under otherwise comparable conditions absent presence of (e.g., prior to and / or after) a particular agent or treatment, or in presence of an appropriate comparable reference agent. In some embodiments, an appropriate reference measurement may be or comprise a measurement in comparable system known or expected to respond in a particular way, in presence of the relevant agent or treatment. In some embodiments, an appropriate reference is a negative reference; in some embodiments, an appropriate reference is a positive reference.

[0068] Isolated: As used herein, refers to a substance and / or entity that has been (1) separated from at least some of the components with which it was associated when initiallyproduced (whether in nature and / or in an experimental setting), and / or (2) designed, produced, prepared, and / or manufactured by the hand of man. In some embodiments, an isolated substance or entity may be enriched; in some embodiments, an isolated substance or entity may be pure. In some embodiments, isolated substances and / or entities may be separated from about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% of the other components with which they were initially associated. In some embodiments, isolated agents are about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure. As used herein, a substance is "pure" if it is substantially free of other components. In some embodiments, as will be understood by those skilled in the art, a substance may still be considered “enriched”, "isolated" or even "pure", after having been combined with certain other components such as, for example, one or more carriers or excipients (e.g., buffer, solvent, water, etc.); in such embodiments, percent isolation or purity of the substance is calculated without including such carriers or excipients. Those skilled in the art are aware of a variety of technologies for isolating (e.g., enriching or purifying) substances or agents (e.g., using one or more of fractionation, extraction, precipitation, or other separation).

[0069] Level: As used herein, the term “level” refers to a scale of amount or quantity of a substance (e.g., a metabolite). In some embodiments, a level can be simply the presence or absence of a substance. A level of a substance may be represented in multiple ways or formats. For example, in some embodiments, a level may be represented as a percentage (%), a measure of weight (e.g., mg, µg, ng, etc.), a measure of concentration (e.g., mg / mL, µg / mL, ng / mL, etc.), a measure of volume (e.g., mL, µL, nL, etc.), in % change, etc.

[0070] Metabolite: As used herein, the term “metabolite” refers to a substance (e.g., a small molecule, macromolecule, organic compound, or inorganic compound) made or used during metabolism. Metabolism is generally understood as a process by which a substance (e.g., food, drug, chemical, cell, or tissue) is chemically broken down. In some embodiments, a metabolite is an end product. In some embodiments, a metabolite is an intermediate. Exemplary metabolites are provided herein, e.g., in Appendix 1-1, 1-3, 3, and 4. Exemplary metabolic pathways are provided herein, e.g., in Appendix 1-2. In some embodiments, a metabolite may be produced or made by an organism. In some embodiments, a metabolite may be produced or made by a microorganism (e.g. microbialstrain). In some embodiments, a microbial metabolite produced or made by a microbial strain. In some embodiments, a metabolite may be produced or made naturally (e.g. by an organism (e.g. microorganism (e.g. microbial strain))). In some embodiments, a metabolite may be produced or made synthetically (e.g. from a source that is not a microbial strain (e.g., synthetically generated)).

[0071] Pharmaceutical composition: As used herein, the term “pharmaceutical composition” refers to a composition in which an active agent is formulated together with one or more pharmaceutically acceptable carriers. In some embodiments, the active agent is present in unit dose amount appropriate for administration in a therapeutic regimen that shows a statistically significant probability of achieving a predetermined therapeutic effect when administered to a relevant population. In some embodiments, a pharmaceutical composition may be specially formulated for administration in solid or liquid form, including those adapted for the following: ophthalmic administration, intravitreal administration, suprachoroidal administration, oral administration, subcutaneous administration, intravenous administration, intramuscular administration, intracerebral administration, intrathecal administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue, capsules, powders, etc. In some embodiments, an active agent may be or comprise a cell or population of cells (e.g., a culture, for example of an Ellagitannin-Enzyme-Synthesizing (EES) microbe); in some embodiments, an active agent may be or comprise an extract or component of a cell or population (e.g., culture) of cells. In some embodiments, an active agent may be or comprise an isolated, purified, or pure compound. In some embodiments, an active agent may have been synthesized in vitro (e.g., via chemical and / or enzymatic synthesis). In some embodiments, an active agent may be or comprise a natural product (whether isolated from its natural source or synthesized in vitro).

[0072] Pharmaceutically acceptable: As used herein, the term "pharmaceutically acceptable" which, for example, may be used in reference to a carrier, diluent, or excipient used to formulate a pharmaceutical composition as disclosed herein, means that the carrier, diluent, or excipient is compatible with the other ingredients of the composition and not deleterious to the recipient thereof.

[0073] Pharmaceutically acceptable carrier: As used herein, the term “pharmaceutically acceptable carrier” means a pharmaceutically-acceptable material,composition or vehicle, such as a liquid or solid filler, diluent, excipient, or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be is “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the subject (e.g., patient). Some examples of materials which can serve as pharmaceutically-acceptable carriers include: sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer’s solution; ethyl alcohol; pH buffered solutions; polyesters, polycarbonates and / or polyanhydrides; and other non-toxic compatible substances employed in pharmaceutical formulations.

[0074] Prebiotic: As used herein, a “prebiotic” refers to an ingredient that allows or promotes specific changes, both in the composition and / or activity in the gastrointestinal microbiota that may (or may not) confer benefits upon the host. In some embodiments, a prebiotic can include one or more of the following: the prebiotic comprises a pome extract, berry extract and walnut extract.

[0075] Prevention: The term “prevention”, as used herein, refers to a delay of onset, and / or reduction in frequency and / or severity of one or more symptoms of a particular disease, disorder or condition. In some embodiments, prevention is assessed on a population basis such that an agent is considered to “prevent” a particular disease, disorder or condition if a statistically significant decrease in the development, frequency, and / or intensity of one or more symptoms of the disease, disorder or condition is observed in a population susceptible to the disease, disorder, or condition. In some embodiments, prevention may be considered complete, for example, when onset of a disease, disorder or condition has been delayed for a predefined period of time.

[0076] Reference: As used herein describes a standard or control relative to which a comparison is performed. For example, in some embodiments, an agent, animal, individual, population, sample, sequence or value of interest is compared with a reference or controlagent, animal, individual, population, sample, sequence or value. In some embodiments, a reference or control is tested and / or determined substantially simultaneously with the testing or determination of interest. In some embodiments, a reference or control is a historical reference or control, optionally embodied in a tangible medium. Typically, as would be understood by those skilled in the art, a reference or control is determined or characterized under comparable conditions or circumstances to those under assessment. Those skilled in the art will appreciate when sufficient similarities are present to justify reliance on and / or comparison to a particular possible reference or control. In some embodiments, a reference is a negative control reference; in some embodiments, a reference is a positive control reference.

[0077] Risk: As will be understood from context, “risk” of a disease, disorder, and / or condition refers to a likelihood that a particular individual will develop the disease, disorder, and / or condition. In some embodiments, risk is expressed as a percentage. In some embodiments, risk is from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or up to 100%. In some embodiments risk is expressed as a risk relative to a risk associated with a reference sample or group of reference samples. In some embodiments, a reference sample or group of reference samples have a known risk of a disease, disorder, condition and / or event. In some embodiments a reference sample or group of reference samples are from individuals comparable to a particular individual. In some embodiments, relative risk is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more.

[0078] Sample: As used herein, the term “sample” typically refers to an aliquot of material obtained or derived from a source of interest. In some embodiments, a source of interest is a biological or environmental source. In some embodiments, a source of interest may be or comprise a cell or an organism, such as a microbe, a plant, or an animal (e.g., a human). In some embodiments, a source of interest is or comprises biological tissue or fluid. In some embodiments, a biological tissue or fluid may be or comprise amniotic fluid, aqueous humor, ascites, bile, bone marrow, blood, breast milk, cerebrospinal fluid, cerumen, chyle, chime, ejaculate, endolymph, exudate, feces, gastric acid, gastric juice, lymph, mucus, pericardial fluid, perilymph, peritoneal fluid, pleural fluid, pus, rheum, saliva, sebum, semen, serum, smegma, sputum, synovial fluid, sweat, tears, urine, vaginal secretions, vitreous humour, vomit, plasma, mucous, digestive fluid, stool, and / or combinations or component(s) thereof. In some embodiments, a biological fluid may be or comprise an intracellular fluid, an extracellular fluid, an intravascular fluid (blood plasma), an interstitialfluid, a lymphatic fluid, and / or a transcellular fluid. In some embodiments, a biological fluid may be or comprise a plant exudate. In some embodiments, a biological tissue or sample may be obtained, for example, by aspirate, biopsy (e.g., fine needle or tissue biopsy), swab (e.g., oral, nasal, skin, or vaginal swab), scraping, surgery, washing or lavage (e.g., bronchioalveolar, ductal, nasal, ocular, oral, uterine, vaginal, or other washing or lavage). In some embodiments, a biological sample is or comprises cells obtained from an individual. In some embodiments, a sample is a “primary sample” obtained directly from a source of interest by any appropriate means. In some embodiments, as will be clear from context, the term “sample” refers to a preparation that is obtained by processing (e.g., by removing one or more components of and / or by adding one or more agents to) a primary sample. For example, filtering using a semi-permeable membrane. Such a “processed sample” may comprise, for example nucleic acids or proteins extracted from a sample or obtained by subjecting a primary sample to one or more techniques such as amplification or reverse transcription of nucleic acid, isolation and / or purification of certain components, etc.

[0079] Small molecule: As used herein, the term “small molecule” refers to small organic or inorganic molecules of molecular weight below about 3,000 Daltons. In general, small molecules may have a molecular weight of less than 3,000 Daltons (Da). Small molecules can be, e.g., from at least about 100 Da to about 3,000 Da (e.g., between about 100 to about 3,000 Da, about 100 to about 2500 Da, about 100 to about 2,000 Da, about 100 to about 1,750 Da, about 100 to about 1,500 Da, about 100 to about 1,250 Da, about 100 to about 1,000 Da, about 100 to about 750 Da, about 100 to about 500 Da, about 200 to about 1500, about 500 to about 1000, about 300 to about 1000 Da, or about 100 to about 250 Da).

[0080] Subject: As used herein, the term “subject” refers to an individual to which a provided treatment is administered. In some embodiments, a subject is animal. In some embodiments, a subject is a mammal, e.g., a mammal that experiences or is susceptible to a disease, disorder, or condition as described herein. In some embodiments, an animal is a vertebrate, e.g., a mammal, such as a non-human primate, (particularly a higher primate), a sheep, a dog, a rodent (e.g. a mouse or rat), a guinea pig, a goat, a pig, a cat, a rabbit, or a cow. In some embodiments, an animal is a non-mammal animal, such as a chicken, an amphibian, a reptile, or an invertebrate model C. elegans. In some embodiments, a subject is a human. In some embodiments, a subject is suffering from or susceptible to one or more diseases, disorders or conditions as described herein. In some embodiments, a subject displays one or more symptoms of a one or more diseases, disorders or conditions asdescribed herein. In some embodiments, a subject has been diagnosed with one or more diseases, disorders or conditions as described herein. In some embodiments, the subject is receiving or has received certain therapy to diagnose and / or to treat a disease, disorder, or condition. In another embodiment, the subject is an experimental animal or animal substitute as a disease model.

[0081] Substantially: As used herein, refers to the qualitative condition of exhibiting total or near-total extent or degree of a characteristic or property of interest. One of ordinary skill in the biological arts will understand that biological and chemical phenomena rarely, if ever, go to completion and / or proceed to completeness or achieve or avoid an absolute result. The term “substantially” is therefore used herein to capture the potential lack of completeness inherent in many biological and chemical phenomena.

[0082] Therapeutic regimen: A “therapeutic regimen”, as that term is used herein, refers to a dosing regimen whose administration across a relevant population may be correlated with a desired or beneficial therapeutic outcome.

[0083] Therapeutically effective amount: As used herein, is meant an amount that produces the desired effect for which it is administered. In some embodiments, the term refers to an amount that is sufficient, when administered to a population suffering from or susceptible to a disease, disorder, and / or condition in accordance with a therapeutic dosing regimen, to treat the disease, disorder, and / or condition. In some embodiments, a therapeutically effective amount is one that reduces the incidence and / or severity of, and / or delays onset of, one or more symptoms of the disease, disorder, and / or condition. Those of ordinary skill in the art will appreciate that the term "therapeutically effective amount" does not in fact require successful treatment be achieved in a particular individual. Rather, a therapeutically effective amount may be that amount that provides a particular desired pharmacological response in a significant number of subjects when administered to subjects (e.g., patients) in need of such treatment. In some embodiments, reference to a therapeutically effective amount may be a reference to an amount as measured in one or more specific tissues (e.g., a tissue affected by the disease, disorder or condition) or fluids (e.g., blood, saliva, serum, sweat, tears, urine, etc.). Those of ordinary skill in the art will appreciate that, in some embodiments, a therapeutically effective amount of a particular agent or therapy may be formulated and / or administered in a single dose. In some embodiments, a therapeutically effective agent may be formulated and / or administered in a plurality of doses, for example, as part of a dosing regimen.

[0084] Treatment: As used herein, the term treatment” (also “treat” or “treating”) refers to any administration of a therapy that partially or completely alleviates, ameliorates, relives, inhibits, delays onset of, reduces severity of, and / or reduces incidence of one or more symptoms, features, and / or causes of a particular disease, disorder, and / or condition. In some embodiments, such treatment may be of a subject who does not exhibit signs of the relevant disease, disorder and / or condition and / or of a subject who exhibits only early signs of the disease, disorder, and / or condition. Alternatively, or additionally, such treatment may be of a subject who exhibits one or more established signs of the relevant disease, disorder and / or condition. In some embodiments, treatment may be of a subject who has been diagnosed as suffering from the relevant disease, disorder, and / or condition. In some embodiments, treatment may be of a subject known to have one or more susceptibility factors that are statistically correlated with increased risk of development of the relevant disease, disorder, and / or condition. BRIEF DESCRIPTION OF THE DRAWING

[0085] Fig.1 shows mice treated with CT6 or CT6m are significantly lighter than vehicle-treated animals. (a) All mice gained weight with aging. (b) TDP43-Q331K transgenic animals are significantly (p < 0.002) heavier than non-transgenic littermate control. (c) mice treated with CT6m exhibited a significant reduction (p < 0.045) in body weight after 57 days of treatment. (d) Both CT6 and CT6m treatments had a significant impact on body weight after 163 days of treatment, (e) which became more pronounced for CT6m (p < 0.0092) treatments at the end of the study. Statistics generated using one-way Anova with Dunnett’s tests for multiple comparisons against group 2. *p < 0.05; ** p < 0.01; *** p < 0.001; ****p < 0.0001

[0086] Fig.2 shows treatment with CT6 or CT6m prevents accumulation of lipids and fat in livers of TDP43 transgenic mice. (a) macroscopic image of the whole liver of a vehicle-treated TDP43-transgenic mouse displaying accumulation of lipid droplets in the liver. (b) macroscopic image of a CT6m-treated liver showing healthy color and morphology. (c) Liver samples from all four groups demonstrating treated-livers lack the appearance of lipid accumulation as seen in group 1 (ntg, vehicle-treated) & group 2 (TDP43 + vehicle).

[0087] Fig.3 shows treatment with CT6 or CT6m prevents lipid accumulation in livers of TDP43 mice. H&E section of livers from TDP43-transgenic & non-transgenic mice. Each panel represents different livers with n=3 livers for each treatment group. TDP43 vehicle-treated animals (2nd column) have the most pronounced lipid accumulation in livers while non-transgenic animals show some degree of fatty liver. Animals treated with CT6 or CT6m have the most normal liver, morphologically.

[0088] Fig.4 shows TDP43-Q331K animals treated with CT6 or CT6m have significantly lower plasma cholesterol compared to control animals. (a) Plasma LDL cholesterol levels in ntg and TDP43-Tg animals at the terminal end-of-study. A significant reduction in LDL levels can be seen in G3 animals treated with CT6 or G4 animals that were treated with CT6m compared to control animals in G1 & G2. (b) Plasma HDL cholesterol levels in the same plasma sample set as in Fig.4a demonstrate that CT6 & CT6m also has profound effects in positively modulating plasma HDL levels. (c) Cholesterol LDL / HDL ratio was calculated by dividing the LDL levels from Fig.4a by the HDL levels from Fig. 4b. (d) To test the lipid-lowering effects of CT6 & CT6m more vigorously, we measured circulating triglyceride levels in the same plasma sample set used for measuring LDL & HDL cholesterol levels. Each data point represents a biological replicate with group 1 having n=19 plasma samples, group 2 with n=16 plasma samples, group 3 with n=19 samples and n=20 for group 4. Statistics generated using one-way Anova with Dunnett’s tests for multiple comparisons against group 2 (TDP43 + Vehicle). *p < 0.05; ** p < 0.01; *** p < 0.001; ****p < 0.0001.

[0089] Fig.5 shows treatment-induced changes in cytokine and chemokine levels from TDP43-Q331K Tg & ntg livers. Each data point represents a biological replicate with G1 (ntg + vehicle) having n=19 liver samples, G2 (TDP43 + vehicle) with n=16 liver samples, G3 (TDP43 + CT6) with n=19 samples and n=20 for G4 (TDP43 + CT6m). Statistics generated using one-way Anova with Dunnett’s tests for multiple comparisons against G2 (TDP43 + Vehicle). *p < 0.05; ** p < 0.01; *** p < 0.001. DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS

[0090] Lipid and Cholesterol Metabolism Associated Diseases, Disorders, and Conditions

[0091] Metabolism is the process by which a body (e.g., a human body) changes food and drink that is consumed into energy. During this process, calories in food and drinks mix with oxygen to make the energy the body needs. Chemicals in the body’s digestive system break the food down into sugars and acids. The body can use this fuel right away, or it can store the energy in the body’s tissues, such as liver, muscles, and body fat.

[0092] A metabolic disorder occurs when abnormal chemical reactions in a body disrupt this process. When this happens, one might have too much of some substances or too little of other ones that one needs to stay healthy. Accordingly, there are different groups of disorders - some affect the breakdown of amino acids, carbohydrates, or lipids. Yet another group, mitochondrial diseases, affects the parts of the cells that produce the energy.

[0093] One can also develop a metabolic disorder when some organs, such as the liver or pancreas, become diseased or do not function normally. For example, diabetes is a metabolic disorder caused by improper function of the pancreas.

[0094] Lipid metabolism disorders involve lipids, which are fats or fat-like substances. They include oils, fatty acids, waxes, and cholesterol. If a person has one of these disorders, they do not have enough enzymes to break down lipids, or the enzymes may not work properly as a result of which a body cannot convert the fats into energy. This results in a build up of a harmful amount of lipids to in a person’s body. Over time, such harmful levels of lipids may cause damage to cells and tissues, especially in the brain, peripheral nervous system, liver, spleen, and bone marrow. Many of these diseases, disorders, or conditions can be very serious, or sometimes even fatal. Some examples of metabolic diseases, disorders, or conditions (e.g. improper lipid metabolism or improper cholesterol metabolism) include but are not limited to lipid-induced metabolic syndrome, cerebral infarction / stroke, myocardial infarction / heart attack, Type II diabetes / diabetes mellitus, glucose intolerance, alcoholism, metabolic syndrome, kidney disease, cardiorenal syndrome, vascular diseases (e.g., hypertension, peripheral arterial disease), Alzheimer’s disease, asthma (e.g., due to abdominal obesity or central / truncal obesity), atherosclerosis, hypothyroidism, liver disease, LDL-hypercholesterolemia, hypertriglyceridemia, mixed hyperlipoproteinemia, coronary heart disease, stroke, peripheral arterial disease, high blood pressure, hyperlipidemia, steatosis, non-alcoholic steatohepatitis (NASH), fatty-liver disease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), liver fibrosis, cirrhosis, or hepatocellular carcinoma.

[0095] The present disclosure provides compositions (e.g. microbiome compositions) and methods that inhibit one or more of the events or processes that take place in metabolism-associated diseases, disorders, or conditions (e.g. lipid and cholesterol metabolism associated diseases, disorders, and conditions). The present disclosure is based in part on the discovery that one or more microbial strains or compositions comprising one or more microbial strains are particularly suitable as therapeutic agents for metabolism- associated diseases, disorders, or conditions.

[0096] Microbial Preparation(s) and / or Component(s)

[0097] The present disclosure provides systems and methods for assessing, characterizing, and identifying one or more microbial strains of a microbiome (e.g. to improve or treat or prevent a metabolism-associated disease, disorder, or condition as described herein). For example, the present disclosure provides systems and methods for assessing, characterizing, and identifying one or more microbial strains of a microbiome that have one or more abilities. Such systems and methods can be useful for assessing, characterizing, and identifying one or more microbial strains that affect the health of humans, livestock, and / or pets. In some embodiments, one or more microbial strains affect the health of humans, livestock, and / or pets by modulating their respective metabolomes, cell viability, ATP levels, one or more other parameters or features (e.g. of an organ of a subject), or a combination thereof to prevent, treat, or reduce the risk of suffering from a disease, disorder, or condition (e.g. metabolism (e.g. lipid and cholesterol metabolism) associated diseases, disorders, and conditions) as disclosed herein. For example, technologies described herein may result in modulating the metabolome, improve cell viability, increase ATP levels, modulate one or more other parameters or features (e.g. level of cell viability, level or activity of a nucleic acid or protein, or form thereof, body weight gain, lipid accumulation in liver, accumulation of visceral fat, elevated blood triglyceride levels, blood-cholesterol levels, oxidative stress, hypercholesterolemia, inflammation, etc.), or a combination thereof of the subject that results in a decrease in production of toxic components and / or components that suggest or are a marker for cellular damage (e.g. liver cell damage (e.g. lipid (e.g. fat) accumulation in liver) in a subject (e.g. in blood of a subject).

[0098] The present disclosure also provides systems and methods for manufacturing a pharmaceutical composition that comprise assessing, characterizing, and identifying one or more microbial strains of a microbiome.

[0099] In some embodiments, assessing, characterizing, and identifying one or more microbial strains from a microbiome of a snake, lizard, fish, or bird. In some embodiments, assessing, characterizing, and identifying one or more microbial strains from a mammalian microbiome. A mammalian microbiome can be a canine, a feline, an equine, a bovine, an ovine, a caprine, or a porcine microbiome. In some embodiments, a microbiome used in a system or method described herein may prevent or treat a disease or condition.

[0100] A microbiome can be isolated from any system or tissue of an organism that supports microbial growth. For example, a microbiome can be a cutaneous microbiome, an oral microbiome, a nasal microbiome, a gastrointestinal microbiome, a brain microbiome, a pulmonary microbiome, or a urogenital microbiome. A list of exemplary microbial strains found in a gastrointestinal microbiome is included below in Table 1. A microbiome sample can be obtained by various ways. For example, a cutaneous, oral, nasal, pulmonary, or urogenital microbiome sample could be obtained using a swab or tissue scrapping. In some embodiments, a gastrointestinal microbiome could be sampled from feces. A cutaneous microbiome, an oral microbiome, a nasal microbiome, a gastrointestinal microbiome, a brain microbiome, a pulmonary microbiome, or a urogenital microbiome sample could be obtained via a biopsy.

[0101] In some embodiments, a microbiome is a microbiome of a healthy individual or an individual who does not suffer from or is not at risk of developing a particular disease or disorder. In some embodiments, a microbiome is a microbiome of an individual that suffers from or is at risk of developing a particular disease, disorder, or condition. In some embodiments, a microbiome is a microbiome of an individual who is known to suffer from a particular disease, disorder, or condition. In some embodiments, a human microbiome is a microbiome of a human with an unknown risk for one or more diseases, disorders, or conditions.

[0102] In some embodiments, a microbiome is a reference microbiome. A reference microbiome can be a microbiome of a healthy individual or an individual who does not suffer from or is not at risk of developing a particular disease, disorder, or condition. In some instances, a reference microbiome may be from the same individual as a microbiometo be assessed or characterized, but was obtained at a different time. In some instances, a reference microbiome may be from the same individual as a microbiome to be assessed or characterized, but was obtained from a different system or tissue.

[0103] In some embodiments, an individual microbial strain or a combination of microbial strains may be assessed, characterized, or identified in a different relative amount than such strain or strains are found in a microbiome. For example, the effect of modulation of a cell or organism in response to a single strain may be assessed, characterized, or identified using in vitro methods (e.g. mammalian cells) or in vivo methods using mammals (e.g. mice, humans, etc.) as described herein. In some embodiments, for example, the effect of modulation of a cell or organism to treat, prevent, or reduce the risk on a disease, disorder, or condition (e.g. a metabolism-associated disease, disorder, or condition as described herein) may be assessed, characterized, or identified using in vitro methods (e.g. mammalian cells) or in vivo methods using mammals (e.g. mice, humans, etc.) as described herein. In some embodiments, for example, the effect of modulation of a cell or organism to treat, prevent, or reduce the risk on a disease, disorder, or condition (e.g. a metabolism- associated disease, disorder, or condition as described herein) by modulating one or more metabolites of the cell or organism, one or features or parameters (e.g. level of cell viability, level or activity of a nucleic acid or protein, or form thereof, body weight gain, lipid accumulation in liver, accumulation of visceral fat, elevated blood triglyceride levels, blood- cholesterol levels, oxidative stress, hypercholesterolemia, inflammation, etc.) of the cell or organism, or a combination thereof may be assessed, characterized, or identified using in vitro methods (e.g. mammalian cells) or in vivo methods using mammals (e.g. mice, humans, etc.) as described herein. As another example, the effect of modulation (e.g. of levels of one or more metabolites) of a cell or organism to treat, prevent, or reduce the risk on a disease, disorder, or condition, as described herein, in response to two microbial strains may be assessed, characterized, or identified together using methods described herein.

[0104] An extract, component, or compound of a microbial strain may also be assessed, characterized, or identified using methods described herein. In some cases, an extract, component, or compound of a microbial strain that has been determined to treat, prevent, or reduce the risk on a disease, disorder, or condition, as described herein, in an organism (e.g. mammal) may be assessed, characterized, or identified. Assessing, characterizing or identifying an extract, component, or compound of a microbial strain that treats, prevents, or reduces the risk on a disease, disorder, or condition in an organism (e.g.mammal) may provide additional information about potential biomarkers, targets, or protective agents in a microbiome.

[0105] A variety of technologies can be used to prepare extracts of microbial strains, and / or to isolate extracts, components, or compounds therefrom, or to process (e.g., to isolate and / or purify one or more components or compounds from). To give but a few examples, such technologies may include, for example, one or more of organic extraction, vacuum concentration, chromatography, and so on.

[0106] Assessing Biological Impact

[0107] The present disclosure provides the insight that compositions (e.g. microbiome compositions) as described herein can be used to treat, prevent, and / or reduce the risk of a disease, disorder, or condition of an organism (e.g. a mammal (e.g. a human)) by contacting the composition(s) (e.g., feeding the compositions to, administering to) with an organism. In some embodiments, an organism may suffer from or be at risk of suffering from a disease, disorder, or condition (e.g. mammalian disease, disorder, or condition). To determine whether one or more compositions treats, prevents, or reduces the risk of a disease, disorder, or condition (e.g. a metabolism-associated disease, disorder, or condition), levels of one or more metabolites can be observed, measured, or assessed in samples that have been contacted with the one or more compositions. For example, levels of the one or more metabolites can be observed, measured, or assessed in samples at different times (e.g. before administration of composition, after administration of composition, during administration of composition, etc.). To determine whether one or more compositions treats, prevents, or reduces the risk of a disease, disorder, or condition (e.g. a metabolism- associated disease, disorder, or condition), one or more features or parameters may be observed, measured, or assessed in samples that have been contacted with the one or more compositions. For example, one or more features or parameters may be observed, measured, or assessed in samples at different times (e.g. before administration of composition, after administration of composition, during administration of composition, etc.).

[0108] In some embodiments, methods described herein utilize a first sample and a second sample. In some embodiments, a first sample is a reference sample. In some embodiments, a reference sample can be a sample obtained from a subject who is contacted with (e.g., administered or fed) a composition, e.g., CT10 composition, CT6 composition, orCT6m composition. In some embodiments, a reference sample can be a sample obtained from a subject who is contacted with (e.g., administered or fed) a composition, e.g., CT10 composition, CT6 composition, or CT6m composition, at a first time point. In some embodiments, a reference sample can be a sample obtained from a subject prior to being contacted with (e.g., administered or fed) a composition, e.g., CT10 composition, CT6 composition, or CT6m composition. In some embodiments, a reference sample can be a sample obtained from a healthy individual. In some embodiments, a reference sample can be a sample obtained from an individual who is suffering from or may have a risk for a disease, disorder, or condition (e.g. metabolism-associated disease, disorder, or condition). In some embodiments, a reference sample is a control sample. In some embodiments, a reference sample is a negative control sample. In some embodiments, a reference sample is a positive control sample. In some embodiments, a reference sample may be a historic reference (e.g. value across control samples). In some embodiments, a reference sample may be from a printed publication (e.g. a text book, a journal, etc.).

[0109] In some embodiments, a second sample can be a test sample. In some embodiments, a test sample may be a sample obtained from a subject who is contacted with (e.g., administered or fed) a composition, e.g., CT10 composition, CT6 composition, or CT6m composition. In some instances, a subject (e.g. patient or population) may be suffering from or at risk of a disease, disorder, or condition (e.g. a metabolism-associated disease, disorder, or condition). In some instances, a subject (e.g. patient or population) may have an unknown risk for one or more diseases, disorders, or conditions as described herein. In some embodiments, a test can be a sample obtained from a subject who is contacted with (e.g., administered or fed) a composition, e.g., CT10 composition, CT6 composition, or CT6m composition, at a second time point.

[0110] In some embodiments, methods described herein comprise comparing one or more metabolite levels (e.g. a metabolome), or one or more parameters or features (e.g. level of cell viability, level or activity of a nucleic acid or protein, or form thereof, body weight gain, lipid accumulation in liver, accumulation of visceral fat, elevated blood triglyceride levels, blood-cholesterol levels, oxidative stress, hypercholesterolemia, inflammation, etc.) obtained from a test sample with one or more metabolite levels (e.g. a metabolome), or one or more parameters or features (e.g. level of cell viability, level or activity of a nucleic acid or protein, or form thereof, body weight gain, lipid accumulation in liver, accumulation of visceral fat, elevated blood triglyceride levels, blood-cholesterol levels, oxidative stress,hypercholesterolemia, inflammation, etc.) obtained from a reference sample. In some embodiments, by comparing one or more metabolite levels, parameters, or features obtained from a test sample with one or more metabolite levels, parameters, or features obtained from a reference sample, a composition described herein can be assessed, characterized or identified as being useful for treating, preventing, or reducing the risk of suffering from a disease, disorder, or condition (e.g. a metabolism-associated disease, disorder, or condition) as described herein. In some embodiments, by comparing one or more metabolite levels, parameters, or features obtained from a test sample with one or more metabolite levels, parameters, or features obtained from a reference sample, it can be determined that a composition as disclosed herein increases the severity or incidence of a disease, disorder, or condition phenotype. In some embodiments, by comparing one or more metabolite levels, parameters, or features obtained from a test sample with one or more metabolite levels, parameters, or features obtained from a reference sample, it can be determined that a composition as disclosed herein decreases the severity or incidence of a disease, disorder, or condition phenotype. In some embodiments, by comparing one or more metabolite levels, parameters, or features obtained from a test sample with one or more metabolite levels, parameters, or features obtained from a reference sample, it can be determined that a composition as disclosed herein has no effect on the severity or incidence of a disease, disorder, or condition phenotype. In some embodiments, by comparing one or more metabolite levels, parameters, or features obtained from a test sample with one or more metabolite levels, parameters, or features obtained from a reference sample, it can be determined that a composition as disclosed herein prevents a disease, disorder, or condition phenotype.

[0111] The present disclosure also provides the recognition that compositions and methods provided herein can be used to monitor progression of a disease, disorder, or condition (e.g. a metabolism-associated disease, disorder, or condition) in an individual. For example, if metabolite levels, parameters or features (e.g. level of cell viability, level or activity of a nucleic acid or protein, or form thereof, body weight gain, lipid accumulation in liver, accumulation of visceral fat, elevated blood triglyceride levels, blood-cholesterol levels, oxidative stress, hypercholesterolemia, inflammation, etc.) determined to increase the severity of a disease, disorder, or condition decrease in relative amount, it may indicate that the disease, disorder, or condition is being attenuated, e.g., by treatment or immune response.

[0112] The present disclosure also provides the insight that compositions and methods provided herein can be used to tailor treatments (e.g., therapies, nutraceuticals, and / or probiotics) to an individual patient. In some embodiments, compositions and methods provided herein can provide “personalized” therapy. In some cases, metabolite levels, features or parameters (e.g. level of cell viability, level or activity of a nucleic acid or protein, or form thereof, body weight gain, lipid accumulation in liver, accumulation of visceral fat, elevated blood triglyceride levels, blood-cholesterol levels, oxidative stress, hypercholesterolemia, inflammation, etc.) within an individual can be assessed, characterized, or identified to determine if they have a disease, disorder, or condition. Based on the results, the individual can be treated with one or more compositions to adjust the metabolite levels (i.e., their metabolome), features or parameters. In some instances, this will affect the disease, disorder, or condition the individual is suffering from or at risk of developing. For example, if an individual is determined to have a relatively low amount of one or more metabolite levels that have been determined to decrease the severity of a disease, disorder, or condition, administration of the one or more compositions that have been determined to decrease the severity of a disease, disorder, or condition to the individual (or an extract, component, or compound thereof) may attenuate the severity of the individual’s disease or condition.

[0113] The present disclosure provides the insight that compositions and methods provided herein can be used recursively to treat, prevent, or ameliorate a disease, disorder, or condition. In some embodiments, for example, one or more compositions disclosed herein may be administered (e.g. fed, injected, etc.) to a subject after determining the effect of one or more compositions on subject’s metabolite levels, or after determining the effect of one or more compositions on subject’s features or parameters (e.g. level of cell viability, level or activity of a nucleic acid or protein, or form thereof, body weight gain, lipid accumulation in liver, accumulation of visceral fat, elevated blood triglyceride levels, blood-cholesterol levels, oxidative stress, hypercholesterolemia, inflammation, etc.). In some embodiments, a composition may be administered once. In some embodiments, a composition may be administered more than once. In some embodiments, a composition may be administered daily, weekly, biweekly, monthly, bimonthly, etc. In each of these instances, levels of one or more metabolites, or changes in features or parameters may be monitored. In some embodiments, levels of one or more metabolites (e.g. metabolome) or changes in features or parameters may be monitored before administration of a composition. In someembodiments, levels of one or more metabolites (e.g. metabolome) or changes in features or parameters may be monitored after administration of a composition.

[0114] Pharmaceutical Compositions

[0115] Provided herein are compositions comprising individual microbial strains or combinations of microbial strains, metabolites thereof, extracts thereof, or components thereof. In some embodiments, a composition comprises individual microbial strains or combinations of microbial strains from a mammalian microbiome, metabolites thereof, extracts thereof, and / or components thereof, which have been assessed, identified, characterized or assayed using methods as described herein. In some embodiments, a composition provided herein comprises one or more, two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more microbial strains from a mammalian microbiome, extracts thereof, metabolites thereof, and / or components thereof, which have been assessed, identified, characterized or assayed using methods as described herein.

[0116] Provided herein are also compositions comprising one or more components or metabolites. In some embodiments, components or metabolites in compositions herein are from a source that is not a microbial strain, e.g., synthetically generated. In some embodiments, components or metabolites in a composition may have been identified from a microbial strain, but are independent from a microbial strain and are not produced by a microbial strain, e.g., they can be synthetically generated.

[0117] In some embodiments, a composition provided herein comprises two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more microbial strains listed in Table 1 below. Table 1: Exemplary Microbial Strains Found in Human Gut Microbiome

[0118] In some embodiments, a composition provided herein comprises Gluconacetobacter sp., Terrisporobacter sp., Coprococcus sp., Lactobacillus sp., Clostridium sp., Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus sp., Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises at least two of, at least three of, at least four of, at least five of, at least six of, at least seven of, at least eight of, at least nine of, or all of Gluconacetobacter sp., Terrisporobacter sp., Coprococcus sp., Lactobacillus sp., Clostridium sp., Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus sp., and Acidaminococcus sp. In some embodiments, for example, a composition comprises all of Gluconacetobacter sp., Terrisporobacter sp., Coprococcus sp., Lactobacillus sp., Clostridium sp., Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus sp., and Acidaminococcus sp.. Suchcompositions may be referred to by different names, including but not limited to, CT10 composition, CT10 cocktail, and so forth.

[0119] In some embodiments, a composition provided herein comprises Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, a composition comprises at least two of, at least three of, at least four of, at least five of, at least six of, at least seven of, at least eight of, at least nine of, or all of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp. In some embodiments, for example, a composition comprises all of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp., and may be referred to by different names, including but not limited to, CT10 composition, CT10 cocktail, and so forth.

[0120] In some embodiments, a composition provided herein comprises Gluconacetobacter sp., Terrisporobacter sp., Coprococcus sp., Lactobacillus sp., Veillonella sp., Bifidobacterium sp., or a combination thereof. In some embodiments, a composition comprises at least two of, at least three of, at least four of, at least five of, or all of Gluconacetobacter sp., Terrisporobacter sp., Coprococcus sp., Lactobacillus sp., Veillonella sp., and Bifidobacterium sp.. In some embodiments, for example, a composition comprises all of Gluconacetobacter sp., Terrisporobacter sp., Coprococcus sp., Lactobacillus sp., Veillonella sp., and Bifidobacterium sp.. Such compositions may be referred to by different names, including but not limited to, CT6 composition, CT6 cocktail, and so forth.

[0121] In some embodiments, a composition provided herein comprises Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, Bifidobacterium breve, or a combination thereof. In some embodiments, a composition comprises at least two of, at least three of, at least four of, at least five of, or all of Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, and Bifidobacterium breve. In some embodiments, for example, a composition comprises all of Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonellaatypica, and Bifidobacterium breve and may be referred to by different names, including but not limited to, CT6 composition, CT6 cocktail, and so forth.

[0122] In some embodiments, a composition provided herein comprises Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., Bifidobacterium sp., or a combination thereof. In some embodiments, a composition comprises at least two of, at least three of, at least four of, at least five of, or all of Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., and Bifidobacterium sp.. In some embodiments, for example, a composition comprises all of Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., and Bifidobacterium sp. and may be referred to by different names, including but not limited to, CT6 composition, CT6 cocktail, and so forth. In some embodiments, a composition provided herein comprises Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, Bifidobacterium breve, or a combination thereof. In some embodiments, a composition comprises at least two of, at least three of, at least four of, at least five of, or all of Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, and Bifidobacterium breve. In some embodiments, for example, a composition comprises all of Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, and Bifidobacterium breve and may be referred to by different names, including but not limited to, CT6 composition, CT6 cocktail, and so forth.

[0123] Exemplary microbiome compositions (e.g. CT10, CT10m, CT10x, CT6, CT6m), as described herein, and their composition details are listed in Tables 2-6 below.

[0124] Table 2: CT10 Composition

[0125] Table 3: CT10m Composition

[0126] Table 4: CT10x Composition

[0127] Table 5: CT6 Composition

[0128] Table 6: CT6m Composition

[0129] In some embodiments, a composition provided herein comprises one or more, two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more metabolites. Metabolites which may be assessed, identified, characterized, or assayed and / or comprised in compositions as disclosed herein, include those listed for example in the Appendices submitted herewith (e.g. Appendix 1-1, 1-2, 1-3, 2, 3, or 4).

[0130] In some embodiments, a metabolite may be Butyrylcamitine, Theobromine, p-Hydroxyphenylpyruvic acid, Propionic acid, Picolinic acid, 2-Hydroxy-4methylvaleric acid, N6-Acetylysine, Urocanic acid, N5-Ethylglutamine, Trigonelline, Stachydrine, Ectoine, 5-Hydroxylysine, Arginine (arg), Cholic acid, 2-(4-Hydroxyphenyl)propionic acid, N-Acetyltryptophan, Hydroxyproline, Argininosuccinic acid, Glutamic acid (Glu), Sarcosine, 5-Methoxyindoleacetic acid, Indole-3-lactic acid, Isovalerylalanine, N- Acetylleucine, 1-Methylhistidine, N-Acetylephenylalanine, Proline (Pro), or any combination thereof.

[0131] In some embodiments, a metabolite may be 4-Hydroxyphenylpyruvic, Ectoine, Gramine, N-Acetyl-L-phenylalanine, Nepsilon-Acetyl-L-lysine, Stachydrine, Trigonelline, 3-Ureidopropionic acid, Theobromine, Hippuric acid, Imidazolepropionic acid, NG-Methyl-L-arginine, trans-Urocanic Acid, N-Acetyl-L-leucine, Sarcosine, Isobutyrylcarnitine, b-Hydroxyisovaleric acid, L-Theanine / N5-Ethylglutamine, 5- Hydroxylysine, Phenaceturic acid, betaine, hydroxyproline, Picolinic acid, 2-Aminoadipic acid, Glycerophosphocholine, carnitine, Glycerol 3-phosphate, Argininosuccinic acid, creatine, Terephthalic acid, Homocitrulline, Mucic acid, Homocysteinesulfinic acid, Trimethyllysine, Spermidine, Glyoxylic acid, XA0013 C6H6O4S, 3-Indoxylsulfuric acid, Nicotinamide, N-Formylglycine, Ureidoglycolate, N-Methylproline, Glucaric acid, Butyrylcarnitine, Methionine sulfoxide, Carboxymethyllysine, Glycolic acid, Phenaceturic acid, Diethanolamine, Phosphorylcholine, Guanidinosuccinic acid, N-Acetylhistidine, Glyceric acid, S-Methylmethionine, Cysteine glutathione disulfide, Kynurenine, N- Acetylphenylalanine, Threonic acid, Malic acid, 7,8-Dihydrobiopterin, Homovanillic acid, Taurocholic acid, 5-Methoxyindoleacetic acid, butyrate, b-Hydroxyisovaleric acid, 2-Oxoglutaric acid, N Acetyltryptophan, Thiaproline, Hypotaurine, Cholic acid, Acetoacetic acid, Ethanolamine, Guanidoacetic acid, S-Sulfocysteine, Myristic acid C14:0 XA0027, or any combination thereof.

[0132] In some embodiments, an individual microbial strain or combinations of microbial strains from a mammalian microbiome that have been killed (e.g., heat killed). Alternatively, in some embodiments, an individual microbial strain or combinations of microbial strains from a mammalian microbiome may include cells that are viable or alive.

[0133] In some embodiments, one or more microbial strains comprise a viable or living individual microbial strain or combinations of microbial strains, e.g., from a mammalian microbiome.

[0134] In some embodiments, one or more microbial strains comprise a viable or living individual microbial strain or combinations of microbial strains, e.g., from a mammalian microbiome, as described herein comprises and / or is formulated through use of one or more cell cultures and / or supernatants or pellets thereof, and / or a powder formed therefrom.

[0135] In some embodiments, compositions for use in accordance with the present disclosure are pharmaceutical compositions, e.g., for administration (e.g., topical, oral, subcutaneous, intravenous, intramuscular, intracerebral, intrathecal, rectal (e.g. rectal intubation), opthalmical, intravitreal, or suprachoroidal administration) to a mammal (e.g., a human). Pharmaceutical compositions typically include an active agent (e.g., individual microbial strains or combinations of microbial strains from a mammalian microbiome, extracts thereof, and / or components thereof), and a pharmaceutically acceptable carrier. Certain exemplary pharmaceutically acceptable carriers include, for instance saline, solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.

[0136] In some embodiments, a pharmaceutical composition for use in accordance with the present disclosure may include and / or may be administered in conjunction with, one or more supplementary active compounds; in certain embodiments, such supplementary active agents can include ginger, curcumin, probiotics (e.g, probiotic strains of one or more of the following genera: Lactobacillus, Bifidobacterium, Saccharomyces, Enterococcus, Streptococcus, Pediococcus, Leuconostoc, Bacillus, and / or Escherichia coli (see Fijan, Int J Environ Res Public Health.2014 May; 11(5): 4745–4767, which is incorporated herein byreference in its entirety); prebiotics (non digestible food ingredients that help support growth of probiotic bacteria, e.g., fructans such as fructooligosaccharides (FOS) and inulins, galactans such as galactooligosaccharides (GOS), dietary fibers such as resistant starch, pectin, beta-glucans, and xylooligosaccharides (Hutkins et al., Curr Opin Biotechnol.2016 Feb; 37: 1–7, which is incorporated herein by reference in its entirety) and combinations thereof.

[0137] In some embodiments, a prebiotic comprises a fructooligosaccharide, an inulin, an isomaltooligosaccharide, a lactilol, a lactosucrose, a lactulose, a soy oligosaccharide, a transgalactooligosaccharide, a xylooligosaccharide, seaweed, or a combination thereof. In some embodiments, a prebiotic comprises seaweed. In some embodiments, a prebiotic comprises a pome extract, berry extract and walnut extract.

[0138] In some embodiments, a probiotic composition can be formulated for oral administration. In some embodiments, a probiotic composition can be a food, a beverage, a feed composition, or a nutritional supplement. In some embodiments, an ellagitannin composition, an enzymatic composition, or both can be a liquid, syrup, tablet, troche, gummy, capsule, powder, gel, or film. In some embodiments, a probiotic composition is an enteric-coated formulation.

[0139] In some embodiments, a probiotic comprises a prebiotic. In some embodiments, a prebiotic comprises a fructooligosaccharide, an inulin, an isomaltooligosaccharide, a lactilol, a lactosucrose, a lactulose, a soy oligosaccharide, a transgalactooligosaccharide, a xylooligosaccharide, seaweed, a pome extract, berry extract and walnut extract. or a combination thereof.

[0140] Pharmaceutical compositions are typically formulated to be compatible with its intended route of administration. Examples of routes of administration include topical, oral, subcutaneous, intravenous, intramuscular, intracerebral, intrathecal, rectal, (e.g. rectal intubation), ophthalmic, intravitreal, or suprachoroidal administration. Methods of formulating suitable pharmaceutical compositions are known in the art, see, e.g., Remington: The Science and Practice of Pharmacy, 21st ed., 2005; and the books in the series Drugs and the Pharmaceutical Sciences: a Series of Textbooks and Monographs (Dekker, NY), which is incorporated in its entirety by reference herein. Oral compositions generally include an inert diluent or an edible carrier (e.g. pharmaceutically acceptable diluent, pharmaceutically acceptable carrier). To give but a few examples, in some embodiments, anoral formulation may be or comprise a syrup, a liquid, a tablet, a troche, a gummy, a capsule, e.g., gelatin capsules, a powder, a gel, a film, etc. Similarly, ocular compositions (e.g. for ophthalmic, intravitreal, or suprachoroidal administration) may include an inert diluent or carrier (e.g. pharmaceutically acceptable diluent, pharmaceutically acceptable carrier), various additives such as viscosity enhancers, permeations enhancers, cyclodextrins, etc. Examples of viscosity enhancers include hydroxy methyl cellulose, hydroxy ethyl cellulose, sodium carboxy methyl cellulose, hydroxypropyl methyl cellulose and polyalcohol. Example of permeation enhancers include chelating agents, preservatives, surface active agents, bile salts, Benzalkonium chloride, polyoxyethylene glycol ethers (lauryl, stearyl and oleyl), ethylenediaminetetra acetic acid sodium salt, sodium taurocholate, saponins and cremophor EL, etc. For example, in some embodiments ocular formulations may be or comprise suspensions, emulsions (e.g. water-in-oil or oil-in water), nanocarriers, (e.g. nanoparticles, nanosuspensions, liposomes, nanomicelles, dendrimers, etc.) ointments, gels, eye drops, etc. Cerebral compositions (e.g. for intracerebral or intrathecal administration) may include an inert diluent or carrier, and / or additives. In some embodiments, cerebral compositions are free of preservatives. In some embodiments, cerebral compositions are sterile.

[0141] In some embodiments, pharmaceutically compatible binding agents, and / or adjuvant materials can be included as part of a pharmaceutical composition. In some particular embodiments, a pharmaceutical composition can contain, e.g., any one or more of the following inactive ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring. In some embodiments, the compositions can be taken as-is or sprinkled onto or mixed into a food or liquid (such as water). In some embodiments, a composition that may be administered to mammals as described herein may be or comprise an ingestible item (e.g., a food or drink) that comprises (e.g., is supplemented) with an individual microbial strain or combinations of microbial strains from a mammalian microbiome, extracts thereof, and / or components thereof.

[0142] In some embodiments, a food can be or comprise one or more of bars, candies, baked goods, cereals, salty snacks, pastas, chocolates, and other solid foods, as wellas liquid or semi-solid foods including yogurt, soups and stews, and beverages such as smoothies, shakes, juices, and other carbonated or non-carbonated beverages. In some embodiments, foods are prepared by a subject by mixing in individual microbial strains or combinations of microbial strains from a mammalian microbiome, extracts thereof, and / or components thereof.

[0143] Compositions can be included in a kit, container, pack, or dispenser, together with instructions for administration or for use in a method described herein.

[0144] Those skilled in the art, reading the present disclosure, will appreciate that, in some embodiments, a composition (e.g., a pharmaceutical composition) as described herein may be or comprise one or more cells, tissues, or organisms (e.g., plant or microbe cells, tissues, or organisms) that produce (e.g., have produced, and / or are producing) a relevant compound.

[0145] Those skilled in the art will appreciate that, in some embodiments, technologies for preparing compositions and / or preparations, and / or for preparing (and particularly for preparing pharmaceutical compositions) may include one or more steps of assessing or characterizing a compound, preparation, or composition, e.g., as part of quality control. In some embodiments, if an assayed material does not meet pre-determined specifications for the relevant assessment, it is discarded. In some embodiments, if such assayed material does meet the pre-determined specifications, then it continues to be processed as described herein.

[0146] In some embodiments, a pharmaceutical composition provided herein can promote the colonization of an individual microbial strain or combinations of microbial strains from a mammalian microbiome, particularly microbial strain(s) that have been identified, characterized, or assessed as decreasing the severity or incidence of a mammalian disease, disorder, or condition, in a mammal suffering from or at risk of the mammalian disease, disorder, or condition. In some embodiments, a pharmaceutical composition provided herein can attenuate the colonization of an individual microbial strain or combinations of microbial strains from a mammalian microbiome, particularly microbial strain(s) that have been identified, characterized, or assessed as increasing the severity or incidence of a mammalian disease, disorder, or condition, in a mammal suffering from or at risk of the mammalian disease, disorder, or condition (e.g. a metabolism-associated disease, disorder, or condition as described herein). In some embodiments, a pharmaceuticalcomposition provided herein can promote the colonization of an individual microbial strain or combinations of microbial strains from a mammalian microbiome, particularly microbial strain(s) that have been identified, characterized, or assessed as not affecting the severity or incidence of the mammalian disease, disorder, or condition but have been identified, characterized, or assessed as being capable of outcompeting one or more microbial strains that have been identified, characterized, or assessed as increasing the severity or incidence of a mammalian disease, disorder or condition, in a mammal suffering from or at risk of the mammalian disease, disorder, or condition.

[0147] In some embodiments, each of the one or more microbial strains in a composition comprises 101colony forming units (CFUs) to 1020CFU. In some embodiments, each of the one or more microbial strains in a composition comprises 101colony forming units (CFUs) to 1015CFU. In some embodiments, each of the one or more microbial strains in a composition comprises 106CFU to 1015CFUs. In some embodiments, each of the one or more microbial strains in a composition comprises about 101CFU to 1015CFU, or about 102CFU to 1014CFU, or about 103CFU to 1013CFU, or about 104CFU to 1013CFU, or about 105CFU to 1012CFU, or about 106CFU to 1011CFU, or about 107CFU to 1010CFU, or about 108CFU to 109CFU, or about 105CFU to 1010CFU, or about 108CFU to 1012CFU. In some embodiments, each of the one or more microbial strains in a composition comprises at least about 101, 5 x 101, 102, 5 x 102, 103, 5 x 103, 104, 5 x 104, 105, 5 x 105, 106, 5 x 106, 107, 5 x 107, 108, 5 x 108, 109, 5 x 109, 1010, 5 x 1010, 1011, 5 x 1011, 1012, or more CFUs. In some embodiments, each of the one or more microbial strains in a composition comprises at most about 1015, 5 x 1014, 1014, 5 x 1013, 1013, 5 x 1012, 1012, 5 x 1011, 1011, 5 x 1010, 1010, 5 x 109, 109, 5 x 108, 108, or less CFUs. In some embodiments, each of the one or more microbial strains in a composition comprises the same number of CFUs. In some embodiments, some of the one or more microbial strains in a composition comprises a different number of CFUs.

[0148] In some embodiments, a composition comprises a total of 101CFU to 1020CFUs. In some embodiments, a composition comprises a total of 106CFU to 1015of CFUs. In some embodiments, a composition can include about 101CFU to 1020CFU, or about 105CFU to 1015CFU, or about 105CFU to 1012CFU, about 105CFU to 1010CFU, or about 108CFU to 1012CFU of one or more microbial strains. In some embodiments, a composition can include about 101CFU to 1015CFU, or about 102CFU to 1014CFU, or about 103CFU to 1013CFU, or about 104CFU to 1013CFU, or about 105CFU to 1012CFU, or about 106CFU to 10 CFU, or about 10 CFU to 10 CFU, or about 108CFU to 109CFU, or about 105CFU to 1010CFU, or about 108CFU to 1012CFU of one or more microbial strains. In some embodiments, a composition can include at least 101, 5 x 101, 102, 5 x 102, 103, 5 x 103, 104, 5 x 104, 105, 5 x 105, 106, 5 x 106, 107, 5 x 107, 108, 5 x 108, 109, 5 x 109, 1010, 5 x 1010, 1011, 5 x 1011, 1012, or more CFUs of one or more microbial strains. In some embodiments, a composition can include at most 1015, 5 x 1014, 1014, 5 x 1013, 1013, 5 x 1012, 1012, 5 x 1011, 1011, 5 x 1010, 1010, 5 x 109, 109, 5 x 108, 108, or less CFUs of one or more microbial strains.

[0149] In some embodiments, a pharmaceutical composition is tailored to a specific mammal (e.g., a specific human, e.g., a patient) based on that mammal’s (e.g., human’s) microbiome. In some embodiments, a pharmaceutical composition is specific for a microbiome of an individual mammal (e.g., human). In some embodiments, a pharmaceutical composition is specific for microbiomes of a population of mammals (e.g., humans). Populations of mammals can include, but are not limited to: families, mammals in the same regional location (e.g., neighborhood, city, state, or country), mammals with the same disease or condition, mammals of a particular age or age range, mammals that consume a particular diet (e.g., food, food source, or caloric intake).

[0150] Methods of Treatment

[0151] The present disclosure recognizes that compositions described herein can be useful in the treatment of subjects. Methods provided by the present disclosure include methods for the treatment of certain diseases, disorders and conditions. In some embodiments, relevant diseases, disorders and conditions may be or include a metabolism- associated disease, disorder, or condition. In some embodiments, a metabolism-associated disease, disorder, or condition may be, but not limited to, lipid-induced metabolic syndrome, cerebral infarction / stroke, myocardial infarction / heart attack, Type II diabetes / diabetes mellitus, glucose intolerance, alcoholism, metabolic syndrome, kidney disease, cardiorenal syndrome, vascular diseases (e.g., hypertension, peripheral arterial disease), Alzheimer’s disease, asthma (e.g., due to abdominal obesity or central / truncal obesity), atherosclerosis, hypothyroidism, liver disease, LDL-hypercholesterolemia, hypertriglyceridemia, mixed hyperlipoproteinemia, coronary heart disease, stroke, peripheral arterial disease, high blood pressure, hyperlipidemia, steatosis, non-alcoholic steatohepatitis (NASH), fatty-liverdisease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), liver fibrosis, cirrhosis, or hepatocellular carcinoma etc..

[0152] Generally, methods of treatment provided by the present disclosure involve administering a therapeutically effective amount of a composition as described herein alone or in combination with other compositions and / or treatments to a subject who is in need of, or who has been determined to be in need of, such treatment.

[0153] In some embodiments, methods of treatment provided herein are prophylactic or preventative, e.g., may be administered to subjects prior to display of significant symptoms and / or to exposure to a particular expected inducement that is associated with metabolism-associated diseases, disorders, or conditions described herein. In some embodiments, methods of treatment provided herein are therapeutic, e.g., may be administered to subjects after development of significant symptoms associated with metabolism-associated diseases, disorders, or conditions.

[0154] In some embodiments, provided methods of treatment are administered to a subject that is a mammal, e.g., a mammal that experiences a disease, disorder, or condition as described herein; in some embodiments, a subject is a human or non-human veterinary subject, e.g., an ape, cat dog, monkey, or pig.

[0155] In many embodiments, treatment involves ameliorating at least one symptom of a disease, disorder, or condition associated with metabolism-associated diseases, disorders, or conditions. In some embodiments, a method of treatment can be prophylactic.

[0156] In some embodiments, the methods can include administration of a therapeutically effective amount of compositions disclosed herein before, during (e.g., concurrently with), or after administration of a treatment that is expected to be associated with metabolism-associated diseases, disorders, or conditions.

[0157] In some embodiments, subjects who receive treatment as described herein may be receiving and / or may have received other treatment (e.g., pharmacological treatment / therapy, surgical, etc.), for example that may be intended to treat one or more symptoms or features of a disease disorder or condition as described herein (e.g. metabolism-associated diseases, disorders, or conditions), so that provided compositions are administered in combination with such other therapy (i.e. treatment) to treat the relevant disease, disorder, or condition.

[0158] In some embodiments, the compositions described herein can be administered in a form containing one or more pharmaceutically acceptable carriers. Suitable carriers have been described previously and vary with the desired form and mode of administration of a composition. For example, pharmaceutically acceptable carriers can include diluents or excipients such as fillers, binders, wetting agents, disintegrators, surface- active agents, glidants, and lubricants. Typically, a carrier may be a solid (including powder), liquid, or any combination thereof. Each carrier is preferably “acceptable” in the sense of being compatible with other ingredients in the composition and not injurious to a subject. A carrier can be biologically acceptable and inert (e.g., it permits the composition to maintain viability of the biological material until delivered to the appropriate site).

[0159] Tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, primogel, or corn starch; a lubricant such as magnesium stearate or sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, orange flavoring, or other suitable flavorings. These are for purposes of example only and are not intended to be limiting.

[0160] Oral compositions can include an inert diluent or an edible carrier. For purposes of oral therapeutic administration, an active compound can be incorporated with excipients and used in the form of tablets, lozenges, pastilles, troches, or capsules, e.g., gelatin capsules. Oral compositions can also be prepared by combining a composition of the present disclosure with a food. In some embodiments, microbes (e.g. one or more microbial strains) can be formulated in a food item. Some non-limiting examples of food items to be used with the methods and compositions described herein include: popsicles, cheeses, creams, chocolates, milk, meat, drinks, pickled vegetables, kefir, miso, sauerkraut, etc. In other embodiments, food items can be juices, refreshing beverages, tea beverages, drink preparations, jelly beverages, and functional beverages; alcoholic beverages such as beers; carbohydrate-containing foods such as rice food products, noodles, breads, and pastas; paste products such as fish, hams, sausages, paste products of seafood; retort pouch products such as curries, food dressed with a thick starchy sauce, and Chinese soups; soups; dairy products such as milk, dairy beverages, ice creams, and yogurts; fermented products such as fermented soybean pastes, fermented beverages, and pickles; bean products; variousconfectionery products including biscuits, cookies, and the like, candies, chewing gums, gummies, cold desserts including jellies, cream caramels, and frozen desserts; instant foods such as instant soups and instant soy-bean soups; and the like. It is preferred that food preparations not require cooking after admixture with microbial strain(s) to avoid killing any microbes. In one embodiment a food used for administration is chilled, for example, iced flavored water. In certain embodiments, the food item is not a potentially allergenic food item (e.g., not soy, wheat, peanut, tree nuts, dairy, eggs, shellfish or fish). Pharmaceutically compatible binding agents, and / or adjuvant materials can be included as part of the composition.

[0161] Ocular formulations (e.g. for ophthalmic, intravitreal, or suprachoroidal administration) can include an inert diluent or a carrier. For purposes of ocular therapeutic administration, an active compound can be incorporated with excipients and used in the form of suspensions, emulsions (e.g. water-in-oil or oil-in water), nanocarriers, (e.g. nanoparticles, nanosuspensions, liposomes, nanomicelles, dendrimers, etc.) ointments, gels, eye drops, etc. In some embodiments, administration of such formulations is topical (e.g. eye drops). In some embodiments, administration of such formulations is via injection (e.g. intravitreal, suprachoroidal, etc.).

[0162] Cerebral formulations (e.g. for intracerebral or intrathecal administration) can include an inert diluent or a carrier. For purposes of cerebral therapeutic administration, an active compound can be incorporated with excipients and used in the form of suspensions, emulsions (e.g. water-in-oil or oil-in water), nanocarriers, (e.g. nanoparticles, nanosuspensions, liposomes, nanomicelles, dendrimers, etc.) ointments, gels, etc. In some embodiments, administration of such formulations is topical (e.g. ointments). In some embodiments, administration of such formulations is via injection (e.g. intracerebral, intrathecal, etc.).

[0163] In some such embodiments, a composition described herein is administered to a subject according to a dosing regimen that achieves population of the subject’s microbiome with administered cells. In some embodiments, a composition is administered to a subject in a single dose. In some embodiments, a composition is administered to a subject in a plurality of doses. In some embodiments, a dose of a composition is administered to a subject twice a day, daily, weekly, or monthly.

[0164] In some embodiments, each of the one or more microbial strains in a dose comprises 101to 1015colony forming units (CFUs). In some embodiments, each of the one or more microbial strains in a dose comprises 106to 1015CFUs. In some embodiments, each of the one or more microbial strains in a dose comprises the same number of CFUs. In some embodiments, some of the one or more microbial strains in a dose comprises a different number of CFUs.

[0165] In some embodiments, a dose of one or more microbial strains comprises a total of 106to 1015CFUs. In some embodiments, a dose of one or more microbial strains comprises a total of 107to 1015CFUs. In some embodiments, a dose of one or more microbial strains comprises 5-200 billion CFUs. In some embodiments, a dose of one or more microbial strains comprises 5-50 billion CFUs. In some embodiments, a dose of one or more microbial strains comprises 5-20 billion CFUs. In some embodiments, a dose of one or more microbial strains comprises 50-100 billion CFUs. In some embodiments, a dose of one or more microbial strains comprises 100-200 billion CFUs.

[0166] In some embodiments, efficacy can be assessed by measuring the degree of oxidative stress of cells in a biological sample prior to and following administration of a composition as described herein. The degree of oxidative stress of cells can be assessed by, for example, measuring the expression of oxidative stress biomarkers, such as reactive oxygen species (ROS) levels, or lipid, protein, and nucleic acid damage levels, or by determining the ratio of oxidized to reduced forms of one or more biomarkers. High levels of oxidative stress can be cytotoxic, so the degree of oxidative stress can be measured by assessing the concentration of intracellular proteins present in the systemic circulation from inflamed or lysed cells (e.g. nerve cells). EXEMPLIFICATION

[0167] Example 1: Evaluation of efficacy of microbiome compositions in affecting body weight in mouse model

[0168] This Example provides an evaluation of the efficacy of microbiome compositions, specifically CT6 and CT6m compositions, in affecting body weight in in vivo mouse model.

[0169] Mouse Model: TDP43 Q331K male mice that were 8 weeks old were used for these experiments. Wild type mice were used as a control in all experiments.

[0170] Study: TDP43-Q331K mice were divided into three groups of 17-20 animals per group, and were provided mock (DPBS) or microbiome composition (CT6 or CT6m; composition details listed in Tables 2, 3, and 4) by daily oral gavage for approximately 220 days. The groups were: (i) G1: Wild type mice treated with DPBS (n=19); (ii) G2: TDP43- Q331K transgenic mice treated with DPBS (n=17); (iii) G3: TDP43-Q331K transgenic mice treated with CT6 composition (n=19); and (iv) G4: TDP43-Q331K transgenic mice treated with CT6m composition (n=20). The body weights of the animals were recorded twice a week until the end of study.

[0171] Results: Fig.1 shows the results of this experiment. Figs.1a-e show average body weight at different timepoints during the study. At study start, TDP43 mice had significantly heavier body weights compared to non-transgenic (ntg) i.e. wild type littermates (p < 0.002). When mice were 8 weeks old all treatment groups exhibited weight gain with aging, regardless of genotype or treatment (see Fig.1a-b). After 57 days of dosing vehicle-treated ntg mice and CT6m treated mice were significantly lighter compared to vehicle-treated TDP43 mice (p < 0.0002 & p < 0.045, respectively) (Fig.1c). After 163 days, both CT6 & CT6m-treated animals showed significantly lower body weights (p < 0.041 & p < 0.035, respectively) compared to vehicle-treated TDP43 mice, whereas body weights of vehicle-treated ntg mice were no longer significantly different to vehicle-treated TDP43 mice (Fig.1d). There were no differences between vehicle-treated ntg and vehicle- treated TDP43 mice at the end of study (> 220 days of dosing). Conversely, CT6 or CT6m- treated mice had significantly lower body weights (p < 0.028 & p < 0.0092, respectively) compared to vehicle-treated TDP43 mice (Fig.1e). Moreover, none of the treated animals presented body weight loss exceeding 10% from baseline, demonstrating that daily treatments were well-tolerated, thus providing substantial evidence that these therapies are safe.

[0172] Example 2: Evaluation of efficacy of microbiome compositions in affecting fat accumulation in livers in mouse model

[0173] This Example provides an evaluation of the efficacy of microbiome compositions, specifically CT6 and CT6m compositions, in affecting fat accumulation in livers in in vivo mouse model.

[0174] Mouse Model: TDP43-Q331K male mice that were 8 weeks old were used for these experiments. Wild type mice were used as a control in all experiments.

[0175] Study: TDP43-Q331K mice were divided into three groups of 20 animals per group, and were provided mock (DPBS) or microbiome composition (CT6 or CT6m; composition details listed in Tables 2, 3, and 4) by daily oral gavage for 224 days. The groups were: (i) G1: Wild type mice treated with DPBS (n=20); (ii) G2: TDP43-Q331K transgenic mice treated with DPBS (n=20); (iii) G3: TDP43-Q331K transgenic mice treated with CT6 composition (n=20); and (iv) G4: TDP43-Q331K transgenic mice treated with CT6m composition (n=20). The animals were sacrificed at the end of the study, following which histological analyses were performed.

[0176] Results: Fig.2 shows the results of this experiment. During harvesting of tissues, it was observed that a large proportion of vehicle-treated TDP43-trangenic and vehicle-ntg animals had grossly observable fatty livers (Fig.2a). On the contrary, less than 10% of animals treated with CT6 or CT6m exhibited grossly observable fatty livers (Fig. 2b), demonstrating that treatments with CT6 and / or CT6m provides protection against non- alcoholic fatty liver disease in TDP43-Q331K male animals. Fig.2c shows photographs of liver samples from each of the four groups demonstrating microbiome composition treated- livers lack the appearance of lipid accumulation that is seen in G1 (ntg, vehicle-treated) & G2 (TDP43 + vehicle) mice.

[0177] To examine the degree of fatty liver disease, hematoxylin & eosin (H&E) staining was performed on formalin-fixed paraffin-embedded livers sections by Horus Scientific, a histology CRO in Worcester, MA. Microscopic evaluation of the H&E sections showed that vehicle-treated animals, regardless of genotype, exhibited a more pronounced and severe degree of lipid deposition in the livers compared to animals treated with CT6 or CT6m (see Fig.3).

[0178] These observations that CT6 & CT6m treatment protects the liver from fat accumulation is in accordance with the significant difference in body weight between vehicle-treated and CT6 / CT6m-treated animals (see Example 1), indicating that CT6 & CT6m has utility and efficacy in treating metabolic disorders.

[0179] Example 3: Evaluation of efficacy of microbiome compositions in affecting LDL- cholesterol, HDL cholesterol, and circulating triglyceride levels in mouse model

[0180] This Example provides an evaluation of the efficacy of microbiome compositions, specifically CT6 and CT6m compositions, in affecting low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, and circulating triglyceride levels in in vivo mouse model.

[0181] Mouse Model: TDP43-Q331K male mice that were 8 weeks old were used for these experiments. Wild type mice were used as a control in all experiments.

[0182] Study: TDP43-Q331K mice were divided into three groups of 16-20 animals per group, and were provided mock (DPBS) or microbiome composition (CT6 or CT6m; composition details listed in Tables 2, 3, and 4) by daily oral gavage for 224 days. The groups were: (i) G1: Wild type mice treated with DPBS (n=19); (ii) G2: TDP43-Q331K transgenic mice treated with DPBS (n=16); (iii) G3: TDP43-Q331K transgenic mice treated with CT6 composition (n=19); and (iv) G4: TDP43-Q331K transgenic mice treated with CT6m composition (n=20).

[0183] To evaluate the impact of CT6 and CT6m treatments on other aspects of metabolic disorders, a lipid panel using mouse-specific, plate-based colorimetric LDL & HDL assay kits to measure the levels of circulating cholesterol from plasma collected at the end-of-study under non-fasting conditions was performed. Plate-based enzymatic assays kits were purchased from Crystal Chem for measuring Mouse HDL-cholesterol (Cat. # 79990) and Mouse LDL-cholesterol (Cat. # 79980) in plasma samples collected at end of study. The assays were carried out in 96-well plates following the assay kit protocol instructions. The optical density (OD) was measured at 600 nM twice with the Promega GloMax Explorer plate reader, per protocol instructions. The first OD reading was done after a 5 minute incubation of modified polyvinyl sulfonic acid and polyethylene-glycol methyl ether (PVS / PEGME) detergent with 3 µL of plasma samples in a 96 well plate

[0184] Results: Fig.4 shows the results of this experiment. Measurement & quantification of LDL cholesterol, which is also commonly referred to as ‘bad’ cholesterol, revealed no significant differences between vehicle-treated transgenic & non-transgenic animals (mean [LDL] = 42.6 + / - 15.1 mg / dL vs.47.1 + / - 13.6 mg / dL, respectively; see Fig.4a). However, treatment with CT6 led to a significant reduction (p = 0.03) in LDL levels compared to vehicle-treated transgenic mice (34.7 + / - 12.2 mg / dL vs 47.1 + / - 13.6 mg / dL, respectively). This reduction was even more robust and significant (p = 0.0002) in animals treated with CT6m, which had a mean LDL concentration of 26.8 + / - 16.2 mg / dL (see Fig. 4a). When LDL level is elevated or too high, the cholesterol can build up along the walls of blood vessels leading to a higher risk for heart disease and stroke.

[0185] HDL cholesterol is known as the ‘good’ cholesterol because it absorbs cholesterol and carries it back to the liver where it gets flushed from the body. Contrary to LDL levels, high levels of HDL cholesterol can lower risks for cardiovascular disease / heart attack and stroke. Therefore, it was determined if CT6 or CT6m treatments imparts any effect on raising HDL levels. Indeed, a significant increase in plasma HDL cholesterol levels was observed in animals treated with CT6 (p= 0.021) or CT6m (p=0.008) compared to vehicle treated TDP43 transgenic animals (mean [HDL] = 46.1mg / dL vs.47.8 mg / dL vs. 31.1 mg / dL, respectively) (see Fig.4b). Intriguingly, it was found that among the four treatment groups, vehicle-treated ntg animals in group 1 (G1) had the highest and most significantly (p <0.0001) elevated HDL levels, with a mean of 58.6 mg / dL.

[0186] Very often the total cholesterol to HDL ratio is used for assessing one’s risk to developing heart disease or stroke. In fact, studies suggests that the total cholesterol to HDL ratio is a better marker and risk indicator for atherosclerosis (commonly referred as heart disease) or stroke compared to looking at LDL or total cholesterol alone. Higher ratio of LDL / HDL indicate a higher risk for developing heart disease or stroke whereas lower ratio of LDL / HDL indicate lower cardiovascular / stroke risk. Indeed, it was observed that animals in G2 (TDP43 + vehicle) had the highest ratio of LDL / HDL compared to animals in groups G1, G3 and G4 (see Fig.4c).

[0187] Furthermore, to test the lipid-lowering effects of CT6 & CT6m compositions, circulating triglyceride levels were measured in the same plasma sample set used for measuring LDL & HDL cholesterol levels (see Fig.4d). It was observed that animals in G2 (TDP43 + vehicle) had the highest plasma triglyceride levels compared to animals in groups G1, G3 and G4 (see Fig.4d). Furthermore, both CT6 and CT6m treated TDP43 mice showed the significantly lower plasma triglyceride levels compared to vehicle treated TDP43 mice. These results suggest microbiome compositions, for example CT6 and CT6m compositions, decrease bad cholesterol and fats in the body thereby reducing risks for cardiovascular disease and stroke.

[0188] Example 4: Evaluation of efficacy of microbiome compositions in affecting inflammation in mouse model

[0189] This Example provides an evaluation of the efficacy of microbiome compositions, specifically CT6 and CT6m compositions, in affecting inflammation, specifically pro-inflammatory cytokines and chemokines levels, in in vivo mouse model.

[0190] Mouse Model: TDP43-Q331K male mice that were 8 weeks old were used for these experiments. Wild type mice were used as a control in all experiments.

[0191] Study: TDP43-Q331K mice were divided into three groups of 16-20 animals per group, and were provided mock (DPBS) or microbiome composition (CT6 or CT6m; composition details listed in Tables 2, 3, and 4) by daily oral gavage for 224 days. The groups were: (i) G1: Wild type mice treated with DPBS (n=19); (ii) G2: TDP43-Q331K transgenic mice treated with DPBS (n=16); (iii) G3: TDP43-Q331K transgenic mice treated with CT6 composition (n=19); and (iv) G4: TDP43-Q331K transgenic mice treated with CT6m composition (n=20). The animals were sacrificed at the end of the study, following which histological analyses were performed. To assess the effects of CT6 or CT6m treatment on inflammation, the levels of pro-inflammatory cytokines and chemokines in liver lysates of mice were assessed.

[0192] Results: Fig.5 shows the results of this experiment. The levels of pro- inflammatory cytokines and chemokines in liver lysates of mice were measured using the Mouse Cytokine / Chemokine 31-Plex Discovery Assay, which was outsourced to and performed by Eve Technologies (Calgary, AB, Canada). As seen from Fig.5, various pro- inflammatory cytokine and chemokines were found to be significantly lower in the CT6 and CT6m treated TDP43 mice compared to the control groups G1 and G2. These results suggest microbiome compositions, for example CT6 and CT6m compositions, decrease pro- inflammatory cytokine and chemokine levels. OTHER EMBODIMENTS

[0193] It is to be appreciated by those skilled in the art that various alterations, modifications, and improvements to the present disclosure will readily occur to those skilled in the art. Such alterations, modifications, and improvements are intended to be part of thepresent disclosure, and are intended to be within the spirit and scope of the invention. Accordingly, the foregoing description and drawing are by way of example only and any invention described in the present disclosure if further described in detail by the claims that follow.

[0194] Those skilled in the art will appreciate typical standards of deviation or error attributable to values obtained in assays or other processes as described herein. The publications, websites and other reference materials referenced herein to describe the background of the invention and to provide additional detail regarding its practice, including those listed in the above References section, are hereby incorporated by reference in their entireties.

[0195] It is to be understood that while embodiments of the invention have been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.EQUIVALENTS

[0196] Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. The scope of the present invention is not intended to be limited to the above Description, but rather is as set forth in the following claims:2-Deoxyuridine 20α-Hydroxyprogesterone 21-Deoxycortisol-2 21-Hydroxypregnenolone 3-(4-Hydroxyphenyl)propionic acid 2-(4-Hydroxyphenyl)propionic acid 3-(3-Hydroxyphenyl)propionic acid 3-(4-Hydroxyphenyl)propionic acid;2-(4-Hydroxyphenyl)propionic acid;3-(3-Hydroxyphenyl)propionic acid;Tropic acid;3-(2-Hydroxyphenyl)propionic acid;m-Ethoxybenzoic acid;3-Phenyllactic acid;p- Methoxyphenylacetic acid 3-cis-Hydroxy-b,e-Caroten-3'-one 3-Guanidinopropanoate 3-Hydroxy-2-methyl-4-pyrone 3-Hydroxy-3-methylglutaric acid 3-Hydroxy-3',4'-didehydro-β,γ-carotene 3-Hydroxybutyric acid 3-Hydroxybutyric acid;2-Hydroxybutyric acid;2-Hydroxyisobutyric acid 3-Hydroxybutyric acid;2-Hydroxyisobutyric acid 3-Hydroxyglutaric acid 3-Hydroxytetradecanoic acid-1 3-Indoxylsulfuric acid 3-Mercaptolactic acid 3-Methylhistamine;1-Methylhistamine 3-Methylhistidine;1-Methylhistidine 3-oxocholic acid 3-Phosphoglyceric acid 3-Ureidopropionic acid 3,4-Dihydroxyhydrocinnamic acid;Homovanillic acid;Hydroxyphenyllactic acid 4-Acetamidobutanoic acid 4-Guanidinobutyric acid 4-Hydroxyquinoline 4-Methyl-2-oxovaleric acid 3-Methyl-2-oxovaleric acid 2-Oxohexanoic acid 4-Methyl-2-oxovaleric acid;3-Methyl-2-oxovaleric acid;2-Oxohexanoic acid 4-Oxopyrrolidine-2-carboxylic acid 5-Amino-4-hydroxynaphthalene-1,3-disulfonic acid 5-Amino-4-oxovaleric acid 5-Hydroxyindoleacetic acid 5-Hydroxylysine 5-Hydroxypentanoic acid;ƒÀ-Hydroxyisovaleric acid;2-Hydroxyvaleric acid 5-Hydroxytryptophan 5-Isopropyl-2'-deoxyuridine triphosphate5-Methoxyindoleacetic acid;Indole-3-lactic acid 5-Methyl-2'-deoxycytidine 5-Oxoproline 5α-Cholestan-3-one-1 5α-Cholestan-3-one-2 5α-Pregnane-3,20-dione 6-Hydroxyhexanoic acid 6-Hydroxyhexanoic acid;2-Hydroxy-4-methylvaleric acid 6-Hydroxynicotinic acid 7-Dehydrocholesterol 7-Dehydrocholesterol 7-Dehydrocholesterol-2 Desmosterol-2 7-Dehydrocholesterol-3 Desmosterol-3 7-Methoxy-2-methylisoflavone 7-Methylguanine 7-Methylguanine;3-Methylguanine 7,8-Dihydrobiopterin 7,8-Dihydroneopterin Abietic acid Abietic acid-1 Abietic acid-3 AC(10:0) AC(12:0)-1 AC(12:0)-2 AC(12:1) AC(12:1)-1 AC(12:1)-3 AC(13:1) AC(13:1)-1 AC(14:0)-1 AC(14:0)-2 AC(14:1)-1 AC(14:1)-2 AC(14:1)-3 AC(14:1)-4 AC(14:2)-1 AC(14:2)-2 AC(14:2)-3 AC(14:3)-1 AC(14:3)-2AC(14:3)-3 AC(14:3)-4 AC(15:0)-1 AC(15:0)-2 AC(16:1) AC(16:2)-1 AC(16:2)-2 AC(17:0)-1 AC(17:0)-2 AC(17:1) AC(18:0) AC(18:1) AC(18:2)-1 AC(18:2)-2 AC(20:0) AC(20:1) AC(22:0) Acetohydroxamic acid;Gly ADMA;SDMA ADP ADP-ribose AEA(22:6) Ala ala ser / gly thr Aminoacetone AMP AMP;dGMP Anandamide ANDS(C-SCOPE IS) Anserine Arachidic acid Arachidonic acid Arg Argininosuccinic acid Ascorbic acid Asiatic acid Asiatic acid-1 Asn Asp Asp Asp Pro Ser Asp Gly His Asp Asp Leu Asn Arg Asp-ProATP Baicalein Behenic acid Betaine Betaine aldehyde_+H2O Betulinic acid Betulinic acid-2 Biopterin Biotin Butyrylcarnitine C;C C3H8N4O C4H7NO4 C5H12N2O2 C5H6O7 C6H10O8 C6H11NO2 C6H12N2O3 C7H9N3O2 C8H17NO C8H18N2O3 C9H18N2O cAMP Campesterol Carbachol Carboxymethyllysine Carnitine Carnosine Carnosine;His-Ala;Ala-His Chenodeoxycholic acid Cholesterol Cholesterol sulfate Cholic acid Choline cis-11-Eicosenoic acid cis-11,14-Eicosadienoic acid-1 cis-11,14-Eicosadienoic acid-2 cis-4,7,10,13,16,19-Docosahexaenoic acid cis-5,8,11,14,17-Eicosapentaenoic acid epa cis-8,11,14-Eicosatrienoic acid cis-Aconitic acid Citric acid CitrullineCorosolic acid Cortexolone Corticosterone 21-Deoxycortisol-1 Cortisol 18-Hydroxycorticosterone Humulone Creatine Creatinine Crotonic acid CSA;CSA Cyclodopa glucoside Cyclohexylamine Cys Cys Csy Asn Asn Cystathionine Cysteine glutathione disulfide Cystine Cytidine Cytosine Daidzein Dansyl acid(C-SCOPE IS) Deoxycholic acid Dethiobiotin dGDP;ADP dGTP;ATP Diethanolamine Dimethylaminoethanol DOPA DPA;DPA Dyphylline Ectoine Erucic acid Ethanolamine Ethanolamine phosphate Ethyl arachidonate Ethyl glucuronide FA 16:1 FA C18:1 FA(12:0) FA(13:0) FA(14:1) FA(14:1)-2FA(14:2)-1 FA(14:2)-2 FA(14:3) FA(15:0) FA(15:0)-1 FA(15:1) FA(15:1)-2 FA(16:2)-1 FA(16:2)-2 FA(16:3 FA(16:3)-2 FA(17:0) FA(17:1) FA(17:2) FA(17:3) FA(19:0) FA(19:0)-1 FA(19:1) FA(19:2) FA(20:3) FA(22:2) FA(22:3)-1 FA(22:3)-2 FA(22:4)-1 FA(22:4)-2 FA(22:5)-1 FA(22:5)-2 FA(24:0) FA(24:2) FA(24:4) FA(24:5)-1 FA(24:5)-2 Flavanone Formiminoglutamic acid Formononetin Fucosyl tryptophan Fucosyl-Lysine Fumaric acid ƒÀ-Ala ƒÁ-Butyrobetaine ƒÁ-Glu-Gly ƒÁ-Glu-Met ƒÁ-Glu-PheƒÁ-Glu-Ser ƒÁ-Glu-Tyr ƒÁ-Glu-Val-Gly GABA GABA;3-Aminoisobutyric acid Galactosylhydroxylysine Galacturonic acid-1 Glucuronic acid-1 Galacturonic acid;Glucuronic acid Gamma-Glu-Gln GDP Genistein Gln Glu Glu;Isoglutamic acid;threo-ƒÀ-Methylaspartic acid;N-Methylaspartic acid;N-Acetylserine Glucaric acid Gluconic acid Gluconolactone Glucosamine Glucosamine 6-sulfuric acid Glucose 6-phosphate Glucosyl-glycerol Glutaric acid Methylsuccinic acid Glutaric acid;Methylsuccinic acid Glutathione (GSSG)_divalent Gly Gly Lys Gly-Ala Gly-Asp Gly-Asp;Asp-Gly Gly-Leu;N-Acetyllysine;Val-Ala;Ala-Val;Leu-Gly Glyceric acid Glycerol Glycerol 3-phosphate Glycerophosphocholine Glycitein Glycochenodeoxycholic acid Glycocholic acid Glycodeoxycholic acid Glyoxylic acid GMPGuanidinosuccinic acid Guanidoacetic acid Gulonolactone;Gluconolactone Hecogenin Heneicosanoic acid 19-Methylarachidic acid Heptadecanoic acid-1 FA(17:0)-1 Heptadecanoic acid-2 FA(17:0)-2 Heptanoic acid Hexanoic acid Hippuric acid Hippuric acid (benzyl glycine) His His Pro Ser Val Arg Tyr Thr His-Asp Histamine Homo Arginine Homo Proline Betaine Homocarnosine Homocitrulline Homocysteinesulfinic acid Homoserine Homovanillic acid Hydroxyphenyllactic acid Hydroxyindole Hydroxyoctanoic acid Hydroxyprogesterone caproate Hydroxyproline Hydroxytetradecanoic acid Hyodeoxycholic acid Hypotaurine IDP Ile Ile;Leu;Alloisoleucine Ile;Leu;ƒÀ-Leucine;Alloisoleucine;6-Aminohexanoic acid Imidazole-4-acetic acid Imidazolelactic acid IMP Indole-3-acetic acid Indole-3-carboxaldehydeIndole-3-lactic acid-1 5-Methoxyindoleacetic acid-1 Indole-3-lactic acid;5-Methoxyindoleacetic acid Indole-3-propionic acid Indole-3-propionic acid (IPA) Inosine 2',3'-cyclic phosphate cIMP Isethionic acid Isobutyrylcarnitine;Butyrylcarnitine Isocitric acid Isoglutamic acid Isoliquiritigenin-1 Isoliquiritigenin-2 Isoliquiritigenin-3 Isonicotinamide;Nicotinamide Isovalerylalanine-2 N-Acetylleucine-2 Isovalerylalanine;N-Acetylleucine Isovalerylcarnitine Kynurenic acid Kynurenine Lactamide Lactic acid Lanosterol Lauric acid Leu Leukotriene B4 Linoleic acid Linolenic acid Linoleyl ethanolamide Liquiritigenin Lithocholic acid Luteolin Lys Lys-Asp Lys-Val Malic acid Mannosamine MCA Met Methionine sulfone Methionine sulfoxide Methylmalonic acid;Succinic acidMorpholine Mucic acid Myristic acid Myristic acid 14:0 Myristoleic acid N-(1-Deoxy-1-fructosyl)valine N-Acetyl-beta-alanine N-Acetyl-β-alanine N-Acetylalanine N-Acetylalanine;N-Acetyl-ƒÀ-alanine N-Acetylasparagine N-Acetylaspartic acid N-Acetylgalactosamine;N-Acetylglucosamine;N-Acetylmannosamine N-Acetylglucosamine N-Acetylglutamic acid N-Acetylglutamine N-Acetylglycine N-Acetylhistidine N-Acetylleucine N-Acetyllysine N-Acetylmethionine N-Acetylneuraminic acid N-Acetylornithine N-Acetylphenylalanine N-Acetyltryptophan N-Acetyltyrosine N-Carbamylglutamate N-Carboxymethylserine N-Ethylmaleimide_+H2O N-Formylaspartic acid N-Formylglycine N-Formylmethionine N-Glycolylneuraminic acid N-Hydroxy-L-tryptophan N-Methylethanolamine phosphate N-Methylproline N,N-Dimethylglycine N’-Formylkynurenine N1-Acetylspermidine N1-Acetylspermidine;N8-Acetylspermidine N1-Methyl-4-pyridone-5-carboxamide N1-Methylguanosine N5-EthylglutamineN5-Ethylglutamine;N-Acetylornithine N6-Acetyllysine N6-Methyl-2'-deoxyadenosine N6-Methyllysine N6,N6,N6-Trimethyllysine Naringenin Nervonic acid Nervonyl carnitine Propyl Betaine (Triethylamine) N f-Formylkynurenine Nicotinamide no matches Norophthalmic acid Norvaline;2-Amino-2-methylbutyric acid;5-Aminovaleric acid;Val Nω-Methylarginine O-Acetylcarnitine O-Acetylhomoserine o-Coumaric acid p-Coumaric acid o-Hydroxybenzoic acid Oleanolic acid Oleic acid Oleoyl ethanolamide AEA(18:1) Ophthalmic acid Ornithine Orotidine;Uridine;Pseudouridine p-Hydroxyphenylpyruvic acid p-Hydroxyphenylpyruvic acid;Caffeic acid Palmitic acid Palmitoleic acid Palmitoylcarnitine Palmitoylethanolamide Pantothenic acid Penicillamine Penicillamine;Met Pentadecanoic acid Phe Phe Met His Glu Phe Phe Trp Trp Phe-Thr Phenaceturic acid PhenolPhenyl Sulfate Phenylpyruvic acid Phosphocreatine Phosphoenolpyruvic acid Phosphorylcholine Picolinic acid Pipecolic acid Pipecolic acid;N-Methylproline;1-Aminocyclopentanecarboxylic acid Piperidine Pro Pro-Gly;Gly-Pro Progesterone Proline Betaine Propionylcarnitine XC0061 Propionylcarnitine;XC0061 Prostaglandin E1-1 Prostaglandin D1-1 Prostaglandin E1-2 Prostaglandin D1-2 Putrescine Pyridoxal Pyrrolidine Pyruvic acid Retinol Vit A Retinol-2 Riboflavin Ribose 5-phosphate Ribulose 5-phosphate Ribulose 5-phosphate;Ribose 1-phosphate;Xylulose 5-phosphate Ricinoleic acid Ricinoleic acid 18:1 Hydroxy Ricinoleic acid-2 Ricinoleic acid-3 S-Acetyldihydrolipoamide (XC0086) S-Adenosylhomocysteine S-Adenosylmethionine S-Carboxymethylcysteine S-Methylcysteine S-Methylglutathione S-Methylmethionine S-SulfocysteineSarcosine SDMA Sedoheptulose 7-phosphate Ser Ser Ala / Thr gly Ser Glu Pro Thr Asp Pro Serotonin Sitosterol Spermidine Spermine Sphinganine Sphingomyelin(d18:1 / 16:0)-1 Sphingomyelin(d18:1 / 16:0)-2 Sphingomyelin(d18:1 / 18:0)-1 Sphingomyelin(d18:1 / 18:0)-2 Sphingosine Stearic acid Stearidonic acid Stearoyl ethanolamide Stigmasterol-1 Stigmasterol-2 Succinic acid Sulfaguanidine(C-SCOPE IS) Sulfolithocholylglycine Taurine Taurochenodeoxycholic acid Taurocholic acid Taurodeoxycholic acid Taurolithocholic acid Tauroursodeoxycholic acid Terephthalic acid Theobromine;Aminophylline;Paraxanthine Thiamine Thiamine phosphate Thr Thr Ala Ala Thr Asp or Ser Glu threo-3-Hydroxyaspartic acid threo-3-Hydroxyaspartic acid-1 threo-3-Hydroxyaspartic acid-2 Threonic acid Thymidine Thyroxinetrans-Glutaconic acid trans-Glutaconic acid;Itaconic acid Tricosanoic acid Trigonelline Trilaurin Trimesic acid;Trimesic acid Trimethylamine Trimethylamine N-oxide Trimethylaminoacetone Trp Tyr UDP-galactose UDP-glucose Uracil Urea Uric acid Uridine Uridine;Pseudouridine Urocanic acid Ursodeoxycholic acid Val XA0005 XA0008 XA0009 XA0011 XA0017 XA0019 XA0023 XA0026 XA0033 XA0034 XA0037 XA0039 XA0052 Xanthosine XC0016 XC0039 XC0040 XC0047 XC0049 XC0054;XC0055;ƒÁ-Glu-Gly XC0056 XC0060XC0063 XC0064 XC0065 XC0067 XC0070 XC0075 XC0088 XC0094 XC0101 XC0103 XC0107;ƒÁ-Glu-Gln XC0114;ƒÁ-Glu-His XC0117 XC0118 XC0119 XC0120 XC0126 XC0133 XC0135 XC0138 XC0139 XC0140 Zeaxanthin α-Tocopherol α-Tocopherol acetate β-Ala β-Estradiol 17α-Estradiol β-Hydroxyisovaleric acid γ-Butyrobetaine γ-Glu-Ala γ-Glu-Arg γ-Glu-Asn γ-Glu-Asp γ-Glu-Citrulline γ-Glu-Gln γ-Glu-Glu γ-Glu-Gly γ-Glu-His γ-Glu-Leu γ-Glu-Lys γ-Glu-Met γ-Glu-Ornitineγ-Glu-Phe γ-Glu-Ser γ-Glu-Taurine γ-Glu-Thr γ-Glu-Trp γ-Glu-Tyr γ-Glu-Val γ-Glu-Val-Gly γ-TocopherolAppendix 2. Known-Unknown PeaksAppendix 2. Known-Unknown Peaks

Claims

CLAIMSWe claim:

1. A method comprising: administering to a subject a composition comprising one or more microbial strains or microbial components, wherein the subject has been diagnosed with or is at high risk of a lipid disease, disorder, or condition, wherein the lipid disease, disorder, or condition includes one or more of body weight gain, lipid accumulation in liver, accumulation of visceral fat, elevated blood triglyceride levels, hypercholesterolemia, inflammation, and / or high blood- cholesterol levels (e.g. Low Density Lipoprotein (LDL) levels).

2. A method comprising: administering to a subject a composition comprising one or more microbial metabolites, wherein the subject has been diagnosed with or is at high risk of a lipid disease, disorder, or condition, wherein the lipid disease, disorder, or condition includes one or more of body weight gain, lipid accumulation in liver, accumulation of visceral fat, elevated blood triglyceride levels, hypercholesterolemia, inflammation, and / or high blood-cholesterol levels (e.g. LDL levels).

3. A method comprising: administering to a subject a composition comprising:(i) one or more microbial strains or microbial components, or(ii) one or more microbial metabolites, wherein the subject has been diagnosed with or is at high risk of a metabolic disease, disorder, or condition.

4. The method of any one of the preceding claims, wherein the subject has been diagnosed with or is at high risk of lipid-induced metabolic syndrome, cerebral infarction / stroke, myocardial infarction / heart attack, Type II diabetes / diabetes mellitus, glucose intolerance, alcoholism, metabolic syndrome, kidney disease, cardiorenal syndrome, vascular diseases (e.g., hypertension, peripheral arterial disease), Alzheimer’s disease, asthma (e.g., due to abdominal obesity or central / truncal obesity), atherosclerosis, hypothyroidism, liver disease, LDL-hypercholesterolemia, hypertriglyceridemia, mixed hyperlipoproteinemia, coronary heart disease, stroke, peripheral arterial disease, high blood pressure, hyperlipidemia, steatosis, non-alcoholic steatohepatitis (NASH), fatty-liver disease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), liver fibrosis, cirrhosis, or hepatocellular carcinoma.

5. The method of any one of the preceding claims, wherein the subject is a mammal.

6. The method of any one of the preceding claims, wherein the subject is a human.

7. The method of any one of claims 1 or 3-6, wherein the one or more microbial strains are from a mammalian microbiome.

8. The method of any one of claims 1 or 3-7, wherein the one or more microbial strains are from a human microbiome.

9. The method of claim 8, wherein the human microbiome is the microbiome of the subject.

10. The method of claim 9, wherein the human microbiome is administered to maintain or modulate the microbiome of the subject.

11. The method of any one of the preceding claims, wherein one or more microbial components or microbial metabolites are selected from Appendix 1, Appendix 3, or Appendix 4.

12. The method of any one of the preceding claims, wherein the one or more microbial metabolites is or comprises a bile acid, Cholesterol, chenodeoxycholic acid, 16α- chenodeoxycholic acid (CDCA), oxysterols, taurochenodeoxycholic acid, cholic acid, lithocholic acid, ursodeoxycholic acid, triglycerides, very-low density lipoprotein (VLDL), VLDL-TG, cholesterol, eicosanoids, arachidonic acid, docosahexaenoic acid, eicosapentaenoic acid, trimethylamines (TMA), trimethylamine-N-oxide (TMAO), endogenous ethanol, acetone, acetaldehyde, butyrate, choline, or any combination thereof.

13. The method of any one of the preceding claims, wherein the one or more microbial metabolites is or comprises Tauroursodeoxycholic acid, taurocholic acid, long-chain acyl- CoA dehydrogenase (LCAD), deoxycholic acid (DCA), lithocholic acid (LCA), taurochenodeoxycholic acid, ursodeoxycholic acid, 7α-hydroxycholesterol, chenodeoxycholic acid, 27-hydroxycholesterol, 7α-hydroxy-4-cholestene-3-one, or any combination thereof.

14. The method of any one of the preceding claims, wherein one or more microbial components or microbial metabolites is Butyrylcamitine, Theobromine, p- Hydroxyphenylpyruvic acid, Propionic acid, Picolinic acid, 2-Hydroxy-4methylvaleric acid, N6-Acetylysine, Urocanic acid, N5-Ethylglutamine, Trigonelline, Stachydrine, Ectoine, 5- Hydroxylysine, Arginine (arg), Cholic acid, 2-(4-Hydroxyphenyl)propionic acid, N- Acetyltryptophan, Hydroxyproline, Argininosuccinic acid, Glutamic acid (Glu), Sarcosine,5 Methoxyindoleacetic acid, Indole 3 lactic acid, Isovalerylalanine, N-Acetylleucine, 1- Methylhistidine, N-Acetylephenylalanine, Proline (Pro), or any combination thereof.

15. The method of any one of the preceeding claims, wherein one or more microbial components or microbial metabolites is 4-Hydroxyphenylpyruvic, Ectoine, Gramine, N- Acetyl-L-phenylalanine, Nepsilon-Acetyl-L-lysine, Stachydrine, Trigonelline, 3- Ureidopropionic acid, Theobromine, Hippuric acid, Imidazolepropionic acid, NG-Methyl-L- arginine, trans-Urocanic Acid, N-Acetyl-L-leucine, Sarcosine, Isobutyrylcarnitine, b- Hydroxyisovaleric acid, L-Theanine / N5-Ethylglutamine, 5-Hydroxylysine, Phenaceturic acid, betaine, hydroxyproline, Picolinic acid, 2-Aminoadipic acid, Glycerophosphocholine, carnitine, Glycerol 3-phosphate, Argininosuccinic acid, creatine, Terephthalic acid, Homocitrulline, Mucic acid, Homocysteinesulfinic acid, Trimethyllysine, Spermidine, Glyoxylic acid, XA0013 C6H6O4S, 3-Indoxylsulfuric acid, Nicotinamide, N- Formylglycine, Ureidoglycolate, N-Methylproline, Glucaric acid, Butyrylcarnitine, Methionine sulfoxide, Carboxymethyllysine, Glycolic acid, Phenaceturic acid, Diethanolamine, Phosphorylcholine, Guanidinosuccinic acid, N-Acetylhistidine, Glyceric acid, S-Methylmethionine, Cysteine glutathione disulfide, Kynurenine, N- Acetylphenylalanine, Threonic acid, Malic acid, 7,8-Dihydrobiopterin, Homovanillic acid, Taurocholic acid, 5-Methoxyindoleacetic acid, butyrate, b-Hydroxyisovaleric acid, 2- Oxoglutaric acid, N-Acetyltryptophan, Thiaproline, Hypotaurine, Cholic acid, Acetoacetic acid, Ethanolamine, Guanidoacetic acid, S-Sulfocysteine, Myristic acid C14:0 XA0027, or any combination thereof.

16. The method of any one of claims 1 or 3-15, wherein the one or more microbial strains are or comprise Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof.

17. The method of any one of claims 1 or 316, wherein the one or more microbial strains are or comprise Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., Bifidobacterium sp., or a combination thereof.

18. The method of any one of claims 1 or 3-17, wherein the one or more microbial strains are or comprise Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, Bifidobacterium breve, or a combination thereof.

19. The method of any one of claims 1 or 3-18, wherein the one or more microbial strains is or comprises Bacillus subtilis.

20. The method of any one of claims 1 or 3-19, wherein the composition comprises two or more microbial strains.

21. The method of any one of claims 1 or 3-20, wherein the composition comprises five or more microbial strains.

22. The method of any one of claims 1 or 3-21, wherein the composition comprises ten or more microbial strains.

23. The method of any one of the preceding claims, wherein the composition is administered topically, orally, subcutaneously, intravenously, intramuscularly, intracerebrally, intrathecally, rectally, opthalmically, intravitreally, or suprachoroidally.

24. The method of claim 20, wherein the composition is administered orally.

25. The method of claim 20, wherein the composition is administered intravenously.

26. The method of any one of the preceding claims, wherein the composition is formulated as a syrup, a liquid, a tablet, a troche, a gummy, a capsule, a powder, a gel, a film, an injection, or an eye drop.

27. The method of any one of claims 1 or 3-26, wherein each microbial strain of the one or more microbial strains is present in the composition at a concentration from 101to 1015CFU.

28. The method of any one of claims 1 or 3-27, wherein each microbial strain of the one or more microbial strains is present in the composition at a concentration of at least 106CFU.

29. A composition for use in treating a metabolic disease, disorder, or condition comprising one or more microbial strains or microbial components.

30. A composition for use in treating a metabolic disease, disorder, or condition comprising one or more microbial metabolites.

31. The composition of claim 29, wherein the one or more microbial strains are from a mammalian microbiome.

32. The composition of claim 29 or 31, wherein the one or more microbial strains are from a human microbiome.

33. The composition of claim 32, wherein the human microbiome is the microbiome of the subject.

34. The composition of claim 33, wherein the human microbiome is administered to maintain or modulate the microbiome of the subject.

35. The composition of any one of claims 29-34, wherein one or more microbial components or microbial metabolites are selected from Appendix 1, Appendix 3, or Appendix 4.

36. The composition of any one of claims 29-35, wherein the one or more microbial metabolites is or comprises a bile acid, Cholesterol, chenodeoxycholic acid, 16α- chenodeoxycholic acid (CDCA), oxysterols, taurochenodeoxycholic acid, cholic acid, lithocholic acid, ursodeoxycholic acid, triglycerides, very-low density lipoprotein (VLDL), VLDL-TG, cholesterol, eicosanoids, arachidonic acid, docosahexaenoic acid, eicosapentaenoic acid, trimethylamines (TMA), trimethylamine-N-oxide (TMAO), endogenous ethanol, acetone, acetaldehyde, butyrate, choline, or any combination thereof.

37. The composition of any one of claims 29-36, wherein the one or more microbial metabolites is or comprises Tauroursodeoxycholic acid, taurocholic acid, long-chain acyl- CoA dehydrogenase (LCAD), deoxycholic acid (DCA), lithocholic acid (LCA), taurochenodeoxycholic acid, ursodeoxycholic acid, 7α-hydroxycholesterol, chenodeoxycholic acid, 27-hydroxycholesterol, 7α-hydroxy-4-cholestene-3-one, or any combination thereof.

38. The composition of any one of claims 29-35, wherein one or more microbial components or microbial metabolites is Butyrylcamitine, Theobromine, p- Hydroxyphenylpyruvic acid, Propionic acid, Picolinic acid, 2-Hydroxy-4methylvaleric acid, N6-Acetylysine, Urocanic acid, N5-Ethylglutamine, Trigonelline, Stachydrine, Ectoine, 5- Hydroxylysine, Arginine (arg), Cholic acid, 2-(4-Hydroxyphenyl)propionic acid, N- Acetyltryptophan, Hydroxyproline, Argininosuccinic acid, Glutamic acid (Glu), Sarcosine, 5-Methoxyindoleacetic acid, Indole-3-lactic acid, Isovalerylalanine, N-Acetylleucine, 1- Methylhistidine, N-Acetylephenylalanine, Proline (Pro), or any combination thereof.

39. The composition of any one of claims 29-35, wherein one or more microbial components or microbial metabolites is 4-Hydroxyphenylpyruvic, Ectoine, Gramine, N- Acetyl-L-phenylalanine, Nepsilon-Acetyl-L-lysine, Stachydrine, Trigonelline, 3- Ureidopropionic acid, Theobromine, Hippuric acid, Imidazolepropionic acid, NG-Methyl-L- arginine, trans-Urocanic Acid, N-Acetyl-L-leucine, Sarcosine, Isobutyrylcarnitine, b- Hydroxyisovaleric acid, L-Theanine / N5-Ethylglutamine, 5-Hydroxylysine, Phenaceturic acid, betaine, hydroxyproline, Picolinic acid, 2-Aminoadipic acid, Glycerophosphocholine, carnitine, Glycerol 3-phosphate, Argininosuccinic acid, creatine, Terephthalic acid, Homocitrulline, Mucic acid, Homocysteinesulfinic acid, Trimethyllysine, Spermidine, Glyoxylic acid, XA0013 C6H6O4S, 3-Indoxylsulfuric acid, Nicotinamide, N- Formylglycine, Ureidoglycolate, N-Methylproline, Glucaric acid, Butyrylcarnitine, Methionine sulfoxide, Carboxymethyllysine, Glycolic acid, Phenaceturic acid, Diethanolamine, Phosphorylcholine, Guanidinosuccinic acid, N-Acetylhistidine, Glyceric acid, S-Methylmethionine, Cysteine glutathione disulfide, Kynurenine, N- Acetylphenylalanine, Threonic acid, Malic acid, 7,8-Dihydrobiopterin, Homovanillic acid, Taurocholic acid, 5-Methoxyindoleacetic acid, butyrate, b-Hydroxyisovaleric acid, 2- Oxoglutaric acid, N-Acetyltryptophan, Thiaproline, Hypotaurine, Cholic acid, Acetoacetic acid, Ethanolamine, Guanidoacetic acid, S-Sulfocysteine, Myristic acid C14:0 XA0027, or any combination thereof.

40. The composition of any one of claims 29 or 31-39, wherein the one or more microbial strains are or comprise Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof.

41. The composition of any one of claims 29 or 31-40, wherein the one or more microbial strains are or comprise Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., Bifidobacterium sp., or a combination thereof.

42. The composition of any one of claims 29 or 31-41, wherein the one or more microbial strains are or comprise Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, Bifidobacterium breve, or a combination thereof.

43. The composition of any one of claims 29 or 31-42, wherein the one or more microbial strains is or comprises Bacillus subtilis.

44. The composition of any one of claims 29 or 31-43, wherein the composition comprises two or more microbial strains.

45. The composition of any one of claims 29 or 31-44, wherein the composition comprises five or more microbial strains.

46. The composition of any one of claims 29 or 31-45, wherein the composition comprises ten or more microbial strains.

47. The composition of any one of claims 29-46, wherein the composition is for topical, oral, subcutaneous, intravenous, intramuscular, intracerebral, intrathecal, rectal, opthalmical, intravitreal, or suprachoroidal administration.

48. The composition of claim 47, wherein the composition is for oral administration.

49. The composition of claim 47, wherein the composition is for intravenous administration.

50. The composition of any one of claims 29-49, wherein the composition is formulated as a syrup, a liquid, a tablet, a troche, a gummy, a capsule, a powder, a gel, a film, an injection, or an eye drop.

51. The composition of any one of claims 29 or 31-50, wherein each microbial strain of the one or more microbial strains is present in the composition at a concentration from 101to 1015CFU.

52. The composition of any one of claims 29 or 31-50, wherein each microbial strain of the one or more microbial strains is present in the composition at a concentration of at least 106CFU.

53. Use of a composition of any one of claims 29-52 for modulating one or more microbial metabolites in a subject.

54. Use of a composition of any one of claims 29-52 for modulating one or more features in a subject.

55. Use of a composition of claim 54, wherein the one or more features is or comprises: (i) level of cell viability; (ii) level or activity of a nucleic acid or protein, or form thereof; (iii) body weight gain; (iv) lipid accumulation in liver; (v) accumulation of visceral fat; (vi) elevated blood triglyceride levels; (vii) blood-cholesterol levels; (viii) oxidative stress; (ix) hypercholesterolemia; or (x) inflammation.

56. Use of a composition of any one of claims 29-52 for characterizing the ability of one more microbial strains to modulate one or more microbial metabolites in a subject.

57. Use of a composition of any one of claims 29-52 for treating or ameliorating a disease, disorder, or condition in a subject, wherein the disease, disorder, or condition is a metabolic disease, disorder, or condition associated with one or more microbial metabolites.

58. The use of a composition of claim 57, wherein the disease, disorder, or condition is lipid-induced metabolic syndrome, cerebral infarction / stroke, myocardial infarction / heart attack, Type II diabetes / diabetes mellitus, glucose intolerance, alcoholism, metabolic syndrome, kidney disease, cardiorenal syndrome, vascular diseases (e.g., hypertension, peripheral arterial disease), Alzheimer’s disease, asthma (e.g., due to abdominal obesity or central / truncal obesity), atherosclerosis, hypothyroidism, liver disease, LDL- hypercholesterolemia, hypertriglyceridemia, mixed hyperlipoproteinemia, coronary heart disease, stroke, peripheral arterial disease, high blood pressure, hyperlipidemia, steatosis, non-alcoholic steatohepatitis (NASH), fatty-liver disease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), liver fibrosis, cirrhosis, or hepatocellular carcinoma.

59. The use of a composition of claim 58, wherein the disease, disorder, or condition is fatty-liver disease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), steatosis, non-alcoholic steatohepatitis (NASH), liver fibrosis, cirrhosis, or hepatocellular carcinoma.

60. A method of screening a microbial strain, comprising: contacting the microbial strain to a culture comprising liver cells or liver cell lines that model a metabolic disease, disorder, or condition, and determining whether the microbial strain altered a feature of the culture, wherein the feature is associated with the metabolic disease, disorder, or condition.

61. The method of claim 60, wherein the step of determining comprises comparing the feature before and after performance of the step of contacting.

62. The method of claim 60, wherein the step of determining comprises comparing the feature after the step of contacting with a comparable reference.

63. The method of claim 62, wherein the comparable reference is a historical reference.

64. The method of claim 63, wherein the comparable reference is a negative control reference.

65. The method of claim 63, wherein the comparable reference is a positive control reference.

66. The method of any one of claims 60-65, wherein the feature is a level of cell viability.

67. The method of any one of claims 60-65, wherein the feature is level or activity of a nucleic acid or protein, or form thereof.

68. The method of any one of claims 60-65, wherein the feature is or comprises weight gain.

69. The method of any one of claims 6065, wherein the feature is or comprises lipid accumulation in liver cells.

70. The method of any one of claims 60-65, wherein the feature is or comprises accumulation of visceral fat.

71. The method of any one of claims 60-65, wherein the feature is or comprises triglyceride levels.

72. The method of any one of claims 60-65, wherein the feature is or comprises cholesterol levels.

73. The method of any one of claims 60-65, wherein the feature is or comprises inflammation.

74. The method of any one of claims 60-65, wherein the microbial strain altered one or more features of the culture, wherein the one or more features is associated with the metabolic disease, disorder, or condition, and wherein the one or more features is or comprises (i) level of cell viability; (ii) level or activity of a nucleic acid or protein, or form thereof; (iii) body weight gain; (iv) lipid accumulation in liver; (v) accumulation of visceral fat;(vi) elevated blood triglyceride levels; (vii) blood-cholesterol levels; (viii) oxidative stress; (ix) hypercholesterolemia; or (x) inflammation.

75. A method comprising: administering to a subject a composition comprising one or more microbial strains or microbial components.

76. A method comprising: administering to a subject a composition comprising one or more microbial metabolites.

77. The method of claim 75 or 76, wherein the subject is a mammal.

78. The method of any one claims 75-77, wherein the subject is a human.

79. The method of any one claims 75 or 77-78, wherein the one or more microbial strains are from a mammalian microbiome.

80. The method of any one claims 75 or 77-79, wherein the one or more microbial strains are from a human microbiome.

81. The method of claim 80, wherein the human microbiome is the microbiome of the subject.

82. The method of claim 81, wherein the human microbiome is administered to maintain or modulate the microbiome of the subject.

83. The method of any one claims 75-82, wherein one or more microbial components or microbial metabolites are selected from Appendix 1, Appendix 3, or Appendix 4.

84. The method of any one claims 75-83, wherein the one or more microbial metabolites is or comprises a bile acid, Cholesterol, chenodeoxycholic acid, 16α-chenodeoxycholic acid (CDCA), oxysterols, taurochenodeoxycholic acid, cholic acid, lithocholic acid, ursodeoxycholic acid, triglycerides, very-low density lipoprotein (VLDL), VLDL-TG, cholesterol, eicosanoids, arachidonic acid, docosahexaenoic acid, eicosapentaenoic acid, trimethylamines (TMA), trimethylamine-N-oxide (TMAO), endogenous ethanol, acetone, acetaldehyde, butyrate, choline, or any combination thereof.

85. The method of any one claims 75-84, wherein the one or more microbial metabolites is or comprises Tauroursodeoxycholic acid, , taurocholic acid, long-chain acyl-CoA dehydrogenase (LCAD), deoxycholic acid (DCA), lithocholic acid (LCA), taurochenodeoxycholic acid, ursodeoxycholic acid, 7α-hydroxycholesterol, chenodeoxycholic acid, 27-hydroxycholesterol, 7α-hydroxy-4-cholestene-3-one, or any combination thereof.

86. The method of any one of claims 75-83, wherein one or more microbial components or microbial metabolites is Butyrylcamitine, Theobromine, p-Hydroxyphenylpyruvic acid,Propionic acid, Picolinic acid, 2 Hydroxy 4methylvaleric acid, N6-Acetylysine, Urocanic acid, N5-Ethylglutamine, Trigonelline, Stachydrine, Ectoine, 5-Hydroxylysine, Arginine (arg), Cholic acid, 2-(4-Hydroxyphenyl)propionic acid, N-Acetyltryptophan, Hydroxyproline, Argininosuccinic acid, Glutamic acid (Glu), Sarcosine, 5- Methoxyindoleacetic acid, Indole-3-lactic acid, Isovalerylalanine, N-Acetylleucine, 1- Methylhistidine, N-Acetylephenylalanine, Proline (Pro), or any combination thereof.

87. The method of any one of claims 75-83, wherein one or more microbial components or microbial metabolites is 4-Hydroxyphenylpyruvic, Ectoine, Gramine, N-Acetyl-L- phenylalanine, Nepsilon-Acetyl-L-lysine, Stachydrine, Trigonelline, 3-Ureidopropionic acid, Theobromine, Hippuric acid, Imidazolepropionic acid, NG-Methyl-L-arginine, trans- Urocanic Acid, N-Acetyl-L-leucine, Sarcosine, Isobutyrylcarnitine, b-Hydroxyisovaleric acid, L-Theanine / N5-Ethylglutamine, 5-Hydroxylysine, Phenaceturic acid, betaine, hydroxyproline, Picolinic acid, 2-Aminoadipic acid, Glycerophosphocholine, carnitine, Glycerol 3-phosphate, Argininosuccinic acid, creatine, Terephthalic acid, Homocitrulline, Mucic acid, Homocysteinesulfinic acid, Trimethyllysine, Spermidine, Glyoxylic acid, XA0013 C6H6O4S, 3-Indoxylsulfuric acid, Nicotinamide, N-Formylglycine, Ureidoglycolate, N-Methylproline, Glucaric acid, Butyrylcarnitine, Methionine sulfoxide, Carboxymethyllysine, Glycolic acid, Phenaceturic acid, Diethanolamine, Phosphorylcholine, Guanidinosuccinic acid, N-Acetylhistidine, Glyceric acid, S-Methylmethionine, Cysteine glutathione disulfide, Kynurenine, N-Acetylphenylalanine, Threonic acid, Malic acid, 7,8- Dihydrobiopterin, Homovanillic acid, Taurocholic acid, 5-Methoxyindoleacetic acid, butyrate, b-Hydroxyisovaleric acid, 2-Oxoglutaric acid, N-Acetyltryptophan, Thiaproline, Hypotaurine, Cholic acid, Acetoacetic acid, Ethanolamine, Guanidoacetic acid, S- Sulfocysteine, Myristic acid C14:0 XA0027, or any combination thereof.

88. The method of any one claims 75 or 77-87, wherein the one or more microbial strains are or comprise Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof.

89. The method of any one claims 75 or 77-88, wherein the one or more microbial strains are or comprise Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., Bifidobacterium sp., or a combination thereof.

90. The method of any one claims 75 or 77-89, wherein the one or more microbial strains are or comprise Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, Bifidobacterium breve, or a combination thereof.

91. The method of any one claims 75 or 77-90, wherein the one or more microbial strains is or comprises Bacillus subtilis.

92. The method of any one claims 75 or 77-91, wherein the composition comprises two or more microbial strains.

93. The method of any one claims 75 or 77-92, wherein the composition comprises five or more microbial strains.

94. The method of any one claims 75 or 77-93, wherein the composition comprises ten or more microbial strains.

95. The method of any one claims 75-94, wherein the composition is administered topically, orally, subcutaneously, intravenously, intramuscularly, intracerebrally, intrathecally, rectally, opthalmically, intravitreally, or suprachoroidally.

96. The method of claim 95, wherein the composition is administered orally.

97. The method of claim 95, wherein the composition is administered intravenously.

98. The method of any one claims 75-97, wherein the composition is formulated as a syrup, a liquid, a tablet, a troche, a gummy, a capsule, a powder, a gel, a film, an injection, or an eye drop.

99. The method of any one claims 75 or 77-98, wherein each microbial strain of the one or more microbial strains is present in the composition at a concentration from 101to 1015CFU.

100. The method of any one claims 75 or 77-99, wherein each microbial strain of the one or more microbial strains is present in the composition at a concentration of at least 106CFU.

101. The method of any one of claims 75 -100, the microbial strain or the microbial metabolite altered a feature of the subject.

102. The method of claim 101, wherein the feature is a level of cell viability.

103. The method of claim 101, wherein the feature is level or activity of a nucleic acid or protein, or form thereof.

104. The method of claim 101, wherein the feature is or comprises body weight gain.

105. The method of claim 101, wherein the feature is or comprises lipid accumulation in liver.

106. The method of claim 101, wherein the feature is or comprises accumulation of visceral fat.

107. The method of claim 101, wherein the feature is or comprises triglyceride levels.

108. The method of claim 101, wherein the feature is or comprises cholesterol levels.

109. The method of claim 101, wherein the feature is or comprises inflammation.

110. The method of claim 101, wherein the microbial strain altered one or more features of the subject, and wherein the one or more features is or comprises (i) level of cell viability; (ii) level or activity of a nucleic acid or protein, or form thereof; (iii) body weight gain; (iv) lipid accumulation in liver; (v) accumulation of visceral fat;(vi) elevated blood triglyceride levels; (vii) blood-cholesterol levels; (viii) oxidative stress; (ix) hypercholesterolemia; or (x) inflammation.

111. The method of any one of claims 101-110, wherein the feature is associated with the metabolic disease, disorder, or condition.

112. A method of characterizing a microbial strain, comprising: adding the microbial strain to a culture comprising liver cells or liver cell lines that model a metabolic disease, disorder, or condition, and determining whether the microbial strain affects levels of one or more features of the liver cells or liver cell lines, wherein the one or more features are associated with the metabolic disease, disorder, or condition.

113. A method of manufacturing a pharmaceutical treatment comprising characterizing one or more microbial strains, microbial components, or microbial metabolites comprising the steps of: adding the one or more microbial strains to a culture comprising liver cells or liver cell lines that model a metabolic disease, disorder, or condition, and determining whether the one or more microbial strains affect levels of one or more features of the liver cells or liver cell lines, wherein the one or more features are associated with the metabolic disease, disorder, or condition.

114. A method of manufacturing a pharmaceutical treatment comprising: adding one or more microbial strains or microbial components, to a syrup, a liquid, a tablet, a troche, a gummy, a capsule, a powder, a gel, a film, an injection, or an eye drop.

115. A method of manufacturing a pharmaceutical treatment comprising: adding one or more microbial metabolites, to a syrup, a liquid, a tablet, a troche, a gummy, a capsule, a powder, a gel, a film, an injection, or an eye drop.

116. A method of assessing a microbial strain for the ability to affect one or more features of a culture, comprising: adding the microbial strain to the culture comprising liver cells or liver cell lines that model a metabolic disease, disorder, or condition, and determining whether the microbial strain affects levels of one or more features of the liver cells or liver cell lines, wherein the one or more features are associated with the metabolic disease, disorder, or condition.

117. The method of any one of claims 112-114 or 116, further comprising: before adding the microbial strain to the culture, determining levels of one or more features of the liver cells or liver cell lines in the culture, after adding the microbial strain to the culture, determining the levels of the same one or more features of the liver cells or liver cell lines in the culture, and comparing the levels of one or more features determined before adding the microbial strain with the levels of one or more features determined after adding the microbial strain.

118. The method of any one of claims 112117, wherein the one or more features includes: (i) level of cell viability; (ii) level or activity of a nucleic acid or protein, or form thereof; (iii) body weight gain; (iv) lipid accumulation in liver; (v) accumulation of visceral fat; (vi) elevated blood triglyceride levels; (vii) blood-cholesterol levels; (viii) oxidative stress; (ix) hypercholesterolemia; (x) inflammation; or (xi) a combination thereof.

119. The method of any one of claims 60-118, wherein the disease, disorder, or condition is lipid-induced metabolic syndrome, cerebral infarction / stroke, myocardial infarction / heart attack, Type II diabetes / diabetes mellitus, glucose intolerance, alcoholism, metabolic syndrome, kidney disease, cardiorenal syndrome, vascular diseases (e.g., hypertension, peripheral arterial disease), Alzheimer’s disease, asthma (e.g., due to abdominal obesity or central / truncal obesity), atherosclerosis, hypothyroidism, liver disease, LDL- hypercholesterolemia, hypertriglyceridemia, mixed hyperlipoproteinemia, coronary heart disease, stroke, peripheral arterial disease, high blood pressure, hyperlipidemia, steatosis, non-alcoholic steatohepatitis (NASH), fatty-liver disease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), liver fibrosis, cirrhosis, or hepatocellular carcinoma.

120. A composition for use in treating or preventing a metabolic disease, disorder, or condition, comprising one or more microbial strains or microbial components.

121. A composition for use in treating or preventing a metabolic disease, disorder, or condition, comprising one or more microbial metabolites.

122. The use of claim 120, wherein the one or more microbial strains are from a mammalian microbiome.

123. The use of claim 120 or 122, wherein the one or more microbial strains are from a human microbiome.

124. The use of claim 123, wherein the human microbiome is the microbiome of the subject.

125. The use of claim 124, wherein the human microbiome is administered to maintain or modulate the microbiome of the subject.

126. The use of any one of claims 120-125, wherein one or more microbial components or microbial metabolites are selected from Appendix 1, Appendix 3, or Appendix 4.

127. The use of any one of claims 120-126, wherein the one or more microbial metabolites is or comprises a bile acid, Cholesterol, chenodeoxy cholic acid, 16a- chenodeoxycholic acid (CDCA), oxysterols, taurochenodeoxy cholic acid, cholic acid,lithocholic acid, ursodeoxycholic acid, triglycerides, very-low density lipoprotein (VLDL), VLDL-TG, cholesterol, eicosanoids, arachidonic acid, docosahexaenoic acid, eicosapentaenoic acid, trimethylamines (TMA), trimethylamine-N-oxide (TMAO), endogenous ethanol, acetone, acetaldehyde, butyrate, choline, or any combination thereof.

128. The use of any one of claims 120-127, wherein the one or more microbial metabolites is or comprises Tauroursodeoxycholic acid, , taurocholic acid, long-chain acyl- CoA dehydrogenase (LCAD), deoxycholic acid (DCA), lithocholic acid (LCA), taurochenodeoxycholic acid, ursodeoxycholic acid, 7α-hydroxycholesterol, chenodeoxycholic acid, 27-hydroxycholesterol, 7α-hydroxy-4-cholestene-3-one, or any combination thereof.

129. The use of any one of claims 120-126, wherein one or more microbial components or microbial metabolites is Butyrylcamitine, Theobromine, p-Hydroxyphenylpyruvic acid, Propionic acid, Picolinic acid, 2-Hydroxy-4methylvaleric acid, N6-Acetylysine, Urocanic acid, N5-Ethylglutamine, Trigonelline, Stachydrine, Ectoine, 5-Hydroxylysine, Arginine (arg), Cholic acid, 2-(4-Hydroxyphenyl)propionic acid, N-Acetyltryptophan, Hydroxyproline, Argininosuccinic acid, Glutamic acid (Glu), Sarcosine, 5- Methoxyindoleacetic acid, Indole-3-lactic acid, Isovalerylalanine, N-Acetylleucine, 1- Methylhistidine, N-Acetylephenylalanine, Proline (Pro), or any combination thereof.

130. The use of any one of claims 120-126, wherein one or more microbial components or microbial metabolites is 4-Hydroxyphenylpyruvic, Ectoine, Gramine, N-Acetyl-L- phenylalanine, Nepsilon-Acetyl-L-lysine, Stachydrine, Trigonelline, 3-Ureidopropionic acid, Theobromine, Hippuric acid, Imidazolepropionic acid, NG-Methyl-L-arginine, trans- Urocanic Acid, N-Acetyl-L-leucine, Sarcosine, Isobutyrylcarnitine, b-Hydroxyisovaleric acid, L-Theanine / N5-Ethylglutamine, 5-Hydroxylysine, Phenaceturic acid, betaine, hydroxyproline, Picolinic acid, 2-Aminoadipic acid, Glycerophosphocholine, carnitine, Glycerol 3-phosphate, Argininosuccinic acid, creatine, Terephthalic acid, Homocitrulline, Mucic acid, Homocysteinesulfinic acid, Trimethyllysine, Spermidine, Glyoxylic acid,XA0013 C6H6O4S, 3 Indoxylsulfuric acid, Nicotinamide, N-Formylglycine, Ureidoglycolate, N-Methylproline, Glucaric acid, Butyrylcarnitine, Methionine sulfoxide, Carboxymethyllysine, Glycolic acid, Phenaceturic acid, Diethanolamine, Phosphorylcholine, Guanidinosuccinic acid, N-Acetylhistidine, Glyceric acid, S-Methylmethionine, Cysteine glutathione disulfide, Kynurenine, N-Acetylphenylalanine, Threonic acid, Malic acid, 7,8- Dihydrobiopterin, Homovanillic acid, Taurocholic acid, 5-Methoxyindoleacetic acid, butyrate, b-Hydroxyisovaleric acid, 2-Oxoglutaric acid, N-Acetyltryptophan, Thiaproline, Hypotaurine, Cholic acid, Acetoacetic acid, Ethanolamine, Guanidoacetic acid, S- Sulfocysteine, Myristic acid C14:0 XA0027, or any combination thereof.

131. The use of any one of claims 120 or 122-130, wherein the one or more microbial strains are or comprise Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof.

132. The use of any one of claims 120 or 122-131, wherein the one or more microbial strains are or comprise Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Veillonella sp., Bifidobacterium sp., or a combination thereof.

133. The use of any one of claims 120 or 122-132, wherein the one or more microbial strains are or comprise Gluconacetobacter hanseni, Terrisporobacter glycolicus, Coprococcus catus, Lactobacillus plantarum, Veillonella atypica, Bifidobacterium breve, or a combination thereof.

134. The use of any one of claims 120 or 122-133, wherein the one or more microbial strains is or comprises Bacillus subtilis.

135. The use of any one of claims 120 or 122-134, wherein the composition comprises two or more microbial strains.

136. The use of any one of claims 120 or 122-135, wherein the composition comprises five or more microbial strains.

137. The use of any one of claims 120 or 122-136, wherein the composition comprises ten or more microbial strains.

138. The use of any one of claims 120-137, wherein the composition is for topical, oral, subcutaneous, intravenous, intramuscular, intracerebral, intrathecal, rectal, opthalmical, intravitreal, or suprachoroidal administration.

139. The use of claim 138, wherein the composition is for oral administration.

140. The use of claim 138, wherein the composition is for intravenous administration.

141. The use of any one of claims 120-140, wherein the composition is formulated as a syrup, a liquid, a tablet, a troche, a gummy, a capsule, a powder, a gel, a film, an injection, or an eye drop.

142. The use of any one of claims 120 or 122-141, wherein each microbial strain of the one or more microbial strains is present in the composition at a concentration from 101to 1015CFU.

143. The use of any one of claims 120 or 122-141, wherein each microbial strain of the one or more microbial strains is present in the composition at a concentration of at least 106CFU.

144. The use of any one of claims 120-143, wherein the metabolic disease, disorder, or condition is lipid-induced metabolic syndrome, cerebral infarction / stroke, myocardial infarction / heart attack, Type II diabetes / diabetes mellitus, glucose intolerance, alcoholism, metabolic syndrome, kidney disease, cardiorenal syndrome, vascular diseases (e.g., hypertension, peripheral arterial disease), Alzheimer’s disease, asthma (e.g., due to abdominal obesity or central / truncal obesity), atherosclerosis, hypothyroidism, liver disease, LDL-hypercholesterolemia, hypertriglyceridemia, mixed hyperlipoproteinemia, coronary heart disease, stroke, peripheral arterial disease, high blood pressure, hyperlipidemia, steatosis, non-alcoholic steatohepatitis (NASH), fatty-liver disease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), liver fibrosis, cirrhosis, or hepatocellular carcinoma.

145. The use of claim 144, wherein the metabolic disease, disorder, or condition is fatty- liver disease, metabolic associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD), steatosis, non-alcoholic steatohepatitis (NASH), liver fibrosis, cirrhosis, or hepatocellular carcinoma.

146. An injection comprising the composition of any one of claims 29-52.

147. A food supplement comprising the composition of any one of claims 29-52.

148. A kit comprising the composition of claim any one of claims 29-52 or 120 for use in treating or preventing a metabolic disease, disorder, or condition.

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