Use of gram positive anaerobic bacteria for lipid and insulin regulation

Abstract

Provided herein are compositions comprising one or more substantially pure strains of bacteria as well as methods of making and using the same to treat and / or prevent one or more lipid and / or insulin related disorders and to regulate or alter the metabolism of lipids and / or insulin in a subject in need thereof.

Description

METHODS AND COMPOSITIONS FOR LIPID AND INSULIN REGULATION CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Provisional Patent Application No.63 / 662,076 filed June 20,2024, the disclosure of which is incorporated by reference herein in its entirety. INCORPORATION BY REFERENCE OF SEQUENCE LISTING

[0002] The Sequence Listing submitted in an XML file, in accordance with 37 C.F.R. §§2412 is incorporated herein by reference. The xml file name is “NB42183_WO_PCT_Seq_List.xml”, the date of creation of the xml file is May 07, 2025, and the size of the xml file in bytes is 9,854,076. FIELD OF THE INVENTION

[0003] Provided herein are bacterial compositions useful for treating and / or preventing one or more lipid and / or insulin related disorders and for regulating or altering the metabolism of lipids and / or insulin in a subject in need thereof, as well as methods for making and using the same. BACKGROUND

[0004] Over the recent course of history, the availability and storage of dietary energy in humans has shifted from caloric scarcity and high caloric demands to one with abundant caloric supply and low caloric demands. This shift has had a profound effect on various pathways, including the development of disordered lipid and insulin metabolism, and the rise in lipid and insulin disorders in humans. Lipids and fatty acids are important components of the human body, and therefore play a role in multiple functions of both health and disease, including energy storage, hormone regulation, nerve impulse transmission, fat-soluble nutrient absorption, and insulin resistance. Conversely, insulin resistance is a complex disorder associated with multiple etiological pathways and can lead to cellular changes that converge to promote accumulation of lipids in the liver and skeletal muscle, which can lead to impaired insulin signaling and resistance.

[0005] Although the mechanistic links between disorders of fatty acid / lipid metabolism and insulin resistance has been explored, the etiology of lipid and insulin disorders is still poorlyunderstood, and therefore continues to have significant impacts to human health and healthcare systems.

[0006] What is needed, therefore, are additional compositions and methods to address lipid and insulin disorders for the development of new treatment and therapy options. The subject matter disclosed herein addresses these needs and provides additional benefits as well. SUMMARY

[0007] Provided herein are methods of treating and / or preventing a lipid disorder in a subject in need thereof, which include administering an effective amount of a composition containing a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria to the subject in need thereof. In some embodiments, the Gram-positive anaerobic bacteria include bacteria from the order Eubacteriales. In some embodiments, the bacteria include one or more substantially purified Butyricicoccus or Roseburia.

[0008] In some embodiments, the bacteria include one or more substantially purified Butyricicoccus faecihominis strains. In some embodiments, the Butyricicoccus faecihominis strain includes a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3. In some embodiments, the Butyricicoccus faecihominis strain is the strain deposited under DSM 34943, or strain which includes all the defining characteristics of the strain deposited under DSM 34943.

[0009] In some of any embodiments, the bacteria include one or more substantially purified Roseburia faecis strains. In some embodiments, the Roseburia faecis strain includes a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:1. In some embodiments, the Roseburia faecis strain is the strain deposited under DSM 35024, or strain which includes all the defining characteristics of the strain deposited under DSM 35024.

[0010] In some embodiments, the treating and / or preventing further includes treating and / or preventing an insulin disorder. In some embodiments, the composition does not include any additional butyrate producing bacteria. In some embodiments, the composition is a probiotic, aprebiotic, postbiotic, human milk oligosaccharides, xylitol, betaine, and / or a botanical. In some embodiments, the composition has been pasteurized or heat treated. In some embodiments, the composition is lyophilized or freeze dried or spray dried. In some embodiments, the composition is encapsulated or coated. In some embodiments, the composition is a pharmaceutical composition and further includes at least one pharmaceutically acceptable carrier and / or excipient. In some embodiments, the composition is formulated as a tablet, lozenge, prolonged- release capsule, prolonged-release granule, powder, sachet, nasal spray, ointment, serum, lotion or gummy.

[0011] In some embodiments, the composition is formulated as a food product, nutritional product, food ingredient, dietary supplement, or medicament. In some embodiments, the composition comprises at least about 1 x 104CFU / g to at least about 1 x 1014CFU / g of a biologically pure strain of bacteria. In some embodiments, the treating and / or preventing includes administering the composition for at least one month.

[0012] Also provided herein is a method of treating and / or preventing an insulin disorder in a subject in need thereof, which includes administering an effective amount of a composition which includes a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria to the subject in need thereof. In some embodiments, the Gram-positive anaerobic bacteria include bacteria from the order Eubacteriales. In some embodiments, the bacteria include one or more substantially purified Butyricicoccus or Roseburia.

[0013] Also provided herein is a method of treating and / or preventing a lipid disorder and an insulin disorder in a subject in need thereof, which includes administering an effective amount of a composition containing a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria to the subject in need thereof.

[0014] Provided herein is a method of altering lipid metabolism in a subject, which includes administering an effective amount of a composition having a plurality of substantially pure non- pathogenic Gram-positive anaerobic bacteria. In some embodiments, the Gram-positive anaerobic bacteria include bacteria from the order Eubacteriales. In some embodiments, the bacteria include one or more substantially purified Butyricicoccus or Roseburia.

[0015] In some embodiments, the bacteria include one or more substantially purified Butyricicoccus faecihominis strains. In some embodiments, the Butyricicoccus faecihominis strain includes a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3. In some embodiments, the Butyricicoccus faecihominis strain is the strain deposited under DSM 34943, or strain which includes all the defining characteristics of the strain deposited under DSM 34943.

[0016] In some of any embodiments, the bacteria include one or more substantially purified Roseburia faecis strains. In some embodiments, the Roseburia faecis strain includes a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:1. In some embodiments, the Roseburia faecis strain is the strain deposited under DSM 35024, or strain which includes all the defining characteristics of the strain deposited under DSM 35024.

[0017] In some embodiments, the treating and / or preventing further includes altering insulin metabolism. In some embodiments, the composition does not include any additional butyrate producing bacteria. In some embodiments, the composition is a probiotic, a prebiotic, postbiotic, human milk oligosaccharides, xylitol, betaine, and / or a botanical. In some embodiments, the composition has been pasteurized or heat treated. In some embodiments, the composition is lyophilized or freeze dried or spray dried. In some embodiments, the composition is encapsulated or coated. In some embodiments, the composition is a pharmaceutical composition and further includes at least one pharmaceutically acceptable carrier and / or excipient. In some embodiments, the composition is formulated as a tablet, lozenge, prolonged-release capsule, prolonged-release granule, powder, sachet, nasal spray, ointment, serum, lotion or gummy.

[0018] In some embodiments, the composition is formulated as a food product, nutritional product, food ingredient, dietary supplement, or medicament. In some embodiments, the composition comprises at least about 1 x 104CFU / g to at least about 1 x 1014CFU / g of a biologically pure strain of bacteria. In some embodiments, the treating and / or preventing includes administering the composition for at least one month.

[0019] In some embodiments, the lipid metabolism includes modulating a hormone associated with lipid metabolism. In some embodiments, the hormone is primarily produced by adipocytes. In some embodiments, the hormone is leptin. In some embodiments, the hormone is resistin. In some embodiments, the method further includes modulating one or more of ALT levels, cholesterol production and % body fat.

[0020] Each of the aspects and embodiments described herein are capable of being used together, unless excluded either explicitly or clearly from the context of the embodiment or aspect.

[0021] Throughout this specification, various patents, patent applications and other types of publications (e.g., journal articles, electronic database entries, etc.) are referenced. The disclosure of all patents, patent applications, and other publications cited herein are hereby incorporated by reference in their entirety for all purposes. BRIEF DESCRIPTION OF THE DRAWINGS

[0022] FIG.1 depicts the effect of R. faecis DSM 35024, B. faecihominis DSM 34943 and A. hadrus FLM9MS-51 on resistin levels in a diet induced obesity model. Statistical significance between the different stimulus is presented as ns = not significant, * = p<0.05, ** = p<0.01, *** = p<0.001, and **** = p<0.0001.

[0023] FIG.2 depicts the effect of R. faecis DSM 35024, B. faecihominis DSM 34943 and A. hadrus FLM9MS-51 on leptin levels in a diet induced obesity model. Statistical significance between the different stimulus is presented as ns = not significant, * = p<0.05, ** = p<0.01, *** = p<0.001, and **** = p<0.0001.

[0024] FIG.3 depicts the effect of R. faecis DSM 35024, B. faecihominis DSM 34943 and A. hadrus FLM9MS-51 during an Insulin Tolerance Test (ITT) in a diet induced obesity model. Statistical significance between the different stimulus is presented as ns = not significant, * = p<0.05, ** = p<0.01, *** = p<0.001, and **** = p<0.0001.

[0025] FIG.4 depicts the effect of R. faecis DSM 35024, B. faecihominis DSM 34943 and A. hadrus FLM9MS-51 on Cholesterol levels in a diet induced obesity model. Statisticalsignificance between the different stimulus is presented as ns = not significant, * = p<0.05, ** = p<0.01, *** = p<0.001, and **** = p<0.0001.

[0026] FIG.5 depicts the effect of R. faecis DSM 35024, B. faecihominis DSM 34943 and A. hadrus FLM9MS-51 on alanine transaminase (ALT) levels in a diet induced obesity model. Statistical significance between the different stimulus is presented as ns = not significant, * = p<0.05, ** = p<0.01, *** = p<0.001, and **** = p<0.0001.

[0027] FIG.6 depicts the effect of R. faecis DSM 35024, B. faecihominis DSM 34943 and A. hadrus FLM9MS-51 on non-esterified fatty acids (NEFA) levels in a diet induced obesity model. Statistical significance between the different stimulus is presented as ns = not significant, * = p<0.05, ** = p<0.01, *** = p<0.001, and **** = p<0.0001.

[0028] FIG.7 depicts the effect of R. faecis DSM 35024, B. faecihominis DSM 34943 and A. hadrus FLM9MS-51 on total body fat measured by qNMR in a diet induced obesity model. Statistical significance between the different stimulus is presented as ns = not significant, * = p<0.05, ** = p<0.01, *** = p<0.001, and **** = p<0.0001.

[0029] FIG.8 depicts production of butyrate by R. faecis DSM 35024, B. faecihominis DSM 34943 and A. hadrus FLM9MS-5.

[0030] FIG.9 depicts engraftment of B. faecihominis DSM 34943 in the mice GI tract following oral gavage. Relative abundance of B. faecihominis DSM 34943 in mouse fecal samples at different time points (Days 0, 8, 44 and 84). DETAILED DESCRIPTION

[0031] Lipids have well-defined roles in signaling and gene transcription, as metabolic fuels and as structural components of cells (Metcalfe et al 2019. Journal of Molecular Endocrinology. Vol 62:1). The diversity in chemical structure among lipids results in a vast spectrum of physiochemical properties (Shevchenko & Simons 2010, Li et al.2015, Lydic & Goo 2018), which in turn are associated with a range of lipid disorders with alterations in primary lipoproteins, cholesterol, triglycerides, and the development of secondary lipid metabolism abnormalities (Natesan et. al.2021 Biomol Ther Nov 1;29(6):596-604). While unlimited accessto calorie-dense foods and reductions in physical activity create an environment conducive to excessive lipid accumulation, there are various factors at the cellular level that heighten lipid accumulation in non-adipose tissues and alter adipose tissue function / metabolism. In addition, insulin-resistant individuals have been found to possess a greater proportion of small adipose cells than insulin-sensitive individuals, while their large adipose cells are fewer but larger (Weyer et al.2000, McLaughlin et al.2007, Johannsen et al.2014, McLaughlin et al. 2014, Kim et al.2015). Moreover, adipogenesis is impaired with insulin resistance (Deurenberg et al.1991, Yang et al.2004, McLaughlin et al.2007, 2014) and promotion of adipocyte differentiation has been suggested to have an effect on insulin sensitivity (De Souza et al.2001, McLaughlin et al.2010, Eliasson et al.2014).

[0032] The inventors of the instant application have surprisingly found that several microorganisms derived from fecal microbiota of healthy human donors, including Butyricicoccus faecihominis and Roseburia faecis, can successfully treat lipid and insulin disorders, as well as modulate lipid and insulin metabolism, with additional positive effects on liver health. I. Definitions

[0033] As used herein, "microorganism" or “microbe” refers to a bacterium, a fungus, a virus, a protozoan, and other microbes or microscopic organisms.

[0034] As used here in the term “probiotic” refers to a composition for consumption by animals (i.e. as an or as a component of animal feed) that contains viable (i.e. live) microorganisms, i.e. microorganisms that are capable of living and reproducing that, when administered in adequate amounts, confer a health benefit on a subject (see Hill et al.2014 Nature Revs Gastro & Hep 11, 506-514, incorporated by reference herein in its entirety). A probiotic may include one or more (such as any of 1, 2, 3, or 4) of any of the microbial strains described herein. Probiotics are distinguished from bacterial compositions that have been killed, for example, by pasteurization or heat treatment. Administration of non-viable bacterial compositions for the treatment of one or more immune system related disorders is also contemplated in certain embodiments of the methods disclosed herein.

[0035] A bacterial “strain” as used herein refers to a bacterium which remains genetically unchanged when grown or multiplied. The multiplicity of identical bacteria is included.

[0036] By “at least one strain,” is meant a single strain but also mixtures of strains comprising at least two strains of microorganisms. By “a mixture of at least two strains,” is meant a mixture of two, three, four, five, six or even more strains. In some embodiments of a mixture of strains, the proportions can vary from 1% to 99%. When a mixture comprises more than two strains, the strains can be present in substantially equal proportions in the mixture or in different proportions.

[0037] For purposes of this disclosure, “substantially pure” bacteria or “substantially pure” strain means containing no other bacterial strains in quantities sufficient to interfere with replication of the strain or to be detectable by normal bacteriological techniques. “Isolated” when used in connection with the organisms and cultures described herein includes not only a substantially pure strain, but also any culture of organisms which is grown or maintained other than as it is found in nature. In some embodiments, the strains are mutants, variants, or derivatives of strains of Butyricicoccus species, including Butyricicoccus faecihominis. In some embodiments, the strains are strains having all of the identifying characteristics of strains of a Butyricicoccus species. In some embodiments, the strains are mutants, variants, or derivatives of strains of Roseburia species, including Roseburia faecis. In some embodiments, the strains are strains having all of the identifying characteristics of strains of a Roseburia species. In some embodiments, the strain is a Butyricicoccus faecihominis strain comprising the strain deposited at the German Collection of Microorganisms and Cell Cultures (DSM) under number DSM 34943, or strain comprising all the defining characteristics of the strain deposited at the German Collection of Microorganisms and Cell Cultures (DSM) under number DSM 34943. In some embodiments, the strain is a Roseburia faecis strain comprising the strain deposited at the German Collection of Microorganisms and Cell Cultures (DSM) under number DSM 35024 or strain comprising all the defining characteristics of the strain deposited at the German Collection of Microorganisms and Cell Cultures (DSM) under number DSM 35024. Further, each individual strain or any combination of these strains can also provide one or more of the benefits described herein. In some embodiments, the strains are mutants, variants, or derivatives of strains Butyricicoccus faecihominis and / or a Roseburia faecis displaying at least 70%, 71%, 72%, 73%, 74%, 75%, 76&, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence similarity to a 16S ribosomal RNA sequence of SEQ ID NO: 2, 3 or 1. It will also be clear that addition of other microbial strains, carriers, additives, enzymes, yeast, or the like will also provide one or more benefits or improvement of one or more lipid and insulin disorders as well as modulate lipid and insulin metabolism, with additional positive effects on liver health in a subject and will not constitute a substantially different bacterial strain.

[0038] The term “16S rRNA” or “16S ribosomal RNA” means the rRNA constituting the small subunit of prokaryotic ribosomes. In bacteria, this 16S rRNA gene can be used to identify and characterize operational taxonomic units.

[0039] The term “sequence identity” or “sequence similarity” as used herein, means that two polynucleotide sequences, a candidate sequence and a reference sequence, are identical (i.e. 100% sequence identity) or similar (i.e. on a nucleotide-by-nucleotide basis) over the length of the candidate sequence. In comparing a candidate sequence to a reference sequence, the candidate sequence may comprise additions or deletions (i.e. gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Optimal alignment of sequences for determining sequence identity may be conducted using the any number of publicly available local alignment algorithms known in the art such as ALIGN or Megalign (DNASTAR), or by inspection.

[0040] The term “percent (%) sequence identity” or “percent (%) sequence similarity,” as used herein with respect to a reference sequence is defined as the percentage of nucleotide residues in a candidate sequence that are identical to the residues in the reference polynucleotide sequence after optimal alignment of the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity.

[0041] As used herein, the term “subject” or “patient” is meant a mammal (e.g., a human). In some embodiments, a subject is suffering from a relevant disease, disorder or condition such as, without limitation, one or more lipid and / or insulin related disorders. In some embodiments, a subject is susceptible to a disease, disorder, or condition. In some embodiments, a subject displays one or more symptoms or characteristics of a disease, disorder or condition. In someembodiments, a subject does not display any symptom or characteristic of a disease, disorder, or condition. In some embodiments, a subject is an individual who is at risk of developing disease, disorder, or condition. In some embodiments, a subject is someone with one or more features characteristic of susceptibility to or risk of a disease, disorder, or condition. In some embodiments, a subject is a patient. In some embodiments, a subject is an individual to whom diagnosis and / or therapy is and / or has been administered.

[0042] As used herein, “prevent,” “preventing,” “prevention” and grammatical variations thereof refers to a method of partially or completely delaying, reducing the risk of, or precluding the onset or recurrence of a disorder or condition and / or one or more of its attendant symptoms or barring a subject from acquiring or reacquiring a disorder or condition or reducing a subject’s risk of acquiring or reacquiring a disorder or condition or one or more of its attendant symptoms.

[0043] As used herein, the term “reducing” in relation to a particular trait, characteristic, feature, biological process, or phenomena refers to a decrease in the particular trait, characteristic, feature, biological process, or phenomena. The trait, characteristic, feature, biological process, or phenomena can be decreased by 0.5%, 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100% or greater than 100%.

[0044] As used herein “administer” or “administering” is meant the action of introducing one or more compositions comprising one or more microbial strain, to a subject, such as by feeding or consuming orally, applying topically, administering nasally or a combination thereof. The composition containing one or more microbial strains can also be administered in one or more doses.

[0045] As used herein, “effective amount” means a quantity of a composition containing one or more microbial strains to improve one or more metrics in subject. Improvement in one or more metrics of a subject can be measured as described herein or by other methods known.

[0046] As used herein, “lipid disorders” means a condition, disease or disorder characterized by alterations in lipids. As used herein, lipid disorders include, but are not limited to, primary and secondary lipid disorders. In some embodiments, the lipid disorder is a primary lipid disorder. Insome embodiments, the primary lipid disorder is an inherited lipid disorder. In some embodiments, the lipid disorder of a secondary lipid disorder. In some embodiments, the lipid disorder is dyslipidemia, Tay-Sachs disease and Gaucher disease. In some embodiments, the lipid disorders are associated with skeletal muscle alterations, hepatic alterations, atherosclerosis, pregnancy, nephrotic syndrome, and cardiovascular disease. In some embodiments, the dyslipidemia is characterized by alterations in triglycerides, cholesterol, high density lipoproteins (HLD) and low-density lipoproteins (LDL). In some embodiments, the lipid disorder is not a metabolic disorder. In some embodiments, the lipid disorder is not associated with an insulin disorder. In some embodiments, the lipid disorder is associated with an insulin disorder. In some embodiments, the lipid disorder is not associated with obesity. In some embodiments, the lipid disorder is not genetic. In some embodiments, the lipid disorder is genetic. In some embodiments, the lipid disorder may be additionally treated with any pharmacologic treatment. In some embodiments, the subject is treated with a pharmacological treatment. In some embodiments, the subject is not treated with a pharmacological treatment. In some embodiments, the pharmacological treatment is a lipid lowering therapy, a statin, cholesterol absorption inhibitor or RNA therapy.

[0047] As used herein, “lipid metabolism” refers to the synthesis and degradation of lipids in cells. In some embodiments lipid metabolism includes but is not limited to the breakdown and storage of fats and fatty acids for energy and synthesis of structural and functional lipids. In some embodiments, lipid metabolism includes modulating a hormone associated with lipid metabolism. In some embodiments, the hormone is primarily produced by adipocytes. In some embodiments, the hormone is leptin. In some embodiments, the hormone is resistin. In some embodiments, lipid metabolism further includes modulating one or more of ALT levels, cholesterol production and % body fat.

[0048] As used herein, “insulin disorder” means a condition, disease or disorder characterized by alterations in insulin. As used herein, insulin disorders include, but are not limited to, prediabetes, Metabolic dysfunction-associated fatty liver disease (MAFLD), insulin resistance, and Diabetes Mellitus. In some embodiments, the insulin disorders are associated with skeletal muscle alterations, hepatic alterations, atherosclerosis, and cardiovascular disease. In some embodiments, the insulin disorder is not a metabolic disorder. In some embodiments, the insulindisorder is not associated with a lipid disorder. In some embodiments, the insulin disorder is associated with a lipid disorder. In some embodiments, the insulin disorder is not associated with obesity. In some embodiments, the insulin disorder is not genetic. In some embodiments, the insulin disorder is genetic.

[0049] As used herein, “insulin metabolism” refers to the production and degradation of insulin. In some embodiments, insulin metabolism includes processes involved in the regulation of the metabolism of carbohydrates, fats and proteins by promotion of the absorption of glucose from the blood to the liver, fat and skeletal muscle cells. In some embodiments, the alteration in insulin metabolism improves insulin sensitivity. In some embodiments, improving insulin sensitivity includes decreasing the release of NEFA. In some embodiments, decreasing the release of NEFA increases liver function.

[0050] Certain ranges are presented herein with numerical values being preceded by the term "about." The term "about" is used herein to provide literal support for the exact number that it precedes, as well as a number that is near to or approximately the number that the term precedes. In determining whether a number is near to or approximately a specifically recited number, the near or approximating unrecited number can be a number which, in the context in which it is presented, provides the substantial equivalent of the specifically recited number. For example, in connection with a numerical value, the term “about” refers to a range of -10% to +10% of the numerical value, unless the term is otherwise specifically defined in context.

[0051] As used herein, the singular terms “a,” “an,” and “the” include the plural reference unless the context clearly indicates otherwise.

[0052] It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements or use of a “negative” limitation.

[0053] It is also noted that the term “consisting essentially of,” as used herein refers to a composition wherein the component(s) after the term is in the presence of other knowncomponent(s) in a total amount that is less than 30% by weight of the total composition and do not contribute to or interferes with the actions or activities of the component(s).

[0054] It is further noted that the term "comprising,” as used herein, means including, but not limited to, the component(s) after the term “comprising.” The component(s) after the term “comprising” are required or mandatory, but the composition comprising the component(s) can further include other non-mandatory or optional component(s).

[0055] It is also noted that the term “consisting of,” as used herein, means including, and limited to, the component(s) after the term "consisting of.” The component(s) after the term “consisting of” are therefore required or mandatory, and no other component(s) are present in the composition.

[0056] The term “genome” as used herein, can refer to the entirety of an organism's hereditary information that is encoded in its primary DNA sequence. The genome includes both the genes and the non-coding sequences. For example, the genome, in some aspects, represents a microbial genome. The genetic content of the microbiome can comprise: genomic DNA, RNA, and ribosomal RNA, the epigenome, plasmids, and all other types of genetic information found in the microbes that comprise the microbiome.

[0057] “Nucleic acid sequence” and “nucleotide sequence” as used herein refer to an oligonucleotide or polynucleotide, and fragments or portions thereof, and to DNA or RNA of genomic or synthetic origin which may be single- or double-stranded, and represent the sense or antisense strand. The nucleic acid sequence can be made up of adenine, guanine, cytosine, thymine, and uracil (A, T, C, G, and U) as well as modified versions (e.g. N6-methyladenosine, 5-methylcytosine, etc.). The term “sequencing” as used herein refers to sequencing methods for determining the order of the nucleotide bases—A, T, C, G, and U—in a nucleic acid molecule (e.g., a DNA or RNA nucleic acid molecule).

[0058] It is intended that every maximum numerical limitation given throughout this specification includes every lower numerical limitation, as if such lower numerical limitations were expressly written herein. Every minimum numerical limitation given throughout thisspecification will include every higher numerical limitation, as if such higher numerical limitations were expressly written herein. Every numerical range given throughout this specification will include every narrower numerical range that falls within such broader numerical range, as if such narrower numerical ranges were all expressly written herein.

[0059] Unless defined otherwise herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Other definitions of terms may appear throughout the specification. II. Compositions A. Strains

[0060] Provided herein are Gram-positive anaerobic bacterium which can be used in any of the methods described throughout. In some embodiments, the bacteria belong to the Phylum Bacillota. In some embodiments, the bacteria belong to the Class Clostridia. In some embodiments, the bacteria belong to the Order Eubacteriales. In some embodiments, the bacteria belong to the Family Oscillospiraceae. In some embodiments, the bacteria belong to the Genus Butyricicoccus. In some embodiments, the bacteria belong to the Genus Roseburia. In some embodiments, the bacteria are non-spore forming. In some embodiments, the bacteria can ferment glucose. In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria do not produce butyrate.

[0061] Butyricococcus is a genus of Gram-positive anaerobic bacterium that has been isolated from the gut of various organisms, including humans, and have been associated with the production of butyrate, H2 and CO2 and utilization of acetate in M2GSC broth. (Takada et al. Intl. Journal of Systematic and Evolutionary Microbiology Vol 66:10). The Roseburia genus has, to date, five species, including Roseburia intestinalis, Roseburia hominis, Roseburia inulinivorans, Roseburia faecis, and Roseburia cecicola, all of which produce short-chain fatty acids (SCFAs), such as acetate, propionate, and butyrate (Tamanai-Shacoori et al., 2017).

[0062] The strains provided herein include one or more substantially pure strains of a Butyriciccocus species. In some embodiments, the Butyriciccocus species is Butyricococcus faecihominis. In some embodiments, the Butyricicoccus faecihominis strain comprises a bacterialstrain having a 16S ribosomal RNA sequence displaying at least about 90% , 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3. In some embodiments, the Butyricicoccus faecihominis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3. In some embodiments, the Butyricicoccus faecihominis strain comprises a bacterial strain having the 16S ribosomal RNA of SEQ ID NO:2 or SEQ ID NO:3.

[0063] In some embodiments, the Butyricicoccus faecihominis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% , 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence similarity to the 16S ribosomal RNA sequence of the strain deposited under DSM 34943, or strain comprising all the defining characteristics of the strain deposited under DSM 34943. In some embodiments, the Butyricicoccus faecihominis strain comprises the strain deposited under DSM 34943, or strain comprising all the defining characteristics of the strain deposited under DSM 34943.

[0064] The Butyricicoccus faecihominis strain DSM 34943 was deposited on February 14, 2024 at the German Collection of Microorganisms and Cell Cultures GmbH (DSM), Inhoffenstraße 7B, 38124 Braunschweig, GERMANY and given accession number DSM 34943. The deposits were made under the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure.

[0065] The strains provided herein may also include one or more substantially pure strains of a Roseburia species. In some embodiments, the Roseburia species is Roseburia faecis. In some embodiments, the Roseburia faecis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% , 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:1. In some embodiments, the Roseburia faecis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:1. In some embodiments, the Roseburia faecis strain comprises a bacterial strain having the 16S ribosomal RNA of SEQ ID NO:1.

[0066] In some embodiments, the 16S-rRNA encoding gene sequences of each of these bacteria (SEQ ID NOs: 1-3) are provided in Table 1. Table 1 – 16S-rRNA encoding gene sequences of bacteria of the disclosure

[0067] In some aspects, bacteria of the disclosure comprise a 16S-rRNA encoding gene sequence that is at least about 60%, at least about 61%, at least about 62%, at least about 63%, at least about 64%, at least about 65%, at least about 66%, at least about 67%, at least about 68%, at least about 69%, at least about 70%, at least about 71%, at least about 72%, at least about 73%, at least about 74%, at least about 75%, at least about 76%, at least about 77%, at least about 78%, at least about 79%, at least about 80%, at least about 81%, at least about 82%, atleast about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% homologous or identical (100% homologous) to any one of the nucleotide sequences of SEQ ID NOs: 1-4. In some aspects, bacteria of the disclosure comprise a DNA sequence that is at least about 60%, at least about 61%, at least about 62%, at least about 63%, at least about 64%, at least about 65%, at least about 66%, at least about 67%, at least about 68%, at least about 69%, at least about 70%, at least about 71%, at least about 72%, at least about 73%, at least about 74%, at least about 75%, at least about 76%, at least about 77%, at least about 78%, at least about 79%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% homologous or identical (100% homologous) to any one of the nucleotide sequences of SEQ ID NOs: 5-7. In some aspects, the whole genome sequence of bacteria of the disclosure is found in any one of the nucleotide sequences of SEQ ID NOs: 5-7. Table 2 – Whole genomic DNA sequences of probiotic bacteria of the disclosure**These sequences are provided in the sequence listing which is part of the disclosure.

[0068] In some embodiments, the Roseburia faecis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence similarity to the 16S ribosomal RNA sequence of the strain deposited under DSM 35024, or strain comprising all the defining characteristics of the strain deposited under DSM 35024. In some embodiments, the Roseburia faecis strain comprises thestrain deposited under DSM 35024, or strain comprising all the defining characteristics of the strain deposited under DSM 35024.

[0069] The Roseburia faecis strain DSM 35024 was deposited on May 7, 2024 at the German Collection of Microorganisms and Cell Cultures GmbH (DSM), Inhoffenstraße 7B, 38124 Braunschweig, GERMANY and given accession number DSM 35024. The deposits were made under the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure.

[0070] The compositions can include those that contain one or more substantially pure strains (such as any of about 1, 2, 3, 4, 5, 6, 7, or 8 or more strains) of a Butyricicoccus species and a Roseburia species. The compositions can include those that contain one or more substantially pure strains (such as any of about 1, 2, 3, 4, 5, 6, 7, or 8 or more strains) of a Butyricicoccus species or a Roseburia species. The compositions can include those that contain one or more substantially pure strains (such as any of about 1, 2, 3, 4, 5, 6, 7, or 8 or more strains) of Butyriciccocus faecihominis. The compositions can include those that contain one or more substantially pure strains (such as any of about 1, 2, 3, 4, 5, 6, 7, or 8 or more strains) of Butyriciccocus faecihimonis strain DSM 34943. The compositions can include those that contain one or more substantially pure strains (such as any of about 1, 2, 3, 4, 5, 6, 7, or 8 or more strains) of Roseburia faecis. The compositions can include those that contain one or more substantially pure strains (such as any of about 1, 2, 3, 4, 5, 6, 7, or 8 or more strains) of Roseburia faecis strain DSM 35024.

[0071] The compositions disclosed herein can be used as supplements, food additives, and therapeutics for administration to subjects with and / or at risk of developing lipid related disorders, or as a part of a daily nutritional regimen to prevent disease. Probiotics is another term that can be used for these compositions which contain viable microorganisms. The term "viable microorganism" refers to a microorganism which is metabolically active or able to differentiate. In some embodiments, the compositions disclosed herein include both viable probiotic products and / or, in particular embodiments, compositions that include non-viable bacteria (such as heat- treated or pasteurized compositions). B. Formulations

[0072] Generally, the compositions disclosed herein comprise bacteria, such as one or more bacterial strains. In some embodiments, the composition is formulated in freeze-dried or lyophilized form. For example, the compositions can comprise granules or gelatin capsules, for example hard gelatin capsules, comprising a bacterial strain disclosed herein.

[0073] In some embodiments, the compositions disclosed herein comprise lyophilized bacteria. Lyophilization of bacteria is a well-established procedure in the art. Alternatively, the compositions can comprise a live, active bacterial culture. In some embodiments, the compositions are freeze dried or spray dried.

[0074] In some embodiments, any of the compositions disclosed herein is encapsulated to enable delivery of the bacterial strain to the intestine. Encapsulation protects the composition from degradation until delivery at the target location through, for example, rapturing with chemical or physical stimuli such as pressure, enzymatic activity, or physical disintegration, which may be triggered by changes in pH. Any appropriate encapsulation method may be used. Exemplary encapsulation techniques include entrapment within a porous matrix, attachment or adsorption on solid carrier surfaces, self-aggregation by flocculation or with cross-linking agents, and mechanical containment behind a microporous membrane or a microcapsule.

[0075] The compositions disclosed herein can be administered orally and may be in the form of a tablet, capsule, lozenge, prolonged-release capsule, prolonged-release granule, powder, sachet, or gummy. Other ingredients (such as vitamin C or minerals, for example), may be included as oxygen scavengers and prebiotic substrates to improve the delivery and / or partial or total colonization and survival in vivo. Alternatively, the compositions disclosed herein can be administered orally as a food or nutritional product, such as milk or whey based fermented dairy product, food ingredient, dietary supplement, or as a pharmaceutical product or medicament.

[0076] The compositions disclosed herein can be administered nasally or through the respiratory system and may be in the form of a nasal spray.

[0077] The compositions disclosed herein can be administered topically and may be in the form of an ointment, serum or lotion.

[0078] The compositions disclosed herein can be formulated as a probiotic. Alternatively, the compositions disclosed herein can be formulated as a non-viable bacterial compositions, suchas a pasteurized or heat-treated bacterial composition. In some embodiments, the compositions disclosed herein can be formulated as a prebiotic and / or a postbiotic. In some embodiments, the composition can include human-milk oligosaccharides, βine, xylitol, and / or botanicals. In some embodiments, the composition can include vitamins, minerals and trace elements.

[0079] Any of the compositions disclosed herein may include a therapeutically effective amount of a bacterial strain disclosed herein. A therapeutically effective amount of a bacterial strain is sufficient to exert a beneficial effect upon a patient. A therapeutically effective amount of a bacterial strain may be sufficient to result in delivery to and / or partial or total colonization of the subject’s intestine.

[0080] A suitable daily dose of the bacteria, for example for an adult human, may be from about 1 x 104to about 1 X 1014colony forming units (CFU); for example, from about 1 x 107to about 1 x 1010CFU; in another example from about 1 x 104to about 1 x 1014CFU; in another example from about 1 x 107to about 1 x 1011CFU; in another example from about 1 x 108to about 1 x 1010CFU; in another example from about 1 x 106to about 1 x 1010GPU; in another example from about 1 x 107to about 1 x 1011CFU; in another example from about 1 x 108to about 1 x 1010CFU; in another example from about 1 x 108to about 1 x 1011CFU. In certain embodiments, the dose of the bacteria is at least 109cells per day, such as at least 1010, at least 1011or at least 1012cells per day.

[0081] In certain embodiments, the composition contains the bacterial strain in an amount of from about 1 x 106to about 1 x 1011CFU / g, respect to the weight of the composition; for example, from about 1 x 108to about 1 x 1010CFU / g. The dose may be, for example, 1 g, 3g, 5g, and 10 g.

[0082] In certain embodiments, the amount of the bacterial strain is from about 1 x 103to about 1 x 1011colony forming units per gram with respect to a weight of the composition.

[0083] In certain embodiments, the amount of the bacterial strain is from about 1 x 104to about 1 x 1014colony forming units per gram with respect to a weight of the composition.

[0084] In some embodiments, any of the compositions provided herein contains one or more substantially pure strains of Butyrocicoccus. In some embodiments, any of the one or more substantially pure strains of Butyrocicoccus is substantially pure, and includes at least about10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of a Butyrocicoccus strain. In some embodiments, any of the one or more substantially pure strains of Butyrocicoccus is Butyrocicoccus faecihominis. In some embodiments, any of the one or more substantially pure strains of Butyrocicoccus faecihominis is substantially pure, and includes at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of an Butyrocicoccus faecihominis strain.

[0085] In some embodiments, any of the compositions provided herein contains one or more substantially pure strains of Roseburia. In some embodiments, any of the one or more substantially pure strains of Roseburia is substantially pure, and includes at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of a Roseburia strain. In some embodiments, any of the one or more substantially pure strains of Roseburia is Roseburia faecis. In some embodiments, any of the one or more substantially pure strains of Roseburia faecis is substantially pure, and includes at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of an Roseburia faecis strain.

[0086] In certain embodiments, any of the compositions disclosed herein is administered at a dose of between 500mg and l000mg, between 600mg and 900mg, between 700mg and 800mg, between 500mg and 750mg or between 750mg and l000mg. In certain embodiments, the lyophilized bacteria in any of the compositions disclosed herein is administered at a dose of between 500mg and l00mg, between 600mg and 900mg, between 700mg and 800mg, between 500mg and 750mg or between 750mg and l000mg.

[0087] Typically, a probiotic is optionally combined with at least one suitable prebiotic compound. A prebiotic compound is usually a non-digestible carbohydrate such as an oligo- or polysaccharide, or a sugar alcohol, which is not degraded or absorbed in the upper digestive tract Known prebiotics include commercial products such as inulin and transgalacto- oligosaccharides.

[0088] In certain embodiments, any of the compositions disclosed herein is formulated to include a prebiotic compound in an amount of from about 1 to about 30% by weight respect to the total weight composition, (e.g. from 5 to 20% by weight). Carbohydrates may be selected from the group consisting of: fructo- oligosaccharides (or FOS), short-chain fructo- oligosaccharides, inulin, isomalto- oligosaccharides, pectins, xylo-oligosaccharides (or XOS), chitosan-oligosaccharides (or COS), human milk oligosaccharides (or HMO), beta- glucans, gumarabic modified and resistant starches, polydextrose, D-tagatose, acacia fibers, carob, oats, and citrus fibers. In one aspect, the prebiotics are the short-chain fructo-oligosaccharides (for simplicity shown herein below as FOSs-c.c); said FOSs-c.c. are not digestible carbohydrates, generally obtained by the conversion of the beet sugar and including a saccharose molecule to which three glucose molecules are bonded. In some embodiments, any of the probiotics disclosed herein can be formulated with additional probiotics derived from, but not limited to, the genera Lactobacillus and Bifidobacterium (such as B. lactis B420).

[0089] In certain embodiments, the compositions disclosed herein contain a single bacterial strain or species and do not contain any other bacterial strains or species. Such compositions may comprise only de minimis or biologically irrelevant amounts of other bacterial strains or species. Such compositions may be a culture that is substantially free from other species of organism. In certain embodiments, the compositions of the invention consist of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 bacterial strains or species. In certain embodiments, the compositions consist of from 1 to 10, such as from 1 to 5 bacterial strains or species.

[0090] The composition for use in accordance with the methods disclosed herein may or may not require marketing approval. Pharmaceutical Formulations

[0091] Any of the compositions disclosed herein can further comprise pharmaceutically acceptable excipients, diluents or carriers. Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art. Examples of suitable carriers include, without limitation, lactose, starch, glucose, methyl cellulose, magnesium stearate, mannitol, sorbitol and the like. Examples of suitable diluents include, without limitation, ethanol, glycerol and water. The choice of pharmaceutical carrier, excipient or diluent can be selected with regard to the intended route of administration and standard pharmaceutical practice. The pharmaceutical compositions may comprise as, or in addition to, the carrier, excipient or diluent any suitable binders, lubricants, suspending agents, coating agents (such as a gastric-resistant enteric coating agent that does not dissolve or degrade until reaching the small or large intestine), or solubilizing agents. Examples of suitable binders include, without limitation, starch, gelatin, natural sugars such as glucose, anhydrous lactose, maltodextrin, free-flow lactose, beta-lactose, corn sweeteners, natural and synthetic gums, such as acacia, tragacanth or sodium alginate, carboxymethyl cellulose andpolyethylene glycol. Examples of suitable lubricants include, without limitation, sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride and the like. Preservatives, stabilizers, dyes and even flavoring agents may be provided in the pharmaceutical composition. Examples of preservatives include, without limitation, sodium benzoate, sorbic acid and esters of p-hydroxybenzoic acid. Antioxidants and suspending agents may be also used.

[0092] In some cases, the lyophilized bacterial strain is reconstituted prior to administration. In some cases, the reconstitution is by use of a diluent described herein.

[0093] A pharmaceutically acceptable composition or support may be for example a formulation or support in the form of creams, foams, gels, lotions, and ointments of compressed tablets, tablets, capsules, ointments, suppositories or drinkable solutions.

[0094] In certain embodiments, provided herein is a pharmaceutical composition comprising: a bacterial strain disclosed herein; and a pharmaceutically acceptable excipient, carrier or diluent; wherein the bacterial strain is in an amount sufficient to treat a disorder when administered to a subject in need thereof; and wherein the disorder is selected from the group consisting of lipid disorders and insulin disorders. In some embodiments, the disorder is selected from the group consisting of disorders associated with lipid metabolism and insulin metabolism.

[0095] In certain embodiments, any of the pharmaceutical compositions may contain a carrier selected from the group consisting of lactose, starch, glucose, methyl cellulose, magnesium stearate, mannitol and sorbitol. In certain embodiments, any of the pharmaceutical compositions may contain a diluent selected from the group consisting of ethanol, glycerol and water.

[0096] In certain embodiments, any of the pharmaceutical compositions may contain an excipient selected from the group consisting of starch, gelatin, glucose, anhydrous lactose, free- flow lactose, beta-lactose, corn sweetener, acacia, tragacanth, sodium alginate, carboxymethyl cellulose, polyethylene glycol, sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate and sodium chloride.

[0097] In certain embodiments, any of the pharmaceutical compositions may contain at least one of a preservative, an antioxidant and a stabilizer. In certain embodiments, the preservativeselected from the group consisting of sodium benzoate, sorbic acid and esters of p- hydroxybenzoic acid.

[0098] In certain embodiments, the above pharmaceutical composition, wherein when the composition is stored in a sealed container at about 4°C or about 25°C and the container is placed in an atmosphere having 50% relative humidity, at least 80%, 70%, 60%, 50%, 40%, 30%, 20%, or 10% of the bacterial strain as measured in colony forming units, remains after a period of at least about 1 month, 3 months, 6 months, 1 year, 1.5 years, 2 years, 2.5 years or 3 years.

[0099] The bacterial strains disclosed herein can be cultured using standard microbiology techniques such as those described in the Examples section or that are well known in the art. Food Product

[0100] The composition disclosed herein can be formulated as a food product. For example, a food product may provide nutritional benefit in addition to the therapeutic effect of the invention, such as in a nutritional supplement. Similarly, a food product may be formulated to enhance the taste of the composition of the invention or to make the composition more attractive to consume by being more similar to a common food item, rather than to a pharmaceutical composition. In certain embodiments, the composition is formulated as a milk-based product. The term "milk-based product," as used herein, means any liquid or semi-solid milk- or whey- based product having a varying fat content. The milk- based product can be, e.g., cow's milk, goat's milk, sheep's milk, skimmed milk, whole milk, milk recombined from powdered milk and whey without any processing, or a processed product, such as yoghurt, curdled milk, curd, sour milk, sour whole milk, butter milk and other sour milk products. Another important group includes milk beverages, such as whey beverages, fermented milks, condensed milks, infant or baby milks; flavored milks, ice cream; milk-containing food such as sweets. As used herein, the term "food" is used in a broad sense and covers food for humans as well as food for animals (i.e. a feed). In a preferred aspect, the food is for human consumption.

[0101] The food may be in the form of a solution or as a solid, depending on the use and / or the mode of application and / or the mode of administration. When used as, or in the preparation of, a food, such as functional food, any of the compositions provided herein may be used inconjunction with one or more of: a nutritionally acceptable carrier, a nutritionally acceptable diluent, a nutritionally acceptable excipient, a nutritionally acceptable adjuvant, a nutritionally active ingredient.

[0102] By way of example, any of the compositions provided herein can be used as an ingredient to soft drinks, a fruit juice or a beverage comprising whey protein, health teas, cocoa drinks, milk drinks and lactic acid bacteria drinks, yoghurt and drinking yoghurt, cheese, ice cream, water ices and desserts, confectionery, biscuits cakes and cake mixes, snack foods, balanced foods and drinks, fruit fillings, care glaze, chocolate bakery filling, cheese cake flavored filling, fruit flavored cake filling, cake and doughnut icing, instant bakery filling creams, fillings for cookies, ready-to-use bakery filling, reduced calorie filling, adult nutritional beverage, vegetable milk, acidified soy / juice beverage, aseptic / retorted chocolate drink, bar mixes, beverage powders, calcium fortified soy / plain and chocolate milk, calcium fortified coffee beverage.

[0103] Advantageously, where the product is a food product, the bacterial strains should remain effective through the normal "sell-by" or "expiration" date during which the food product is offered for sale by the retailer. Preferably, the effective time should extend past such dates until the end of the normal freshness period when food spoilage becomes apparent. The desired lengths of time and normal shelf life will vary from foodstuff to foodstuff and those of ordinary skill in the art will recognize that shelf-life times will vary upon the type of foodstuff, the size of the foodstuff, storage temperatures, processing conditions, packaging material and packaging equipment age. Food Ingredients

[0104] Compositions of the present invention may take the form of a food ingredient and / or feed ingredient. As used herein the term "food ingredient" or "feed ingredient" includes a composition which is or can be added to functional foods or foodstuffs as a nutritional and / or health supplement for humans and animals. The food ingredient may be in the form of a liquid, suspension or solid, depending on the use and / or the mode of application and / or the mode of administration.Dietary Supplements

[0105] Any of the compositions provided herein may take the form of dietary supplements or may themselves be used in combination with dietary supplements, also referred to herein as food supplements. The term “dietary supplement” as used herein refers to a product intended for ingestion that contains a "dietary ingredient" intended to add nutritional value or health benefits to (supplement) the diet. A "dietary ingredient" may include (but is not limited to) one, or any combination, of the following substances: bacteria, a probiotic (e.g . probiotic bacteria), a vitamin, a mineral, an herb or other botanical, an amino acid, a dietary substance for use by people to supplement the diet by increasing the total dietary intake, a concentrate, metabolite, constituent, or extract.

[0106] Dietary supplements may be found in many forms such as tablets, capsules, soft gels, gel caps, liquids, or powders. Some dietary supplements can help ensure an adequate dietary intake of essential nutrients; others may help prevent or treat diseases. Medical Food

[0107] Compositions of the present invention may take the form of medical foods. By “medical food” it is meant a food which is formulated to be consumed or administered with or without the supervision of a physician and which is intended for a specific dietary management or condition for which distinctive nutritional requirements, based on recognized scientific principles, are established by medical evaluation. III. Methods A. Methods for Treating or Preventing Disease

[0108] Further provided herein are methods for treating and / or preventing lipid disorders in a subject in need thereof, by administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria to the subject in need thereof. Further provided herein are methods for treating and / or preventing insulin disorders in a subject in need thereof, by administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria to the subject in need thereof. Further provided herein are methods for treating and / or preventing lipid disorders and insulin disorders in a subject in need thereof, by administering an effectiveamount of a composition comprising a plurality of substantially pure non-pathogenic Gram- positive anaerobic bacteria to the subject in need thereof.

[0109] Also provided herein are methods of altering lipid metabolism in a subject comprising administering an effective amount of a composition comprising a plurality of any of the substantially pure non-pathogenic Gram-positive anaerobic bacteria of the disclosure. Also provided herein are methods of altering insulin metabolism in a subject comprising administering an effective amount of a composition comprising a plurality of any of the substantially pure non- pathogenic Gram-positive anaerobic bacteria of the disclosure. Also provided herein are methods of altering lipid metabolism and insulin metabolism in a subject comprising administering an effective amount of a composition comprising a plurality of any of the substantially pure non- pathogenic Gram-positive anaerobic bacteria of the disclosure.

[0110] Commensal microbes impact the activation threshold for pathogenic stimulations, in part by producing molecules that mediate host-microbial interactions (Donia et al. Science. 2015;349:1254766). Various clinical, epidemiological and immunological studies have shown that it is possible that changes in the intestinal microbiota may be an essential factor in the incidence of numerous lipid and / or insulin disorders. However, the role of short chain fatty acids (SCFAs) including butyrate is unclear. In some embodiments, the methods provided herein are independent of the amount of butyrate produced by the bacteria. In some embodiments, the methods of treating and / or preventing the lipid or insulin disorder are independent and / or are not associated with the level of butyrate being produced by the bacteria. In some embodiments, the bacteria do not produce increased levels of butyrate.

[0111] In some embodiments, the lipid disorder is a disease or disorder characterized by alterations in lipids. In some embodiments, lipid disorders include, but are not limited to, dyslipidemia, Tay-Sachs disease and Gaucher disease. In some embodiments, the lipid disorders are associated with skeletal muscle alterations, hepatic alterations, atherosclerosis, and cardiovascular disease. In some embodiments, the dyslipidemia is characterized by alterations in triglycerides, cholesterol, high density lipoproteins (HLD) and low-density lipoproteins (LDL). In some embodiments, the lipid disorder is not a metabolic disorder. In some embodiments, the lipid disorder is not associated with an insulin disorder. In some embodiments, the lipid disorder is associated with an insulin disorder. In some embodiments, the lipid disorder is not associatedwith obesity. In some embodiments, the lipid disorder is not genetic. In some embodiments, the lipid disorder is genetic.

[0112] In some embodiments, lipid metabolism is the synthesis and degradation of lipids in cells. In some embodiments lipid metabolism includes but is not limited to the breakdown and storage of fats and fatty acids for energy and synthesis of structural and functional lipids. In some embodiments, lipid metabolism includes modulating a hormone associated with lipid metabolism. In some embodiments, the hormone is primarily produced by adipocytes. In some embodiments, the hormone is leptin. In some embodiments, the hormone is resistin. In some embodiments, lipid metabolism further includes modulating one or more of ALT levels, cholesterol production and % body fat.

[0113] In some embodiments, the insulin disorder is a condition, disease or disorder characterized by alterations in insulin. As used herein, insulin disorders include, but are not limited to, insulin resistance and Diabetes Mellitus. In some embodiments, the insulin disorders are associated with skeletal muscle alterations, hepatic alterations, atherosclerosis, and cardiovascular disease. In some embodiments, the insulin disorder is not a metabolic disorder. In some embodiments, the insulin disorder is not associated with a lipid disorder. In some embodiments, the insulin disorder is associated with a lipid disorder. In some embodiments, the insulin disorder is not associated with obesity. In some embodiments, the insulin disorder is not genetic. In some embodiments, the insulin disorder is genetic.

[0114] In some embodiments, insulin metabolism is the production and degradation of insulin. In some embodiments, insulin metabolism includes processes involved in the regulation of the metabolism of carbohydrates, fats and proteins by promotion of the absorption of glucose from the blood to the liver, fat and skeletal muscle cells. In some embodiments, the alteration in insulin metabolism improves insulin sensitivity. In some embodiments, improving insulin sensitivity includes decreasing the release of NEFA. In some embodiments, decreasing the release of NEFA increases liver function.

[0115] In some embodiments, any of the compositions provided herein can be administered for at least 1 day. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 2 days. In some embodiments, any of the compositionsprovided herein can be administered for between 1 day and 3 days. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 4 days. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 5 days. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 6 days. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 7 days. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 8 days. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 9 days. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 10 days. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 11 days. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 12 days. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 13 days. In some embodiments, any of the compositions provided herein can be administered for between 1 day and 14 days. In some embodiments, any of the compositions provided herein can be administered for more than 1 day.

[0116] In some embodiments, any of the compositions provided herein can be administered for at least 1 week. In some embodiments, any of the compositions provided herein can be administered for between 1 week and 2 weeks. In some embodiments, any of the compositions provided herein can be administered for between 1 week and 3 weeks. In some embodiments, any of the compositions provided herein can be administered for between 1 week and 4 weeks. In some embodiments, any of the compositions provided herein can be administered for between 1 week and 5 weeks. In some embodiments, any of the compositions provided herein can be administered for between 1 week and 6 weeks. In some embodiments, any of the compositions provided herein can be administered for between 1 week and 7 weeks. In some embodiments, any of the compositions provided herein can be administered for between 1 week and 8 weeks. In some embodiments, any of the compositions provided herein can be administered for more than 8 weeks.

[0117] In some embodiments, any of the compositions provided herein can be administered for at least one month. In some embodiments, any of the compositions provided herein can be administered for between 1 month and 2 months. In some embodiments, any of the compositionsprovided herein can be administered for between 1 month and 3 months. In some embodiments, any of the compositions provided herein can be administered for between 1 month and 4 months. In some embodiments, any of the compositions provided herein can be administered for between 1 month and 5 months. In some embodiments, any of the compositions provided herein can be administered for between 1 month and 6 months. In some embodiments, any of the compositions provided herein can be administered for between 1 month and 7 months. In some embodiments, any of the compositions provided herein can be administered for between 1 month and 8 months. In some embodiments, any of the compositions provided herein can be administered for between 1 month and 9 months. In some embodiments, any of the compositions provided herein can be administered for between 1 month and 10 months. In some embodiments, any of the compositions provided herein can be administered for between 1 month and 11 months. In some embodiments, any of the compositions provided herein can be administered for between 1 month and 12 months. In some embodiments, any of the compositions provided herein can be administered for more than 12 months.

[0118] In some embodiments, the one or more (such as 1, 2, 3, 4, 5, 6, 7 or 8) Butyricococcus strains are administered to subject at a rate of at least about 1×104CFU / subject / day to at least about 1 x 1014CFU / subject / day, such as any of about 1×104CFU / subject / day, 1×105CFU / subject / day, 1×106CFU / subject / day, 1×107CFU / subject / day, 1×108CFU / subject / day, 1×109CFU / subject / day, 1×1010CFU / subject / day, 1×1011CFU / subject / day, 1×1012CFU / subject / day, 1×1013CFU / subject / day, or 1×1014CFU / subject / day, inclusive of all values falling in between these measures. In some embodiments, the one or more (such as 1, 2, 3, 4, 5, 6, 7 or 8) Roseburia strains are administered to subject at a rate of at least about 1×104CFU / subject / day to at least about 1 x 1014CFU / subject / day, such as any of about 1×104CFU / subject / day, 1×105CFU / subject / day, 1×106CFU / subject / day, 1×107CFU / subject / day, 1×108CFU / subject / day, 1×109CFU / subject / day, 1×1010CFU / subject / day, 1×1011CFU / subject / day, 1×1012CFU / subject / day, 1×1013CFU / subject / day, or 1×1014CFU / subject / day, inclusive of all values falling in between these measures. B. Methods for Increasing Relative Abundance

[0119] Also provided herein is method of increasing the relative abundance of Butyricicoccus faecihominis in the gastrointestinal tract of subject in need thereof, comprising administering aneffective amount of a composition comprising a plurality of substantially pure non-pathogenic Butyricicoccus faecihominis bacteria to the subject in need thereof.

[0120] In some embodiments the increase in the relative abundance constitutes engraftment in the gastrointestinal tract of the subject in need thereof.

[0121] Also provided herein is method of engrafting Butyricicoccus faecihominis in the gastrointestinal tract of subject in need thereof, comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Butyricicoccus faecihominis bacteria to the subject in need thereof.

[0122] In some embodiments, the Butyricicoccus faecihominis strain that increases the relative abundance and / or engrafts in the gastrointestinal tract of the subject is a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3.

[0123] In some embodiments, the Butyricicoccus faecihominis strain that increases the relative abundance and / or engrafts in the gastrointestinal tract of the subject is the strain deposited under DSM 34943, or strain comprising all the defining characteristics of the strain deposited under DSM 34943. C. Methods for Preparing a Microbial Composition

[0124] Also provided herein are methods for preparing a composition comprising one substantially pure strain of Butyricococcus. Also provided herein are methods for preparing a composition comprising one substantially pure strain of Butyricococcus faecihominis. Also provided herein are methods for preparing a composition comprising one substantially pure strain of Roseburia. Also provided herein are methods for preparing a composition comprising one substantially pure strains of Roseburia faecis.

[0125] Also provided herein are methods for preparing a composition comprising combining one or more substantially pure strains of Butyricicococcus. Also provided herein are methods for preparing a composition comprising combining one or more substantially pure strains of Butyricococcus faecihominis. Also provided herein are methods for preparing a composition comprising combining one or more substantially pure strains of Roseburia. Also provided herein are methods for preparing a composition comprising combining one or more substantially pure strains of Roseburia faecis.

[0126] Also provided herein are methods for preparing a composition comprising combining one or more substantially pure strains of Butyricoccocus and Roseburia. Also provided herein are methods for preparing a composition comprising combining one or more substantially pure strains of Butyricoccocus faecihominis and Roseburia faecis.

[0127] Additionally, the methods for preparing the composition can further include lyophilizing or freeze drying the microbial composition. The method can additionally include a further step of packaging the feed additive composition for storage or transport. IV. Kits

[0128] Further provided herein are kits containing one or more of microbial strains derived from one or more of the microbial strains disclosed herein. The kits can include one or more of (such as any of 1, 2, 3, or 4,) strains derived from one or more of the microbial strains provided herein including a Butyricoccocus faecihominis strain deposited under DSM 34943, and / or a Roseburia faecis strain deposited under DSM 35024, along with instructions for proper storage, maintenance, and use for administering to a subject for the treatment or prevention of one or more lipid and / or disorders, and / or altering lipid and / or insulin metabolism. In one embodiment, the kit can include Butyricoccocus faecihominis strain DSM 34943. In one embodiment, the kit can include Roseburia faecis strain DSM 35024.

[0129] The invention can be further understood by reference to the following examples, which are provided by way of illustration and are not meant to be limiting. EXEMPLARY EMBODIMENTS 1. A method of treating and / or preventing a lipid disorder in a subject in need thereof, comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria to the subject in need thereof. 2. The method of embodiment 1, wherein the Gram-positive anaerobic bacteria comprise bacteria from the order Eubacteriales. 3. The method of embodiment 1 or embodiment 2, wherein the bacteria comprise one or more substantially purified Butyricicoccus or Roseburia.4. The method of any one of embodiments 1-3, wherein the bacteria comprise one or more substantially purified Butyricicoccus faecihominis strains. 5. The method of embodiment 4, wherein the Butyricicoccus faecihominis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3. 6. The method of embodiment 4 or embodiment 5, wherein the Butyricicoccus faecihominis strain comprises the strain deposited under DSM 34943, or strain comprising all the defining characteristics of the strain deposited under DSM 34943. 7. The method of any one of embodiments 1-6, wherein the bacteria comprise one or more substantially purified Roseburia faecis strains. 8. The method of embodiment 7, wherein the Roseburia faecis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:1. 9. The method of embodiment 7 or embodiment 8, wherein the Roseburia faecis strain comprises the strain deposited under DSM 35024, or strain comprising all the defining characteristics of the strain deposited under DSM 35024. 10. The method of any one of embodiments 1-9, wherein the treating and / or preventing further comprises treating and / or preventing an insulin disorder. 11. The method of any one of embodiments 3-11, wherein the composition does not include any additional butyrate producing bacteria. 12. The method of any one of embodiments 1-11, wherein the composition comprises a probiotic, a prebiotic, postbiotic, human milk oligosaccharides, xylitol, betaine, and / or a botanical. 13. The method of any one of embodiments 1-11, wherein the composition has been pasteurized or heat treated. 14. The method of any one of embodiments 1-12, wherein the composition is lyophilized or freeze dried or spray dried. 15. The method of any one of embodiments 1-14, wherein the composition is encapsulated or coated.16. The method of any one of embodiments 1-15, wherein the composition is a pharmaceutical composition and further comprises at least one pharmaceutically acceptable carrier and / or excipient. 17. The method of any one of embodiments 1-16, wherein the composition is formulated as a tablet, lozenge, prolonged-release capsule, prolonged-release granule, powder, sachet, nasal spray, ointment, serum, lotion or gummy. 18. The method of any one of embodiments 1-17, wherein the composition is formulated as a food product, nutritional product, food ingredient, dietary supplement, or medicament. 19. The method of any one of embodiments 1-18, wherein the composition comprises at least about 1 x 104CFU / g to at least about 1 x 1014CFU / g of a biologically pure strain of bacteria. 20. The method of any one of embodiments 1-19, wherein the treating and / or preventing comprises administering the composition for at least one month. 21. A method of treating and / or preventing an insulin disorder in a subject in need thereof, comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria to the subject in need thereof. 22. The method of embodiment 21, wherein the Gram-positive anaerobic bacteria comprise bacteria from the order Eubacteriales. 23. The method of embodiment 21 or embodiment 22, wherein the bacteria comprise one or more substantially purified Butyricicoccus or Roseburia. 24. The method of any one of embodiments 21-23, wherein the bacteria comprise one or more substantially purified Butyricicoccus faecihominis strains. 25. The method of embodiment 24, wherein the Butyricicoccus faecihominis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3. 26. The method of embodiment 24 or embodiment 25, wherein the Butyricicoccus faecihominis strain comprises the strain deposited under DSM 34943, or strain comprising all the defining characteristics of the strain deposited under DSM 34943. 27. The method of any one of embodiments 21-26, wherein the bacteria comprise one or more substantially purified Roseburia faecis strains.28. The method of embodiment 27, wherein the Roseburia faecis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:1. 29. The method of embodiment 30, wherein the Roseburia faecis strain comprises the strain deposited under DSM 35024, or strain comprising all the defining characteristics of the strain deposited under DSM 35024. 30. The method of any one of embodiments 21-29, wherein the treating and / or preventing further comprises treating and / or preventing a lipid disorder. 31. The method of any one of embodiments 23-30, wherein the composition does not include any additional butyrate producing bacteria. 32. The method of any one of embodiments 21-31, wherein the composition comprises a probiotic, a prebiotic, postbiotic, human milk oligosaccharides, xylitol, betaine, and / or a botanical. 33. The method of any one of embodiments 21-31, wherein the composition has been pasteurized or heat treated. 34. The method of any one of embodiments 21-33, wherein the composition is lyophilized or freeze dried or spray dried. 35. The method of any one of embodiments 21-34, wherein the composition is encapsulated or coated. 36. The method of any one of embodiments 21-35, wherein the composition is a pharmaceutical composition and further comprises at least one pharmaceutically acceptable carrier and / or excipient. 37. The method of any one of embodiments 21-36, wherein the composition is formulated as a tablet, lozenge, prolonged-release capsule, prolonged-release granule, powder, sachet, nasal spray, ointment, serum, lotion or gummy. 38. The method of any one of embodiments 21-37, wherein the composition is formulated as a food product, nutritional product, food ingredient, dietary supplement, or medicament. 39. The method of any one of embodiments 21-38, wherein the composition comprises at least about 1 x 104CFU / g to at least about 1 x 1014CFU / g of a biologically pure strain of bacteria.40. The method of any one of embodiments 21-39, wherein the treating and / or preventing comprises administering the composition for at least one month. 41. A method of treating and / or preventing a lipid disorder and an insulin disorder in a subject in need thereof, comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria to the subject in need thereof. 42. The method of embodiment 41, wherein the Gram-positive anaerobic bacteria comprise bacteria from the order Eubacteriales. 43. The method of embodiment 41 or embodiment 42, wherein the bacteria comprise one or more substantially purified Butyricicoccus or Roseburia. 44. The method of any one of embodiments 41-43, wherein the bacteria comprise one or more substantially purified Butyricicoccus faecihominis strains. 45. The method of embodiment 44, wherein the Butyricicoccus faecihominis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3. 46. The method of embodiment 44 or embodiment 45, wherein the Butyricicoccus faecihominis strain comprises the strain deposited under DSM 34943, or strain comprising all the defining characteristics of the strain deposited under DSM 34943. 47. The method of any one of embodiments 41-46, wherein the bacteria comprise one or more substantially purified Roseburia faecis strains. 48. The method of embodiment 47, wherein the Roseburia faecis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:1. 49. The method of embodiment 47 or embodiment 48, wherein the Roseburia faecis strain comprises the strain deposited under DSM 35024, or strain comprising all the defining characteristics of the strain deposited under DSM 35024. 50. The method of any one of embodiments 44-49, wherein the composition does not include any additional butyrate producing bacteria. 51. The method of any one of embodiments 41-50, wherein the composition comprises a probiotic, a prebiotic, postbiotic, human milk oligosaccharides, xylitol, betaine, and / or a botanical.52. The method of any one of embodiments 41-50, wherein the composition has been pasteurized or heat treated. 53. The method of any one of embodiments 41-52, wherein the composition is lyophilized or freeze dried or spray dried. 54. The method of any one of embodiments 41-53, wherein the composition is encapsulated or coated. 55. The method of any one of embodiments 41-54, wherein the composition is a pharmaceutical composition and further comprises at least one pharmaceutically acceptable carrier and / or excipient. 56. The method of any one of embodiments 41-55, wherein the composition is formulated as a tablet, lozenge, prolonged-release capsule, prolonged-release granule, powder, sachet, nasal spray, ointment, serum, lotion or gummy. 57. The method of any one of embodiments 41-56, wherein the composition is formulated as a food product, nutritional product, food ingredient, dietary supplement, or medicament. 58. The method of any one of embodiments 41-57, wherein the composition comprises at least about 1 x 104CFU / g to at least about 1 x 1014CFU / g of a biologically pure strain of bacteria. 59. The method of any one of embodiments 41-58, wherein the treating and / or preventing comprises administering the composition for at least one month. 60. A method of altering lipid metabolism in a subject, comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram- positive anaerobic bacteria. 61. The method of embodiment 60, wherein altering the lipid metabolism comprises modulating a hormone associated with lipid metabolism. 62. The method of embodiment 61, wherein the hormone is primarily produced by adipocytes. 63. The method of embodiment 61 or embodiment 62, wherein the hormone comprises leptin. 64. The method of any one of embodiments 60-63, further comprising modulating one or more of ALT levels, cholesterol production and % body fat. 65. The method of any one of embodiments 60-64, wherein the Gram-positive anaerobic bacteria comprise bacteria from the order Eubacteriales.66. The method of any one of embodiments 60-65, wherein the bacteria comprise one or more substantially purified Butyricicoccus or Roseburia. 67. The method of any one of embodiments 60-66, wherein the bacteria comprise one or more substantially purified Butyricicoccus faecihominis strains. 68. The method of embodiment 67, wherein the Butyricicoccus faecihominis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3. 69. The method of embodiment 67 or embodiment 68, wherein the Butyricicoccus faecihominis strain comprises the strain deposited under DSM 34943, or strain comprising all the defining characteristics of the strain deposited under DSM 34943. 70. The method of any one of embodiments 60-69, wherein the bacteria comprise one or more substantially purified Roseburia faecis strains. 71. The method of embodiment 70, wherein the Roseburia faecis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:1. 72. The method of embodiment 70 or embodiment 71, wherein the Roseburia faecis strain comprises the strain deposited under DSM 35024, or strain comprising all the defining characteristics of the strain deposited under DSM 35024. 73. The method of any one of embodiments 60-72, wherein the altering further comprises altering insulin metabolism. 74. The method of any one of embodiments 66-73, wherein the composition does not include any additional butyrate producing bacteria. 75. The method of any one of embodiments 60-74, wherein the composition comprises a probiotic, a prebiotic, postbiotic, human milk oligosaccharides, xylitol, betaine, and / or a botanical. 76. The method of any one of embodiments 60-74, wherein the composition has been pasteurized or heat treated. 77. The method of any one of embodiments 60-76, wherein the composition is lyophilized or freeze dried or spray dried. 78. The method of any one of embodiments 60-77, wherein the composition is encapsulated or coated.79. The method of any one of embodiments 60-78, wherein the composition is a pharmaceutical composition and further comprises at least one pharmaceutically acceptable carrier and / or excipient. 80. The method of any one of embodiments 60-79, wherein the composition is formulated as a tablet, lozenge, prolonged-release capsule, prolonged-release granule, powder, sachet, nasal spray, ointment, serum, lotion or gummy. 81. The method of any one of embodiments 60-80, wherein the composition is formulated as a food product, nutritional product, food ingredient, dietary supplement, or medicament. 82. The method of any one of embodiments 60-81, wherein the composition comprises at least about 1 x 104CFU / g to at least about 1 x 1014CFU / g of a biologically pure strain of bacteria. 83. The method of any one of embodiments 60-82, wherein the treating and / or preventing comprises administering the composition for at least one month. 84. A method of altering insulin metabolism in a subject comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram- positive anaerobic bacteria. 85. The method of embodiment 84, further comprising alerting lipid metabolism. 86. The method of embodiment 84 or embodiment 85, further comprising improving insulin sensitivity. 87. The method of embodiment 86, wherein the improving insulin sensitivity comprises decreasing the release of NEFA. 88. The method of embodiment 87, wherein the decreasing the release of NEFA increases liver function. 89. The method of any one of embodiments 84-88, wherein the Gram-positive anaerobic bacteria comprise bacteria from the order Eubacteriales. 90. The method of any one of embodiments 84-89 wherein the bacteria comprise one or more substantially purified Butyricicoccus or Roseburia. 91. The method of any one of embodiments 84-90 wherein the bacteria comprise one or more substantially purified Butyricicoccus faecihominis strains.92. The method of embodiment 91, wherein the Butyricicoccus faecihominis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3. 93. The method of embodiment 91 or embodiment 92, wherein the Butyricicoccus faecihominis strain comprises the strain deposited under DSM 34943, or strain comprising all the defining characteristics of the strain deposited under DSM 34943. 94. The method of any one of embodiments 84-93, wherein the bacteria comprise one or more substantially purified Roseburia faecis strains. 95. The method of embodiment 94, wherein the Roseburia faecis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:1. 96. The method of embodiment 94 or embodiment 95, wherein the Roseburia faecis strain comprises the strain deposited under DSM 35024, or strain comprising all the defining characteristics of the strain deposited under DSM 35024. 97. The method of any one of embodiments 90-96, wherein the composition does not include any additional butyrate producing bacteria. 98. The method of any one of embodiments 84-97, wherein the composition comprises a probiotic, a prebiotic, postbiotic, human milk oligosaccharides, xylitol, betaine, and / or a botanical. 99. The method of any one of embodiments 84-97, wherein the composition has been pasteurized or heat treated. 100. The method of any one of embodiments 84-99, wherein the composition is lyophilized or freeze dried or spray dried. 101. The method of any one of embodiments 84-100, wherein the composition is encapsulated or coated. 102. The method of any one of embodiments 84-101, wherein the composition is a pharmaceutical composition and further comprises at least one pharmaceutically acceptable carrier and / or excipient.103. The method of any one of embodiments 84-102, wherein the composition is formulated as a tablet, lozenge, prolonged-release capsule, prolonged-release granule, powder, sachet, nasal spray, ointment, serum, lotion or gummy. 104. The method of any one of embodiments 84-103, wherein the composition is formulated as a food product, nutritional product, food ingredient, dietary supplement, or medicament. 105. The method of any one of embodiments 84-104, wherein the composition comprises at least about 1 x 104CFU / g to at least about 1 x 1014CFU / g of a biologically pure strain of bacteria. 106. The method of any one of embodiments 84-105, wherein the treating and / or preventing comprises administering the composition for at least one month. 107. A method of altering lipid metabolism and insulin metabolism in a subject comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria. 108. The method of embodiment 107, further comprising improving insulin sensitivity. 109. The method of embodiment 108, wherein the improving insulin sensitivity comprises decreasing the release of NEFA. 110. The method of embodiment 109, wherein the decreasing the release of NEFA increases liver function. 111. The method of any one of embodiments 107-110, wherein the Gram-positive anaerobic bacteria comprise bacteria from the order Eubacteriales. 112. The method of any one of embodiments 107-111 wherein the bacteria comprise one or more substantially purified Butyricicoccus or Roseburia. 113. The method of any one of embodiments 107-112 wherein the bacteria comprise one or more substantially purified Butyricicoccus faecihominis strains. 114. The method of embodiment 113, wherein the Butyricicoccus faecihominis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3.115. The method of embodiment 113 or embodiment 114, wherein the Butyricicoccus faecihominis strain comprises the strain deposited under DSM 34943, or strain comprising all the defining characteristics of the strain deposited under DSM 34943. 116. The method of any one of embodiments 107-115, wherein the bacteria comprise one or more substantially purified Roseburia faecis strains. 117. The method of embodiment 116, wherein the Roseburia faecis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:1. 118. The method of embodiment 116 or embodiment 117, wherein the Roseburia faecis strain comprises the strain deposited under DSM 35024, or strain comprising all the defining characteristics of the strain deposited under DSM 35024. 119. The method of any one of embodiments 112-118, wherein the composition does not include any additional butyrate producing bacteria. 120. The method of any one of embodiments 107-119, wherein the composition comprises a probiotic, a prebiotic, postbiotic, human milk oligosaccharides, xylitol, betaine, and / or a botanical. 121. The method of any one of embodiments 107-119, wherein the composition has been pasteurized or heat treated. 122. The method of any one of embodiments 107-121, wherein the composition is lyophilized or freeze dried or spray dried. 123. The method of any one of embodiments 107-122, wherein the composition is encapsulated or coated. 124. The method of any one of embodiments 107-123, wherein the composition is a pharmaceutical composition and further comprises at least one pharmaceutically acceptable carrier and / or excipient. 125. The method of any one of embodiments 107-124, wherein the composition is formulated as a tablet, lozenge, prolonged-release capsule, prolonged-release granule, powder, sachet, nasal spray, ointment, serum, lotion or gummy. 126. The method of any one of embodiments 107-125, wherein the composition is formulated as a food product, nutritional product, food ingredient, dietary supplement, or medicament.127. The method of any one of embodiments 107-126, wherein the composition comprises at least about 1 x 104CFU / g to at least about 1 x 1014CFU / g of a biologically pure strain of bacteria. 128. The method of any one of embodiments 107-127, wherein the treating and / or preventing comprises administering the composition for at least one month. 129. A method of increasing the relative abundance of Butyricicoccus faecihominis in the gastrointestinal tract of a subject in need thereof, comprising administering an effective amount of a composition comprising a plurality of substantially pure non- pathogenic Butyricicoccus faecihominis bacteria to the subject in need thereof. 130. The method of embodiment 129, wherein the Butyricicoccus faecihominis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:3. 131. The method of embodiment 129 or embodiment 130, wherein the Butyricicoccus faecihominis strain comprises the strain deposited under DSM 34943, or strain comprising all the defining characteristics of the strain deposited under DSM 34943. EXAMPLES Example 1: Isolation of strains Fecal samples from multiple donors were obtained and placed under anaerobic conditions shortly after donation and processed immediately. The fecal samples from the multiple donors were mixed, resuspended 1:10 in M9 minimal media (Na2HPO46 g / L, KH2PO43 g / L, NaCl 0.5 g / L, NH4Cl g / L, CaCl20.1 mM, MgSO 41 mM) and passed through a 100 μm cell sieve to remove larger insoluble material. The samples were washed twice and resuspended in M9 minimal media to the original concentration. The slurries were then serially diluted and 100 μl of each sample were plated onto various microbial culture plates. The culture plates used were Reinforced Clostrial Agar (RCA) (Hardy Diagnostics C8721), Yeast Casitone Fatty Acid agar (YCFA) (Casitone 10 g / L, Yeast Extract 2.5 g / L, NaHCO34 g / L, Cysteine 1 g / L, K2HPO40.45 g / L, KH2PO40.45 g / L, NaCl 0.9 g / L, (NH4)2SO40.9 g / L, MgSO4^7H2O 0.09 g / L, CaCl20.09g / L, Hemin 10 mg / L, Resazurin 1 mg / L, Biotin 10 μg / L, Cabalamin 10 μg / L, p-aminobenzoic acid 30 μL, Folic acid 50 μg / L, Pyridoxine 150 μg / L, Thiamine 50 μg / L, Riboflavin 50 μg / L, Acetic acid 1.9 ml / L, Propionic acid 0.7 ml / L, iso-Butyric acid 90 μL, n-Valeric acid 100 μl / L, iso-Valeric acid 100 μl / L), supplemented with 1% unmodified potato starch (Bob's Red Mill Natural Foods), Enriched Trypticase Soy agar (ETSA) (Anaerobe Systems AS-548), Brain Heart Infusion (BHI) (Anaerobe Systems AS-6426), MTGE (Anaerobe Systems AS-777), M17 (Difco BD 218561), supplemented with 1% unmodified potato starch. The plates were incubated for 48 hours at 37° C., under anaerobic conditions (5% H2, 15% CO2, 80% N2). Morphologically diverse colonies were picked from each plate and put into RCB media (AS-606, Anaerobe Systems) and modified YCFA (i.e., Yeast, Casitone, Fatty Acids) broth (Casitone 10 g / L, Yeast Extract 2.5 g / L, NaHCO34 g / L, Cysteine 1 g / L, K2HPO40.45 g / L, KH2PO40.45 g / L, NaCl 0.9 g / L, (NH4)2SO40.9 g / L, MgSO4.7H2O 0.09 g / L, CaCl20.09 g / L, Hemin 10 mg / L, Resazurin 1 mg / L, Biotin 10 μg / L, Cabalamin 10 μg / L, p-aminobenzoic acid 30 g / L, Folic acid 50 μg / L, Pyridoxine 150 μg / L. Thiamine 50 μg / L, Riboflavin 50 μ / L, 1% potato starch) in 96-deep well plates. After overnight incubation at 37° C. under anaerobic conditions, butyrate, acetate and propionate levels were measured in the supernatants from each well (see analytical method below). Organisms were isolated and identified by MALDI TOF or 16s-rRNA sequence (Accugenix, Charles River Labs, Inc.). Single bacterial colonies were lysed with 1μl of 70% formic acid, dried, and 1μl of matrix on a MALDI TOF plate, dried and loaded onto the instrument where they were ionized by a laser. The matrix absorbs most of the energy and transfers it to the sample. The ionized sample was broken into smaller pieces which were then pulled into a mass analyzer region and were separated based on their mass to charge ratio (m / z). Bacteria were identified by comparing their spectra to the spectra from known bacteria in the instrument's database. Candidates were selected based on the correlation analysis and availability of isolation. Three of these candidates were selected for further study, Roseburia faecis DSM 35024, Butyricicoccus faecihominis DSM 34943 and Anaerostipes hadrus FLM9MS-51 (AH).Example 2: Mouse model for evaluating the efficacy of candidates

[0130] This example describes the establishment of a Diet Induced Obesity (DIO) mouse model for evaluating the efficacy of the candidates Roseburia faecis DSM 35024, Butyricicoccus faecihominis DSM 34943 and Anaerostipes hadrus FLM9MS-51 (A. hadrus).

[0131] Roseburia faecis DSM 35024, Butyricicoccus faecihominis DSM 34943 and Anaerostipes hadrus FLM9MS-51 (A. hadrus) were evaluated for their efficacy in improving lipid and insulin related disorders in a DIO mice model. For the animal study, Group 1 animals were maintained on PMI Nutrition International Certified Rodent Chow No.5 CR4 upon arrival. Group 2 – 6 animals were maintained on Research Diet D12492. Animals were single housed in polycarbonate cages which contained appropriate bedding. Animals were distributed to the treatment groups as mentioned in the Table 1 on study day -1, in such a way as to generate cohorts with no significant differences with respect to body weight and non-fasted blood glucose based on measurements from Day -1. Table 1: Experimental design

[0132] Test articles R.faecis, B. faecihominis, and A. hadrus were prepared daily and administered within one hour of formulation. The Vehicle Control (Group 2) was administered once daily via oral gavage from Days 1 to 84. The dose volume for each animal was 100 µl. Test Articles (Groups 2 – 5) were administered once daily via oral gavage from Days 1 to 84. Thedose volume for each animal was 100 µl. Each dose was administered using a syringe with attached gavage cannula.

[0133] The Control Article Liraglutide (Group 6) was administered to the appropriate animals via subcutaneous injection into the interscapular area once daily from Days 1 to 84. The dose volume for each animal was based on the most recent body weight measurement. Each dose was administered using a using a syringe / needle within the demarcated area. The first day of dosing was designated as Day 1.

[0134] Study parameters included mortality / moribundity checks, daily observations, body weight measurements, food consumption, fecal samples, blood glucose measurements, Oral Glucose Tolerance Test, qNMR assessments, Cytokine assessments, and Clinical Chemistry parameters. Blood samples were taken at designated time points throughout the dosing phase and on the scheduled euthanasia day for biomarker evaluation. Example 3: Mouse model for evaluating formulations

[0135] This example describes evaluation of the efficacy of the candidates Roseburia faecis DSM 35024, Butyricicoccus faecihominis DSM 34943 and Anaerostipes hadrus FLM9MS-51 (A. hadrus) described in Example 2, for improving various parameters associated with lipid and insulin related disorders in an DIO mice model.

[0136] Resistin levels were measured in the serum obtained from mice from the different groups. The Roseburia faecis DSM 35024 and Butyricicoccus faecihominis DSM 34943 gavaged groups showed 27% and 23% decrease, respectively, in leptin levels compared to vehicle control. A. hadrus FLM9MS-51 showed 18% improvement in resistin levels as compared to vehicle control. Mice treated with Liraglutide showed 29% improvement. *P < 0.05 (FIG.1).

[0137] Leptin levels were measured in the serum obtained from mice from different groups. The Roseburia faecis DSM 35024 and Butyricicoccus faecihominis DSM 34943 gavaged groups showed 47% and 42% decrease in leptin levels, respectively, compared to vehicle control. Mice treated with Liraglutide showed 74% improvement. *P < 0.05 (FIG.2).

[0138] An insulin tolerance test (ITT) was conducted similar to the protocols established Melior Discovery; 2019 and Bonora E et. al. (J Clin Endocrinol Metab 1989; 68: 374–378). Briefly, all mice received an intraperitoneal injection of insulin (dose 0.5 U / kg at 5 mL / kg). Blood glucose was checked via tail snip using a hand-held glucometer (Abbott Alpha Trak) at the following times relative to insulin dose: 0 (just prior to insulin dose), 15, 30, 45, 60 and 90 min. Plasma glucose levels were measured in the serum obtained from mice from different groups. Area under the curve was calculated based on the values obtained during the study. As shown in FIG. 3, vehicle control showed an increase in the plasma glucose levels in the animals compared to chow, whereas the Butyricicoccus faecihominis DSM 34943 gavaged group showed 10% improvement as compared to control group. Mice treated with Liraglutide showed 31% improvement. The R. faecis DSM 35024 and A. hadrus gavaged groups showed no improvement in as compared to vehicle control. *P < 0.05.

[0139] Cholesterol levels were measured in the serum obtained from mice from the different groups. R. faecis DSM 35024, B. faecihominis DSM 34943 and A. hadrus FLM9MS-51 gavaged group showed significant decrease in cholesterol levels at the end of the study as compared to vehicle control. Mice treated with Liraglutide showed 30% improvement as compared to control group *P < 0.05 (FIG.4).

[0140] Alanine transaminase (ALT) levels were measured in the serum obtained from mice from the different groups. As shown in FIG.5, the R. faecis DSM 35024 and B. faecihominis DSM 34943 gavaged group showed 13% and 21% decrease in the ALT levels at the end of the study as compared to vehicle control. Mice treated with Liraglutide showed 38% decline in ALT levels as compared to HFD control group.

[0141] Nonesterified fatty acids (NEFA) levels were measured in the serum obtained from mice from the different groups. As shown in FIG.6, the B. faecihominis DSM 34943 gavaged group showed 8% decrease in the NEFA levels at the end of the study as compared to vehicle control. Mice treated with Liraglutide showed 8% decline in NEFA levels as compared to HFD control group.

[0142] Body composition analysis was done by qNMR (Bruker NMR LF90II). Body composition was determined at the start (days -2 and -1) and at the end of the study (Days 83 and 84). As shown in FIG.7, vehicle control showed significant fat accumulation in the animals compared to the chow-only group. The B. faecihominis DSM 34943 gavaged group showed 10 % decrease in the total body fat at the end of the study as compared to vehicle control. And Liraglutide showed 55% decrease as compared to HFD control group *P < 0.05

[0143] Production of short chain fatty acids (SCFA) by Roseburia faecis DSM 35024, Butyricicoccus faecihominis DSM 34943 and Anaerostipes hadrus FLM9MS-51 (A. hadrus) was analyzed after 24 hours of stationary incubation in RCM media at 37°C in an anaerobic environment. Cells were removed from supernatant by centrifugation and filtering. SCFA analysis performed by GC-MS. Butyrate production was observed in the supernatants from all the three strains (FIG.8).

[0144] These results demonstrate that although Roseburia faecis DSM 35024, Butyricicoccus faecihominis DSM 34943 and Anaerostipes hadrus FLM9MS-51 (A. hadrus) are all butyrate producing microorganisms, their effect on various lipid and insulin related markers varies in this model. The B. faecihominis DSM 34943 gavaged group showed improvement across all evaluated parameters compared to R. faecis DSM 35024 and A. hadrus FLM9MS-51. This suggests that the potential health benefits mediated by B. faecihominis DSM 34943 may not be exclusively associated with butyrate production. Example 4: Evaluation of GI tract engraftment

[0145] This example describes evaluation of the ability of Butyricicoccus faecihominis (B. faecihominis) DSM 34943 to engraft in the gastrointestinal tract in a mouse model.

[0146] Briefly, 8-9-weeks-old male C57Bl / 6J DIO and 10 male C57Bl / 6J mice were included in the study (10 animals per group) purchased from Jackson Laboratories (Bar Harbor, ME, USA). Following a two-week acclimation period, all animals were randomly allocated to three treatment groups as mentioned in the Table 1 above.

[0147] Mice were gavaged with either PBS control or B. faecihominis DSM 34943 once a day starting at Day 1 through Day 84.

[0148] 16S rRNA profiling was performed on mouse fecal pellet samples collected from Days 0 (pre), 8, 44, and 84. Using sterile forceps, mouse fecal pellets were placed into the wells of a Bead Plate from the DNeasy PowerSoil HTP 96 Kit (Qiagen, Hilden, Germany), and DNA were extracted by using the manufacturer’s protocol. Analysis was done as described previously. (Kumar et al 2022).

[0149] As shown in FIG.9, B. faecihominis is absent in the gastrointestinal tract of mice. Introduction of B. faecihominis via gavage results in the engraftment of the strain in the mice GI tract as shown by increased signature by day 84.

[0150] These results demonstrate that Butyricicoccus faecihominis is capable of engraftment in the gastrointestinal tract.

Claims

CLAIMS We claim:

1. A method of treating and / or preventing a lipid disorder in a subject in need thereof, comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria to the subject in need thereof.

2. The method of claim 1, wherein the Gram-positive anaerobic bacteria comprise bacteria from the order Eubacteriales.

3. The method of claim 1 or claim 2, wherein the bacteria comprise one or more substantially purified Butyricicoccus or Roseburia.

4. The method of any one of claims 1-3, wherein the bacteria comprise one or more substantially purified Butyricicoccus faecihominis strains.

5. The method of claim 4, wherein the Butyricicoccus faecihominis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:2 or SEQ ID NO:

3.

6. The method of claim 4 or claim 5, wherein the Butyricicoccus faecihominis strain comprises the strain deposited under DSM 34943, or strain comprising all the defining characteristics of the strain deposited under DSM 34943.

7. The method of any one of claims 1-6, wherein the bacteria comprise one or more substantially purified Roseburia faecis strains.

8. The method of claim 7, wherein the Roseburia faecis strain comprises a bacterial strain having a 16S ribosomal RNA sequence displaying at least about 90% sequence similarity to the 16S ribosomal RNA sequence of SEQ ID NO:

1.

9. The method of claim 7 or claim 8, wherein the Roseburia faecis strain comprises the strain deposited under DSM 35024, or strain comprising all the defining characteristics of the strain deposited under DSM 35024.

10. The method of any one of claims 1-9, wherein the composition does not include any additional butyrate producing bacteria.

11. The method of any one of claims 1-10, wherein the composition comprises a probiotic, a prebiotic, postbiotic, human milk oligosaccharides, xylitol, betaine, and / or a botanical.

12. The method of any one of claims 1-11, wherein the composition has been pasteurized or heat treated.

13. The method of any one of claims 1-12, wherein the composition is lyophilized or freeze dried or spray dried.

14. The method of any one of claims 1-13, wherein the composition is a pharmaceutical composition and further comprises at least one pharmaceutically acceptable carrier and / or excipient.

15. The method of any one of claims 1-14, wherein the composition is formulated as a tablet, lozenge, prolonged-release capsule, prolonged-release granule, powder, sachet, nasal spray, ointment, serum, lotion, gummy, food product, nutritional product, food ingredient, dietary supplement, or medicament.

16. The method of any one of claims 1-15, wherein the composition comprises at least about 1 x 104CFU / g to at least about 1 x 1014CFU / g of a biologically pure strain of bacteria.

17. A method of treating and / or preventing an insulin disorder in a subject in need thereof, comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria to the subject in need thereof.

18. A method of treating and / or preventing a lipid disorder and an insulin disorder in a subject in need thereof, comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria to the subject in need thereof.

19. A method of altering lipid metabolism in a subject, comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Gram-positive anaerobic bacteria.

20. The method of claim 19, wherein altering the lipid metabolism comprises modulating a hormone associated with lipid metabolism.

21. The method of claim 19 or claim20, wherein the hormone comprises leptin.

22. A method of increasing the relative abundance of Butyricicoccus faecihominis in the gastrointestinal tract of a subject in need thereof, comprising administering an effective amount of a composition comprising a plurality of substantially pure non-pathogenic Butyricicoccus faecihominis bacteria to the subject in need thereof.

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