Bacterial strains for treating diseases

Abstract

Therapeutic compositions comprising the bacterial strains and methods for the treatment or prevention of diseases are disclosed. More specifically, the present invention also discloses compositions comprising bacterial strains isolated from the human gastrointestinal tract and their use in the treatment or prevention of inflammatory and autoimmune disorders.

Description

[Technical field]

[0001] The present invention relates generally to the field of therapeutic compositions comprising bacterial strains and methods for the treatment or prevention of diseases. More specifically, the present invention relates to compositions comprising bacterial strains isolated from the human gastrointestinal tract and their use in the treatment or prevention of inflammatory and autoimmune disorders. [Background technology]

[0002] The human gut microbiota contains over 500–1000 different phylotypes belonging to several bacterial phyla, including Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Verrucomicrobia. Two major phyla, Bacteroidetes and Firmicutes, generally account for over 90% of the gut microbiota (Arumugam et al., 2011). The favorable symbiotic relationships resulting from bacterial colonization of the human intestinal tract produce a wide variety of metabolic, structural, defensive, and other beneficial functions. Gut bacteria are key regulators of digestion along the gastrointestinal (GI) tract, with commensal bacteria playing key roles in the extraction, synthesis, and absorption of many nutrients and metabolites, including bile acids, lipids, amino acids, vitamins, and short-chain fatty acids (SCFAs). More recently, the immunological importance of the gut microbiota and its products in regulating the development, homeostasis, and function of innate and adaptive immune cells has been recognized (Brestoff and Atris, 2013).

[0003] It is increasingly recognized that the gut microbiome regulates the host's intestinal mucosal immunity and predisposition to inflammation ( Geva-Zatorsky et al., 2017 ; Kabat et al., 2014 ), opening new avenues for novel therapeutic interventions.

[0004] Dramatic changes in microbiota composition have been reported in many inflammatory and autoimmune disorders, including inflammatory bowel disease (IBD). Recognizing the potential positive effects that certain bacterial strains may have on the intestinal tract of animals, various strains have been proposed for use in treating various diseases. Certain strains, including Lactobacillus and Bifidobacterium strains, have been proposed for use in treating various extraintestinal inflammatory and autoimmune disorders (see Goldin & Gorbach, 2008; Azad et al., 2013). However, the exact effects that specific bacterial strains have locally and systemically in the gastrointestinal tract have not been elucidated. As a result, the relationship between different diseases and different bacterial strains in the human gastrointestinal tract has not yet been clearly elucidated.

[0005] IBD (which includes two major disease subtypes, Crohn's disease (CD) and ulcerative colitis (UC)) is characterized by recurrent and disabling inflammation of the gastrointestinal tract. In 2017, it was estimated that 6.8 million people worldwide suffered from IBD, with the highest prevalence in the United States and Europe (GBD 2017; Inflammatory Bowel Disease Collaborators, 2019). Up to 20% of patients are diagnosed before the age of 16, and pediatric-onset IBD (PIBD) is associated with a more complex and active disease, with adverse effects on growth and psychosocial development.

[0006] There is currently no cure for IBD, and long-term clinical management requires effective therapeutic agents with a good safety profile. However, existing treatments have various deficiencies, and remissions are generally short. Furthermore, IBD therapeutic agents are ineffective when early onset coupled with more active disease leads to progressive intestinal damage and the need for surgery. There is an urgent need to develop more effective and safer therapies to improve patients' quality of life, maintain remission over the long term, reduce surgeries, and reduce personal and public health costs.

[0007] Existing treatments for IBD are suboptimal, with strong adverse effects, low compliance (average non-adherence rate 50% (see Chan et al., 2017)), and high costs. Furthermore, there are no effective solutions to maintain long-term disease-free remission. Methalmine is one of the most widely used first-line therapies for relapse and maintenance of remission in mild to moderate ulcerative colitis, with response rates of 40–70% and remission rates of 15–20% (Karagozian & Burakoff, 2007).

[0008] There is a need in the art for new methods of treating inflammatory and autoimmune disorders, and there is also a need to characterize the potential effects of gut bacteria in order to develop new therapies using gut bacteria. Summary of the Invention

[0009] The present invention is based in part on the inventors' identification that bacterial strains of Intestinicoccus colisanans enhance or improve intestinal barrier function. Based on this observation, it is proposed that I. colisanans strains are particularly suitable for therapeutic use for the treatment and prevention of inflammatory and autoimmune disorders, as described below.

[0010] The present inventors have developed new compositions comprising live strains of the species Intestinicoccus colisanans that can be used for the treatment and prevention of inflammatory and autoimmune disorders.

[0011] Thus, in one aspect, the present invention provides a cell of the Intestinicoccus colisanans strain deposited under accession number V21 / 015887 or V21 / 015888, or a derivative thereof.

[0012] In some embodiments, the cells are at least partially isolated.

[0013] In another aspect, the present invention provides a biologically pure culture of the Intestinicoccus colisanans strain deposited under accession number V21 / 015887 or V21 / 015888, or a derivative thereof.

[0014] In another aspect, the invention provides a composition comprising a cell or culture as described above and elsewhere herein.

[0015] In yet another aspect, the invention provides compositions comprising a bacterial strain having a 16S rRNA that is at least about 97.5%, 98%, 98.5%99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to SEQ ID NO: 1; or having a 16S rRNA sequence set forth by SEQ ID NO: 1. In some embodiments, the bacterial strain comprises two or more copies (e.g., 2 copies, 3 copies, 4 copies, 5 copies, 6 copies, 7 copies, 8 copies) of the 16S rRNA sequence in its genome.

[0016] In some embodiments, the composition further comprises a pharma- ceutically acceptable excipient, diluent or carrier.

[0017] In yet another aspect, the present invention provides a pharmaceutical composition comprising a bacterial strain having a 16S rRNA sequence that is at least about 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to a 16S rRNA sequence of a bacterial strain of the species Intestinicoccus colisanans, together with a pharma- ceutically acceptable carrier, diluent or excipient.

[0018] Typically, the bacterial strain is at least partially isolated.

[0019] In some embodiments, the bacterial strain is live. In some alternative embodiments, the bacterial strain is dead.

[0020] In some embodiments, the composition further comprises a prebiotic.

[0021] In some embodiments, the composition is formulated in a dry form. Typically, the composition is dried using a technique selected from freeze drying, spray drying, fluidized bed drying, vacuum drying, or a combination thereof.

[0022] In some embodiments, the compositions are formulated for oral administration.

[0023] In some embodiments, the bacterial strain produces an agent that attenuates or impairs signal transduction and activator of transcription 3 (STAT3) in cells.

[0024] In some embodiments of this type, the agent is a small molecule, a peptide, or a nucleotide.Typically, the agent is released by the bacterial strain.

[0025] In some embodiments, the agent specifically binds to any one of STAT3, JAK2, TYK2, or IL-23.

[0026] In some embodiments, I. colisanans metabolizes one or more agents selected from the group consisting of starch, glucose, fructose, gluconic acid, lactose, trehalose, and lactaldehyde as carbon sources.

[0027] In another aspect, the present invention provides a method of restoring or improving intestinal barrier function in a subject, the method comprising administering to the subject a bacterial strain of the I. colisanans species, thereby restoring or improving intestinal barrier function.

[0028] In some preferred embodiments, restoration or improvement of intestinal barrier function is characterized by at least one of: (i) an increase in the quality and / or quantity of mucin; (ii) improved integrity of tight junction proteins; (iii) a reduction in translocation of luminal contents into the systemic circulation; or (iv) a reduction in intestinal ulcers and / or wounds.

[0029] In some embodiments, the luminal contents comprise lipopolysaccharide (LPS).

[0030] In some embodiments, restoration or improvement of intestinal barrier function results in a reduction in systemic inflammation in the subject. In some embodiments of this type, the systemic inflammation is characterized by elevated levels of inflammatory cytokines (e.g., IL-1β, IL-8, IL-6, and TNF) in the subject compared to the levels of inflammatory cytokines in healthy subjects.

[0031] In some embodiments, the I. colisanans bacterial strain stimulates PBMCs to produce the cytokines IL-10 and IL-12 in a ratio of 5 or greater. For example, the I. colisanans bacterial strain may stimulate PBMCs to produce the cytokines IL-10 and IL-12 in a ratio of 10, 15, 20, 25, or 30 or greater.

[0032] In yet another aspect, the present invention provides a method of maintaining intestinal barrier function in a subject, the method comprising administering to the subject a bacterial strain of the I. colisanans species, thereby maintaining intestinal barrier function in the subject.

[0033] In yet another aspect, the present invention provides a method of reducing inflammation in a subject, comprising administering to the subject a bacterial strain of I. colisanans, thereby reducing inflammation in the subject.

[0034] In some embodiments, the inflammation is local to the intestinal environment or is systemic inflammation.

[0035] In another aspect, the present invention provides a method of inducing or enhancing mucosal healing in a subject, the method comprising administering to the subject an amount of a bacterial strain of the I. colisanans species sufficient to induce epithelial cell migration, proliferation, and / or differentiation, thereby inducing mucosal healing in the subject.

[0036] In some embodiments, mucosal healing in a subject can be measured using one or more fecal or serum markers. As illustrative examples, the one or more fecal markers can be selected from the group including calprotectin, lactoferrin, metalloproteinase (MMP)-9, and lipocalin-2.

[0037] In some embodiments, the bacterial strain reduces inflammation by attenuating the NFκB pathway. In some embodiments of this type, the bacterial strain inhibits the production of one or more transcription factors, cytokines, or chemokines selected from the group including NFκB, TNF, IFN-γ, IL-1β, IL-8, and MCP-1.

[0038] In yet another aspect, the present invention provides a method of blocking or inhibiting STAT3 signaling in a target cell, comprising contacting the cell with at least a soluble component of a bacterial cell preparation of the I. colisanans species to block or inhibit STAT3 signaling in the cell. Typically, the method of this aspect is performed in vitro.

[0039] In some embodiments, the target cell is selected from a reporter cell (e.g., a HEK cell), an immune cell (e.g., a Th17 immune cell), an epithelial cell, or an endothelial cell. In some embodiments, the target cell is a mammalian cell, preferably a human cell.

[0040] In some embodiments, the bacterial cell preparation is a bacterial cell culture. Thus, the soluble component may comprise, consist of, or consist essentially of the soluble fraction of the bacterial cell culture (e.g., cell culture supernatant). The soluble component may further comprise some insoluble components of the bacterial cell culture. For example, the soluble component may comprise substantially all of the bacterial culture. Preferably, the soluble component is substantially depleted of bacterial cells.

[0041] In some alternative embodiments, the bacterial cell preparation is a bacterial cell lysate. In exemplary embodiments of this type, the soluble components may relate to the soluble fraction of the cell lysate. The soluble fraction may be suitably obtained by any method, including centrifugation.

[0042] In yet another aspect, the present invention provides a method of blocking or inhibiting STAT3 signaling in a cell, comprising administering to a subject a bacterial strain of the I. colisanans species, thereby blocking or inhibiting STAT3 signaling in the cell. Typically, the method of this aspect is performed in vivo.

[0043] In some embodiments, the cell is an immune cell (eg, a Th17 immune cell) or an epithelial cell.

[0044] In some embodiments, the cell is an epithelial cell, and the bacterial strain or a metabolic product produced by the bacterial strain increases the production of IL-22 in the subject.

[0045] In some embodiments, the bacterial strain produces a molecule that is a direct or indirect inhibitor of STAT3. For example, the bacterial strain may produce a metabolite that directly inhibits at least one of an IL-23 polypeptide, a JAK2 polypeptide, a TYK2 polypeptide, or a STAT3 polypeptide.

[0046] In some embodiments, the bacterial strains used in the methods described above and elsewhere herein produce the metabolic product acetate.

[0047] In some embodiments, the bacterial strain has a 16S rRNA sequence that is at least about 97.5%, 98.5%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% identical to the 16S rRNA sequence of an I. colisanans bacterial strain.

[0048] In some alternative embodiments, the bacterial strain has a 16S rRNA sequence that is at least about 97.5%, 98.5%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% identical to SEQ ID NO: 1, or the bacterial strain has a 16S rRNA gene sequence set forth by SEQ ID NO: 1. In some embodiments, the bacterial strain comprises two or more copies (e.g., 2 copies, 3 copies, 4 copies, 5 copies, 6 copies, 7 copies, 8 copies) of an independently selected 16S rRNA sequence set forth in SEQ ID NO: 1. In some alternative embodiments, the bacterial strain has a 16S rRNA sequence that is at least about 97.5%, 98.5%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% identical to SEQ ID NO: 2, or the bacterial strain has a 16S rRNA gene sequence set forth by SEQ ID NO: 2. In some embodiments, the bacterial strain comprises two or more copies (e.g., 2 copies, 3 copies, 4 copies, 5 copies, 6 copies, 7 copies, 8 copies) of an independently selected 16S rRNA sequence set forth in SEQ ID NO: 2.

[0049] In some embodiments, the bacterial strain is an I. colisanans strain deposited under accession number V21 / 015887 or V21 / 015888, or a derivative thereof.

[0050] Preferably, the bacterial strain is at least partially isolated.

[0051] In some embodiments, the bacterial strain is formulated as a pharmaceutical composition, further comprising a pharma- ceutically acceptable carrier, diluent or excipient. In some embodiments, the pharmaceutical composition is a dry composition. In some embodiments, the dry composition is selected from the group consisting of particles, granules, and powders. As illustrative examples, the pharmaceutical composition may be freeze-dried, spray-dried, fluid-bed dried, vacuum-dried, or a combination thereof.

[0052] In some embodiments, the pharmaceutical compositions are formulated for oral administration.

[0053] In still yet another aspect, the present invention provides a method of treating an inflammatory or autoimmune disorder in a subject, comprising administering to the subject an effective amount of a bacterial strain of I. colisanans, thereby treating or preventing the inflammatory or autoimmune disorder.

[0054] In some embodiments, the inflammatory or autoimmune disorder is selected from the group comprising inflammatory bowel disease (such as Crohn's disease or ulcerative colitis); asthma (such as allergic asthma or neutrophilic asthma); fatty liver disease (such as non-alcoholic fatty liver disease (NAFLD)); ankylosing spondylitis; systemic lupus erythematosus (SLE); scleroderma; Sjogren's syndrome; and vasculitis. Preferably, the inflammatory or autoimmune disorder is inflammatory bowel disease (IBD).

[0055] In some embodiments, the bacterial strain blocks or inhibits STAT3 signaling in at least a cell of the subject. Typically, the cell is an epithelial cell, an endothelial cell, or an immune cell (e.g., a Th17 immune cell).

[0056] In some embodiments, the bacterial strain has a 16S rRNA sequence that is at least about 98%, 98.5, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to a 16S rRNA sequence of an I. colisanans bacterial strain.

[0057] Alternatively, in some embodiments, the bacterial strain has a 16S rRNA sequence that is at least about 98%, 98.5, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to SEQ ID NO: 1, or the bacterial strain has a 16S rRNA gene sequence set forth by SEQ ID NO: 1. Alternatively, the bacterial strain may have a 16S rRNA sequence that is at least about 98%, 98.5, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to SEQ ID NO:2, or the bacterial strain has a 16S rRNA gene sequence set forth by SEQ ID NO:2.

[0058] In some alternative embodiments, the bacterial strain may have a 16S rRNA sequence that is at least about 98%, 98.5, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to any one of SEQ ID NOs:7-10, or the bacterial strain has a 16S rRNA gene sequence set forth by any one of SEQ ID NOs:7-10.

[0059] Preferably, the bacterial strain is at least partially isolated.

[0060] In some embodiments, the bacterial strain is formulated as a pharmaceutical composition together with a pharma- ceutically acceptable carrier, diluent and / or excipient. In some embodiments, the composition is a dry composition selected from the group consisting of particles, granules, and powders. For example, the composition may be lyophilized. Alternatively, the composition may be spray-dried, fluidized bed dried, or vacuum dried.

[0061] In some embodiments, the compositions are formulated for oral administration.

[0062] In one aspect, the present invention provides a composition comprising a bacterial strain of the genus Intestinicoccus for use in therapy.

[0063] In another aspect, the invention provides a composition comprising a bacterial strain of I. colisanans for use in therapy. In some of the same embodiments and in some other embodiments, the bacterial strain has a 16S rRNA sequence that is at least about 98%, 98.5, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to a 16S rRNA sequence of the bacterial strain of I. colisanans.

[0064] Alternatively, the bacterial strain may have a 16S rRNA sequence that is at least about 98%, 98.5, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to SEQ ID NO:1, or the bacterial strain has a 16S rRNA gene sequence as depicted by SEQ ID NO:1.

[0065] Alternatively, the bacterial strain may have a 16S rRNA sequence that is at least about 98%, 98.5, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to SEQ ID NO:2, or the bacterial strain has a 16S rRNA gene sequence as depicted by SEQ ID NO:2.

[0066] Alternatively, the bacterial strain may have a 16S rRNA sequence that is at least about 98%, 98.5, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to any one of SEQ ID NOs:7-10, or the bacterial strain has a 16S rRNA gene sequence set forth by any one of SEQ ID NOs:7-10.

[0067] In yet another aspect, the present invention provides a composition comprising a bacterial strain of the genus Intestinicoccus for use in the treatment or prevention of an inflammatory or autoimmune disorder.

[0068] In yet another aspect, the present invention provides a composition comprising a bacterial strain of I. colisanans for use in the treatment or prevention of an inflammatory or autoimmune disorder.

[0069] In some embodiments, the bacterial strain is an I. colisanans strain or a derivative thereof.

[0070] In some embodiments, the inflammatory or autoimmune disorder is selected from inflammatory bowel disease (such as Crohn's disease or ulcerative colitis); asthma (such as allergic asthma or neutrophilic asthma); arthritis (such as rheumatoid arthritis, osteoarthritis, psoriatic arthritis, or juvenile idiopathic arthritis); fatty liver disease (such as non-alcoholic fatty liver disease (NAFLD)); ankylosing spondylitis; psoriasis; systemic lupus erythematosus (SLE); scleroderma; Sjogren's syndrome; and type 1 diabetes. In some preferred embodiments, the inflammatory or autoimmune disorder is inflammatory bowel disease (IBD).

[0071] In one aspect, the invention provides a composition for use in treating an inflammatory or autoimmune disorder, the composition comprising a bacterial strain of I. colisanans and an adjunctive treatment.

[0072] In some embodiments, the adjunctive treatment is an anti-inflammatory agent. As illustrative examples, the anti-inflammatory agent is selected from the group including 5-aminosalicylate, corticosteroids, azathioprine, or a combination thereof. In some other embodiments, the adjunctive treatment is an antibody (e.g., a monoclonal antibody). As illustrative examples, the antibody may be selected from infliximab, adalimumab, golimumab, certolizumab pegol, natalizumab, and vedolizumab.

[0073] In another aspect, the present invention provides a composition for use in treating an inflammatory or autoimmune disorder, the composition comprising a bacterial strain of I. colisanans and a nutritional supplement, in this type of embodiment, the nutritional supplement improves the engraftment of the bacterial strain.

[0074] In some related aspects, the technology described herein provides bacterial species and compositions comprising them in the form of probiotics. Preferably, such probiotics are effective in improving the gut microbial ecosystem, alleviating symptoms of microbial dysbiosis, promoting wellness, and / or treating or preventing inflammatory and / or autoimmune disorders. [Brief description of the drawings]

[0075] The following figures form part of the present specification and are included to further demonstrate certain aspects of the present disclosure. The present disclosure may be better understood by reference to one or more of these figures in combination with the detailed description of specific embodiments presented herein.

[0076] [Figure 1] A graphical representation of the association of I. colisanans with representative inflammatory and / or autoimmune disorders is provided. (A) Using high-resolution gut metagenomic data (MDD) from 6,020 subjects, we identified that I. colisanans was significantly less prevalent in various inflammatory and autoimmune disorders (hatched bars) compared to healthy individuals (black bars) (P<0.05, Fisher's exact test). (B) The strongest reduction was observed for IBD, including both major subtypes Crohn's disease (CD) and ulcerative colitis (UC). These observations were validated in an independent IBD cohort previously published by Harvard (Franzosa et al., 2019).

[0077] [Diagram 2] Photographs and graphical representations of the morphology and phylogeny of I. colisanans are provided. (A) Gram-stained I. colisanans isolates showing morphology. (B) Phylogenetic tree constructed with alignment of 120 bacteria-specific single-copy marker genes from a high-quality reference genome (GTDB r89). Nonparametric bootstrap values ​​calculated from 1000 replicates. Intestinococcus was previously designated UBA1417.

[0078] [Diagram 3] Figure 1 provides a graphical representation showing that I. colisanans does not affect healthy intestinal function in untreated C57Bl / 6 mice. (A) Overview of the model used to evaluate the effect of I. colisanans on untreated C57Bl / 6 mice. (B) Treatment with I. colisanans has little effect on body weight in untreated animals. (C)-(D) Treatment with I. colisanans has no effect on colon length or colon weight / length ratio compared to vehicle-treated controls in untreated animals. (E)-(F) Treatment with I. colisanans has no effect on epithelial damage, inflammation, hypervascularization compared to vehicle-treated controls in untreated animals. (G) Treatment with I. colisanans has no effect on intestinal tissue architecture compared to vehicle-treated controls in untreated animals. All data reported as mean and standard deviation. ns not significant.

[0079] [Figure 4-1]A graphical representation is provided that I. colisanans restores intestinal barrier function. (A) Overview of the DSS mouse model used to evaluate the therapeutic efficacy of I. colisanans. (B) Effects of daily treatment with vehicle, prednisone, and I. colisanans in healthy and DSS-treated mice. All treatment groups were compared to the DSS+vehicle group. Significant differences were determined using two-way ANOVA with Tukey's test for multiple comparisons. (C) Endoscopic assessment of colitis assessed on days 1, 2, and 6. All groups were compared to the DSS+vehicle group on individual days using the Kruskal-Wallis test with Dunn's correction for multiple comparisons (day 1) or one-way ANOVA with Dunnett's correction for multiple comparisons (days 2, 6) as appropriate. All data are presented as mean and standard deviation. (D) Representative images of intestinal histology of C57Bl / 6 mice treated with vehicle, prednisone, or I. colisanans. (E) DSS treatment increases histopathological scores, which are ameliorated by treatment with prednisone, F. prausnitzii A2-165, and I. colisanans. All data presented as mean and standard deviation. All groups were compared to the DSS+vehicle group, and significant differences were determined using one-way ANOVA with Dunnett's test for multiple comparisons. (F) DSS treatment increases epithelial damage, which is ameliorated by treatment with prednisone and I. colisanans. All data presented as mean and standard deviation. All groups were compared to the DSS+vehicle group using the Kruskal-Wallis test with Dunn's correction for multiple comparisons. (G) Total histopathological scores of mice, (H) epithelial subscore of total histopathological scores of all mice, (I) inflammation subscore of total histopathological scores of all mice. All groups were compared to the DSS control group using regular one-way ANOVA with Dunnett's multiple comparisons test. The D'Agostino-Pearson omnibus test was applied to all data to test for normal distribution, and all data passed this test. The Brown-Forsyth test was applied to all data to test for significant differences in standard deviations between groups, and all data passed this test.All groups are visually represented with points representing individual mice, and columns and error bars represent the mean and standard deviation of each group. The following annotations are used for statistical significance after correction for multiple comparisons: *, p<0.05; **, p<0.01; ***, p<0.001; ****, p<0.0001. (J) Disease Activity Index scores for healthy mice or DSS-treated mice receiving I. colisanans MH27-2 at the indicated doses and formulations, or the control drugs minocycline and prednisone. All groups treated with I. colisanans MH27-2 or control drugs were compared to DSS-vehicle controls using Brown-Forsythe and Welch analysis of variance and Dunnett's T3 multiple comparison test. (K) Mouse body weights as a percentage of original body weight for healthy mice or DSS-treated mice administered I. colisanans MH27-2 at the indicated doses and formulations, or the control drugs minocycline and prednisone. All groups treated with I. colisanans MH27-2 or control drugs were compared to DSS-vehicle controls using ordinary one-way ANOVA and Dunnett's multiple comparison test. (L) Fecal occult blood scores for healthy mice or DSS-treated mice administered I. colisanans MH27-2 at the indicated doses and formulations, or the control drugs minocycline and prednisone. All groups treated with I. colisanans MH27-2 or control drugs were compared to DSS-vehicle controls using Brown-Forsythe and Welch ANOVA and Dunnett's multiple comparison test. (M-P) Histopathological total and subscores for healthy mice or DSS-treated mice receiving I. colisanans MH27-2 at the indicated doses and formulations, or the control drugs minocycline and prednisone. All groups treated with I. colisanans MH27-2 or control drugs were compared to DSS-vehicle controls using ordinary one-way ANOVA and Dunnett's multiple comparison test. All groups are visually represented with points representing individual mice, and columns and error bars represent the mean and standard deviation of each group.For all statistical analyses, the D'Agostino-Pearson omnibus test was used to determine if the data were normally distributed, and all data passed this test. The Brown-Forsyth test was used to determine if the standard deviations were significantly different between groups, and if this test was significant, the Brown-Forsyth and Welch ANOVA test was used instead of the regular one-way ANOVA. In this case, Dunnett's T3 multiple comparison test was used instead of the Dunnett test. After correction for multiple comparisons, the following annotations are used for statistical significance: *, p<0.05; **, p<0.01; ***, p<0.001; ****, p<0.0001. [Figure 4-2]A graphical representation is provided that I. colisanans restores intestinal barrier function. (A) Overview of the DSS mouse model used to evaluate the therapeutic efficacy of I. colisanans. (B) Effects of daily treatment with vehicle, prednisone, and I. colisanans in healthy and DSS-treated mice. All treatment groups were compared to the DSS+vehicle group. Significant differences were determined using two-way ANOVA with Tukey's test for multiple comparisons. (C) Endoscopic assessment of colitis assessed on days 1, 2, and 6. All groups were compared to the DSS+vehicle group on individual days using the Kruskal-Wallis test with Dunn's correction for multiple comparisons (day 1) or one-way ANOVA with Dunnett's correction for multiple comparisons (days 2, 6) as appropriate. All data are presented as mean and standard deviation. (D) Representative images of intestinal histology of C57Bl / 6 mice treated with vehicle, prednisone, or I. colisanans. (E) DSS treatment increases histopathological scores, which are ameliorated by treatment with prednisone, F. prausnitzii A2-165, and I. colisanans. All data presented as mean and standard deviation. All groups were compared to the DSS+vehicle group, and significant differences were determined using one-way ANOVA with Dunnett's test for multiple comparisons. (F) DSS treatment increases epithelial damage, which is ameliorated by treatment with prednisone and I. colisanans. All data presented as mean and standard deviation. All groups were compared to the DSS+vehicle group using the Kruskal-Wallis test with Dunn's correction for multiple comparisons. (G) Total histopathological scores of mice, (H) epithelial subscore of total histopathological scores of all mice, (I) inflammation subscore of total histopathological scores of all mice. All groups were compared to the DSS control group using regular one-way ANOVA with Dunnett's multiple comparisons test. The D'Agostino-Pearson omnibus test was applied to all data to test for normal distribution, and all data passed this test. The Brown-Forsyth test was applied to all data to test for significant differences in standard deviations between groups, and all data passed this test.All groups are visually represented with points representing individual mice, and columns and error bars represent the mean and standard deviation of each group. The following annotations are used for statistical significance after correction for multiple comparisons: *, p<0.05; **, p<0.01; ***, p<0.001; ****, p<0.0001. (J) Disease Activity Index scores for healthy mice or DSS-treated mice receiving I. colisanans MH27-2 at the indicated doses and formulations, or the control drugs minocycline and prednisone. All groups treated with I. colisanans MH27-2 or control drugs were compared to DSS-vehicle controls using Brown-Forsythe and Welch analysis of variance and Dunnett's T3 multiple comparison test. (K) Mouse body weights as a percentage of original body weight for healthy mice or DSS-treated mice administered I. colisanans MH27-2 at the indicated doses and formulations, or the control drugs minocycline and prednisone. All groups treated with I. colisanans MH27-2 or control drugs were compared to DSS-vehicle controls using ordinary one-way ANOVA and Dunnett's multiple comparison test. (L) Fecal occult blood scores for healthy mice or DSS-treated mice administered I. colisanans MH27-2 at the indicated doses and formulations, or the control drugs minocycline and prednisone. All groups treated with I. colisanans MH27-2 or control drugs were compared to DSS-vehicle controls using Brown-Forsythe and Welch ANOVA and Dunnett's multiple comparison test. (M-P) Histopathological total and subscores for healthy mice or DSS-treated mice receiving I. colisanans MH27-2 at the indicated doses and formulations, or the control drugs minocycline and prednisone. All groups treated with I. colisanans MH27-2 or control drugs were compared to DSS-vehicle controls using ordinary one-way ANOVA and Dunnett's multiple comparison test. All groups are visually represented with points representing individual mice, and columns and error bars represent the mean and standard deviation of each group.For all statistical analyses, the D'Agostino-Pearson omnibus test was used to determine if the data were normally distributed, and all data passed this test. The Brown-Forsyth test was used to determine if the standard deviations were significantly different between groups, and if this test was significant, the Brown-Forsyth and Welch ANOVA test was used instead of the regular one-way ANOVA. In this case, Dunnett's T3 multiple comparison test was used instead of the Dunnett test. After correction for multiple comparisons, the following annotations are used for statistical significance: *, p<0.05; **, p<0.01; ***, p<0.001; ****, p<0.0001.

[0080] [Figure 5-1](A) Overview of the SKG model used to evaluate the therapeutic efficacy of I. colisanans. (B) Curdlan treatment increases histopathological scores, which are ameliorated by treatment with anti-IL-23 antibody and I. colisanans. All data are presented as mean and standard deviation. All groups were compared to the curdlan + vehicle group using analysis of variance and Dunnett's test for multiple comparisons. (C) Curdlan treatment increases IL-6 and IL-12p70, which are ameliorated by treatment with I. colisanans. All data are presented as mean and standard deviation. For IL-6, all groups were compared to the curdlan + vehicle group using ordinary one-way analysis of variance and Dunnett's test for multiple comparisons. For IL-12p70, all groups were compared to the DSS + vehicle group using the Kruskal-Wallis test and Dunn's correction for multiple comparisons. For IL-6, all groups were compared to the Curdlan + Vehicle group using a regular one-way ANOVA test with Dunnett's test for multiple comparisons. For all data, ns is not significant; * is p<0.05; ** is p<0.01; *** is p<0.001, **** is p<0.0001. (E) Overview of the TNBS mouse model used to evaluate the therapeutic efficacy of I. colisanans MH27-2. (F) TNBS treatment increases the gross lesion histopathology score, which is improved by treatment with I. colisanans MH27-2 and Cyclosporine A. The TNBS + Vehicle group was compared to the I. colisanans MH27-2 and Cyclosporine A treated groups using a regular one-way ANOVA test with Sidak's multiple comparison correction. (G) Treatment with I. colisanans MH27-2 results in a significant improvement in the ulcer / inflammation score. TNBS + vehicle group was compared to I. colisanans MH27-2 and cyclosporine A treatment. (H) TNBS treatment increases the total histopathology score, which is ameliorated by treatment with I. colisanans MH27-2 and cyclosporine A.The TNBS + vehicle group was compared to the I. colisanans MH27-2 and cyclosporine A treated groups using Brown-Forsyth and Welch analysis of variance tests with Dunnett's T3 multiple comparison correction. (I-L) Treatment with I. colisanans MH27-2 results in significant improvements in the degree of inflammation, erosion or ulceration, epithelial regeneration, and percent lesion score. The TNBS + vehicle group was compared to the I. colisanans MH27-2 and cyclosporine A treated groups using Kruskal-Wallis tests with Dunn's multiple comparison tests. (M) Treatment with I. colisanans MH27-2 results in a significant reduction in IL-6 concentrations. The TNBS + vehicle group was compared to the I. colisanans MH27-2 and cyclosporine A treated groups. Data were log-transformed and analyzed using the Kruskal-Wallis test with Dunn's multiple comparison test and the ordinary one-way ANOVA test with Sidak's multiple comparison correction (ns, not significant; *, p<0.05; **, p<0.01; ***, p<0.001; ****, p<0.0001). [Figure 5-2](A) Overview of the SKG model used to evaluate the therapeutic efficacy of I. colisanans. (B) Curdlan treatment increases histopathological scores, which are ameliorated by treatment with anti-IL-23 antibody and I. colisanans. All data are presented as mean and standard deviation. All groups were compared to the curdlan + vehicle group using analysis of variance and Dunnett's test for multiple comparisons. (C) Curdlan treatment increases IL-6 and IL-12p70, which are ameliorated by treatment with I. colisanans. All data are presented as mean and standard deviation. For IL-6, all groups were compared to the curdlan + vehicle group using ordinary one-way analysis of variance and Dunnett's test for multiple comparisons. For IL-12p70, all groups were compared to the DSS + vehicle group using the Kruskal-Wallis test and Dunn's correction for multiple comparisons. For IL-6, all groups were compared to the Curdlan + Vehicle group using a regular one-way ANOVA test with Dunnett's test for multiple comparisons. For all data, ns is not significant; * is p<0.05; ** is p<0.01; *** is p<0.001, **** is p<0.0001. (E) Overview of the TNBS mouse model used to evaluate the therapeutic efficacy of I. colisanans MH27-2. (F) TNBS treatment increases the gross lesion histopathology score, which is improved by treatment with I. colisanans MH27-2 and Cyclosporine A. The TNBS + Vehicle group was compared to the I. colisanans MH27-2 and Cyclosporine A treated groups using a regular one-way ANOVA test with Sidak's multiple comparison correction. (G) Treatment with I. colisanans MH27-2 results in a significant improvement in the ulcer / inflammation score. TNBS + vehicle group was compared to I. colisanans MH27-2 and cyclosporine A treatment. (H) TNBS treatment increases the total histopathology score, which is ameliorated by treatment with I. colisanans MH27-2 and cyclosporine A.The TNBS + vehicle group was compared to the I. colisanans MH27-2 and cyclosporine A treated groups using Brown-Forsyth and Welch analysis of variance tests with Dunnett's T3 multiple comparison correction. (I-L) Treatment with I. colisanans MH27-2 results in significant improvements in the degree of inflammation, erosion or ulceration, epithelial regeneration, and percent lesion score. The TNBS + vehicle group was compared to the I. colisanans MH27-2 and cyclosporine A treated groups using Kruskal-Wallis tests with Dunn's multiple comparison tests. (M) Treatment with I. colisanans MH27-2 results in a significant reduction in IL-6 concentrations. The TNBS + vehicle group was compared to the I. colisanans MH27-2 and cyclosporine A treated groups. Data were log-transformed and analyzed using the Kruskal-Wallis test with Dunn's multiple comparison test and the usual one-way ANOVA test with Sidak's multiple comparison correction (ns, not significant; *, p<0.05; **, p<0.01; ***, p<0.001; ****, p<0.0001).

[0081] [Figure 6] 1 provides a graphical representation of I. colisanans MH27-1 and MH27-2 suppressing IL-6-mediated STAT3 activation in vitro. STAT3 signaling is inhibited when HEKBlue IL-6 reporter cells are treated with raw cell-free supernatant or <3 kDa fractionated culture supernatant of (A) I. colisanans MH27-1 and (B) 10% v / v MH27-2 (unpaired t-test, n=18), (C) MH27-3 (unpaired t-test, n=18), (D) MH27-4 v (unpaired t-test, n=18), (E) MH27-5 v (unpaired t-test, n=18), and (F) R. bromii MCB950 (unpaired t-test, n=12). STAT3 activation by IL-6 trans-signaling is inhibited by raw cell-free supernatant of I. colisanans MH27-2.

[0082] [Figure 7]Graphs showing that I. colisanans promotes migration of human intestinal epithelial cells are presented. (A) A transwell migration assay was used to study the effect of sterile culture supernatant extract from I. colisanans on migration of HCT116 colon cancer cells. In serum-starved conditions (0.5% FBS), addition of 0.5x extract of I. colisanans to the bottom of the chamber significantly increased migration of HCT116 cells towards the basolateral side compared to the medium extract control. (Untreated and medium controls n=6 technical replicates, I. colisanans n=4 technical replicates for 3 biological replicates each; unpaired t-test, two-tailed P>0.0001). (B) As a second readout for cell migration, an Incucyte scratch wound assay was performed. Relative wound confluence was measured every 2 hours after scratching the HCT116 cell monolayer. 24 hours after scratching, serum-starved HCT116 cells incubated in 0.3x extract from I. colisanans strain MH27-2 showed significantly higher wound confluence compared to cells treated with medium extract (one-way ANOVA followed by Dunnett's multiple comparison test, * indicates p<0.05).

[0083] [Figure 8] Figure 1 provides a graphical representation of MH27 suppressing IL-23-mediated STAT3 activation. STAT3 signaling is inhibited when the HEK-Blue™ IL 23 reporter cell line is treated with 25% cell-free supernatant or <3 kDa size fractionated I. colisanans, but not with R. bromii supernatant and similarly prepared YG / P medium. Samples were compared using an unpaired t-test (*** is p<0.001; ns is not significant). These data shown are the combined results of three independent experiments. Technical and biological replicates of raw and <3 kDa fractions were pooled together.

[0084] [Figure 9]After treatment with IFNγ (48 h treatment (grey area)), culture supernatant from I. colisanans MH27-2 ameliorated the decrease in TEER compared to YG / V medium control at 168, 192, 216, 240, 288, 312 and 336 h (p<0.05 by two-way ANOVA test). (▲) Untreated, (◆) IFNγ+I. colisanans MH27-2 extract, (·) IFNγ+medium extract, (square) IFNγ.

[0085] [Figure 10] Treatment with I. colisanans MH27-2 culture supernatant extract enhanced IL-6 (96 h treatment (grey area)) and mediated a dose-dependent decrease in TEER compared to media control. Statistical significance was determined by unpaired t-test. (▲) untreated, (◆) IL-6 + I. colisanans MH27-2 extract, (·) IL-6 + media extract, (square) IL-6.

[0086] [Figure 11] Graphs are provided showing that retreatment with I. colisanans MH27 extract ameliorates the decrease in IFNγ-induced ZO1 expression in T84 cells. (A) T84 cells were pretreated with YG / V medium control or extracts of I. colisanans MH27-1, MH27-2, or MH27-3 (1x), or left untreated for 18 h. Cells were then stimulated with recombinant IFNγ for 48 h, stained for ZO1, and imaged by confocal microscopy. Scale bars represent 10 μm. (B) Quantification of the relative brightness of ZO1 normalized to unstimulated cells reveals that pretreatment with I. colisanans MH27 extract significantly attenuates the decrease in IFNγ-induced ZO1 expression in T84 cells. Data are the mean ± SD of one experiment and four replicates. One-way ANOVA with Dunnett's correction for multiple comparisons, *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001.

[0087] [Figure 12]Figure 1 provides a graph showing that pretreatment with I. colisanans MH27 fraction ameliorates the decrease in IFNγ-induced ZO1 expression in T84 cells. Effect of fractionated (A) YG / V and (B) I. colisanans MH27-2 extracts on ZO1 expression. Scale bar represents 40 μm. (C) Quantification of relative intensity of ZO1 normalized to unstimulated cells reveals that pretreatment with 15% and 30% fractions of I. colisanans MH27-2 extract significantly attenuates the decrease in IFNγ-induced ZO1 expression in T84 cells. Data are mean ± SD of one experiment and four replicates. One-way ANOVA with Dunnett's correction for multiple comparisons, ***p<0.001, ****p<0.0001.

[0088] [Figure 13] Graphs showing that I. colisanans MH27-produced metabolites ameliorate the decrease in IFNγ-induced ZO1 expression in T84 cells. (A) T84 cells were pretreated with ornithine, indole-3-acrylic acid (IAyA), or indole-3-propionic acid (IPA) or left untreated for 18 h. Cells were then stimulated with recombinant IFNγ for 48 h, stained for ZO1, and imaged by confocal microscopy. Scale bars represent 10 μm. (B) Quantification of the relative intensity of ZO1 normalized to unstimulated cells reveals that pretreatment with all investigated metabolites significantly attenuates the decrease in IFNγ-induced ZO1 expression in T84 cells.) Data are the mean ± SD of one experiment and four replicates. One-way ANOVA with Dunnett's correction for multiple comparisons, **p<0.01, ***p<0.001, ****p<0.0001. (C) Cyclo(-Phe-Pro) (CPP) inhibits IL-23-mediated STAT3 activation compared to vehicle control. Data are the mean ± SD of three experiments. Data were analyzed using an unpaired t-test. **** indicates p<0.0001.

[0089] [Figure 14]IL-10 / IL-12 ratios of PBMC stimulated with I. colisanans. Data are the mean and SD of single experiments.

[0090] [Figure 15] Treatment of the LS174T-NF-κB cell line with 25% cell-free or <3 kDa size-fractionated I. colisanans supernatant inhibits NF-κB activation compared to similarly prepared medium (A–C), whereas R. bromii MCB950 cell-free supernatant does not inhibit NF-κB activation (D). Samples were compared using unpaired t-tests (*, p<0.05; **, p<0.01; ***, p<0.001; ****, p<0.0001 ns, not significant). Data shown are the combined results of three independent experiments.

[0091] [Figure 16-1] I. colisanans MH27-4 (A), MH27-5 (B), MH27-6 (C) and R. bromii MCB950 (D) were isolated using a gating strategy on a CytoFLEX SRT Benchtop cell sorter. [Figure 16-2] I. colisanans MH27-4 (A), MH27-5 (B), MH27-6 (C) and R. bromii MCB950 (D) were isolated using a gating strategy on a CytoFLEX SRT Benchtop cell sorter. [Figure 16-3] I. colisanans MH27-4 (A), MH27-5 (B), MH27-6 (C) and R. bromii MCB950 (D) were isolated using a gating strategy on a CytoFLEX SRT Benchtop cell sorter. [Figure 16-4] I. colisanans MH27-4 (A), MH27-5 (B), MH27-6 (C) and R. bromii MCB950 (D) were isolated using a gating strategy on a CytoFLEX SRT Benchtop cell sorter. [Table 1] DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0092] 1.Definition Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by those skilled in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, preferred methods and materials are described. For purposes of the present invention, the following terms are defined below.

[0093] The articles "a" and "an" are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, "an element" means one element or more than one element.

[0094] The term "about" as used herein refers to the normal error range for the respective value, which is readily known to one of ordinary skill in the art. Reference herein to "about" a value or parameter includes (and describes) embodiments that are directed to the value or parameter itself.

[0095] As used herein, the term "administering" refers to the placement of an agent (e.g., a bacterium) disclosed herein into a subject by a method or route that results in at least partial delivery of the agent at a desired site. Compositions including compounds disclosed herein can be administered by any suitable route that results in an effective biological activity or therapeutic effect in a subject. In some embodiments, administration includes human physical activity (e.g., injection, ingestion, application, and / or operation of a delivery device or machine). Such activity can be performed (e.g., by a medical professional and / or the subject being treated).

[0096] Specifically, as used herein, "administering" and "administration" encompass embodiments in which one person instructs another person to ingest live bacteria, killed bacteria, spent media from bacteria, bacterial cell pellets, purified metabolic products produced by bacteria, purified proteins produced by bacteria, prebiotics, small molecules, or combinations thereof, in a particular manner and / or for a particular purpose, independent of or distinct from any instructions received from the second person. Non-limiting examples of embodiments include situations in which one person instructs another person to take live bacteria, killed bacteria, spent media derived from bacteria, bacterial cell pellets, purified metabolites produced by bacteria, purified proteins produced by bacteria, prebiotics, small molecules, or combinations thereof in a particular manner and / or for a particular purpose, including when a physician prescribes a course of action and / or treatment to a patient, when a parent instructs a minor user (such as a child) to take such a product, when a trainer advises a user (such as an athlete) to follow a particular course of action and / or treatment, or when a manufacturer, distributor, or marketer recommends conditions of use to an end user, for example, through advertising or labeling on packaging or other materials provided in connection with the sale or marketing of the product. In some embodiments, the disclosed compositions can be administered orally, intravenously, intramuscularly, intrathecally, subcutaneously, sublingually, buccally, rectally, vaginally, ocularly, ocularly, nasally, by inhalation, aerosol, dermal, transdermal, or combinations thereof, and can be formulated for delivery with a pharma- ceutically acceptable excipient, carrier, or diluent. Of note, while the disclosed compositions encompass multiple formulations and delivery modes for treatments to ameliorate dysbiosis and its sequelae, it is noted that live bacterial preparations such as probiotics are not typically administered intravenously, intramuscularly, or intraperitoneally. These delivery modes are likely reserved for small molecule products of bacterial metabolism.

[0097] Terms such as "concurrent administration" or "administering simultaneously" or "co-administration" refer to administration of a single composition containing two or more actives, or administration of each active delivered contemporaneously or simultaneously or sequentially by separate routes within a sufficiently short period of time that effective results are comparable to those obtained when all such actives are administered as a single composition. "Concurrently" means that the actives are administered together at substantially the same time, preferably in the same formulation. "Concurrently" means that the actives are administered close in time, for example, one agent is administered within about one minute to about one day before or after another agent. Any contemporaneity is useful. However, when not administered simultaneously, the agents are often administered within about one minute to about eight hours, preferably within about less than one hour to about four hours. When administered simultaneously, the agents are preferably administered at the same site on the subject. The term "same site" includes the exact same location, but may be within about 0.5 to about 15 centimeters, preferably within about 0.5 to about 5 centimeters. The term "separately" as used herein means that the active agents are administered at intervals, for example, from about one day to several weeks or months. The active agents may be administered in any order. The term "sequentially" as used herein means that the active agents are administered consecutively, for example, at intervals of minutes, hours, days, or weeks. Optionally, the active agents may be administered in a regular repeating cycle.

[0098] The term "agent" includes compounds that induce a desired pharmacological and / or physiological effect. The term also encompasses pharma- ceutically acceptable and pharmacologically active components of the compounds specifically referred to herein, including, but not limited to, salts, esters, amides, prodrugs, active metabolites, analogs, and the like. When the above term is used, it should be understood to include the active agent itself, as well as pharma- ceutically acceptable and pharmacologically active salts, esters, amides, prodrugs, metabolites, analogs, and the like. The term "agent" should not be construed narrowly, but extends to small molecules, proteinaceous molecules, such as peptides, polypeptides, and proteins, and compositions containing them, as well as genetic molecules, such as RNA, DNA, and mimetics and chemical analogs thereof, and cellular agents. The term "agent" includes cells capable of producing and secreting the polypeptides referred to herein, as well as polynucleotides comprising nucleotide sequences encoding the polypeptides. Thus, the term "agent" extends to nucleic acid constructs, including vectors, such as viral or non-viral vectors, expression vectors, and plasmids, for expression and secretion in various cells.

[0099] The "amount" or "level" of a biomarker is the detectable level in a sample. These can be measured by methods known to those of skill in the art and disclosed herein. The expression level or amount of the assessed biomarker can be used to determine response to treatment.

[0100] As used herein, "and / or" refers to and includes any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (or).

[0101] The term "anaerobic" means not requiring oxygen for growth. Anaerobic bacterial strains include bacterial strains that are obligate anaerobes (i.e., those that are harmed by the presence of oxygen), aerotolerant anaerobes (i.e., those that cannot use oxygen to grow but can tolerate its presence), and facultative anaerobes (i.e., those that can grow without oxygen but can use oxygen if it is present).

[0102] "Anaerobic conditions" are defined as conditions in which the oxygen concentration in the fermentation medium is too low for the microorganism to use it as a terminal electron acceptor. "Anaerobic conditions" can be further defined as conditions in which no or only a small amount of oxygen is added to the medium at a rate of less than 3 mmol / L / h, preferably less than 2.5 mmol / L / h, more preferably less than 2 mmol / L / h, and most preferably less than 1.5 mmol / L / h. "Anaerobic conditions" in particular means a completely oxygen-free (=0 mmol / L / h oxygen) or a small amount of oxygen is added to the medium at a rate of, for example, less than 0.5 to less than 1 mmol / L / h. "Anaerobic metabolism" refers to biochemical processes in which oxygen is not the final acceptor of the electrons contained in NADH. Anaerobic metabolism can be divided into anaerobic respiration, in which compounds other than oxygen are the final electron acceptors, and substrate-level phosphorylation, in which electrons from NADH are utilized to generate reduced products via fermentation pathways.

[0103] The term "carbon source" generally refers to a substrate or compound suitable for supporting the growth of microorganisms. Carbon sources can be in various forms, including but not limited to polymers, carbohydrates, alcohols, acids, aldehydes, ketones, amino acids, peptides, and the like. For example, they can include monosaccharides (glucose, fructose, xylose, and the like), oligosaccharides (i.e., sucrose, lactose), polysaccharides (i.e., starch, cellulose, hemicellulose), lignocellulosic materials, fatty acids (i.e., succinic acid, lactic acid, acetic acid), glycerol, and the like, or mixtures thereof. Carbon sources can also be photosynthetic products, such as glucose or cellulose.

[0104] Monosaccharides used as carbon sources may be hydrolysates of polysaccharides, such as acid or enzymatic hydrolysates of cellulose, starch and pectin. The term "energy source" may be used interchangeably herein with carbon source, since in chemoorganotrophic metabolism, the carbon source is used as an electron donor during catabolism and as a carbon source during cell growth.

[0105] Throughout this specification, unless the context requires otherwise, the words "comprise", "comprises" and "comprising" are understood to mean the inclusion of the recited step or element or group of steps or elements, but not the exclusion of any other step or element or group of steps or elements. Thus, the use of terms such as "comprising" indicates that the recited elements are required or essential, while other elements are optional and may or may not be present. "Consisting of" means including and limited to what follows the phrase "consisting of". Thus, the phrase "consisting of" indicates that the recited elements are required or essential, and other elements may not be present. "Consisting essentially of" means including any elements recited following this phrase, with other elements limited to those that do not interfere with or contribute to the activity or function specified in this disclosure for the recited elements. Thus, the phrase "consisting essentially of" indicates that the recited elements are required or essential, but other elements are optional and may or may not be present depending on whether they affect the activity or function of the recited elements.

[0106] As used herein, "culturing," "culture," and the like, refer to a set of procedures used in vitro in which a population of cells (or a single cell) is incubated under conditions shown to support the growth or maintenance of cells in vitro. The art recognizes the numerous formats, media, temperature ranges, gas concentrations, and the like that need to be defined in a culture system. Parameters will vary based on the format selected and the particular needs of the individual practicing the methods disclosed herein. However, it is recognized that the determination of culture parameters is routine in nature.

[0107] The terms "reduction", "decrease", "reduction", "inhibition", "suppression", "attenuation" and the like are all used herein to mean a statistically significant amount of reduction. In some embodiments, these terms typically mean a reduction of at least 10% compared to a reference level (e.g., the absence of a given treatment or agent), and can include, for example, a reduction of at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, at least about 99% or more. As used herein, "reduction", "suppression", and "inhibition" do not require complete inhibition or reduction compared to a reference level. "Complete inhibition", and the like, is 100% inhibition compared to a reference level. Preferably, the decrease is to a level that is accepted as within the normal range (eg, for individuals without a given disorder).

[0108] The terms "increased," "increase," "enhancement," or "activation" are all used herein to mean an increase by a statistically significant amount. In some embodiments, the terms "increased," "increase," "enhancement," or "activation" can refer to an increase of at least 10% as compared to a reference level (e.g., in the absence of a given treatment or agent), including, for example, an increase of at least about 10% as compared to a reference level, e.g., an increase of at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, at least about 99%, or up to and including 100% as compared to a reference level, or any increase between 10-100% as compared to a reference level, or an increase of at least about 2-fold, or at least about 3-fold, or at least about 3-fold, or at least about 4-fold, or at least about 5-fold, or at least about 10-fold as compared to a reference level, or any increase between 2-fold and 10-fold as compared to a reference level. In the context of a marker or condition, an "increase" is a statistically significant increase in such level.

[0109] As used herein, the term "isolated" encompasses bacteria or other entities or substances that (1) have been separated from at least some of the components with which they were originally associated when produced (whether in nature, such as human feces, or in an experimental environment, such as a petri plate dish of artificial growth medium), and / or (2) have been produced, prepared, purified, and / or manufactured by the hand of man. Isolated bacteria, proteins, metabolites, or combinations thereof may be separated from at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or more of the other components with which they were originally associated. In some embodiments, isolated bacteria, proteins, metabolites, or combinations thereof are greater than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or greater than about 99% pure. As used herein, a material is "pure" if it is substantially free of other components (such as other bacterial species). The terms "purify", "purifying" and "purified" refer to a bacterium or other material that has been separated from at least some of the components with which it was associated when it was first produced or produced (e.g., in nature or in a laboratory environment) or at any time after it was first produced, as recognized by those skilled in the art of bacterial culture or related technology (e.g., chemistry). A bacterium or bacterial population can be considered purified if it is isolated from, for example, a material or environment that contains the bacterium or bacterial population at the time or after it is produced; a purified bacterium or bacterial population may contain up to about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90% or more than about 90% other materials and still be considered "isolated". In some embodiments, purified bacteria and bacterial populations are greater than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99% or greater than about 99% pure. In the case of bacterial compositions provided herein, one or more bacterial types present in the composition may be purified independently from one or more other bacteria produced and / or present in the material or environment that contains the bacterial types.In some embodiments, a bacterium or bacterial population is "isolated" if it comprises a single strain of bacteria. In some embodiments, such isolated bacteria can be mixed or administered with other isolated bacteria (e.g., in a defined consortium of isolated bacteria). Bacterial compositions and their bacterial components are generally purified from residual habitat products.

[0110] The term "genome" as used herein includes DNA that contains genes (coding nucleic acid sequences) and non-coding nucleic acid sequences of a microorganism, and thus includes, for example, the introduction of a nucleic acid into the coding and non-coding DNA of a microorganism.

[0111] The term "gram indeterminate" refers to giving a positive and / or negative result in the Gram stain test (i.e., retaining the color of the crystal violet stain). Retention of crystal violet stain by bacteria is related to the thickness of the peptidoglycan layer of the bacterial cell wall. Gram-positive bacteria have a thicker peptidoglycan layer. Gram staining is commonly used to aid in the classification of bacterial strains in the field of microbiology.

[0112] As used herein, the term "intestinal tract" is understood to refer to the human gastrointestinal tract, also known as the digestive tract. The intestinal tract includes the oral cavity, pharynx, esophagus, stomach, small intestine (duodenum, jejunum, ileum), large intestine (cecum and colon) and rectum. Although the entire digestive tract can be colonized by various species of microorganisms, the majority of the gut microbiome, both in terms of number of species and biomass, resides in the intestine (small intestine and large intestine).

[0113] The terms "marker", "biomarker" and the like refer to any compound that can be measured as an indicator of the physiological state of a biological system. The marker can be a biomarker, including amino acid sequences, nucleic acid sequences and fragments thereof. Exemplary biomarkers include, but are not limited to, cytokines, chemokines, growth factors and angiogenesis factors, metastasis-associated molecules, cancer antigens, apoptosis-associated proteins, enzymes, proteases, adhesion molecules, cell signaling molecules and hormones. The marker can also be, in some embodiments, a sugar that cannot be significantly metabolized in the biological system. The sugar can be, for example, mannitol, lactulose, sucrose, sucralose, and any combination of the foregoing.

[0114] "Measuring" or "measurement" means assessing the presence, absence, quantity or amount (which may be an effective amount) of a given substance in a sample, including deriving a qualitative or quantitative concentration level of such substance, or otherwise assessing the value or classification of a clinical parameter of interest. Alternatively, the terms "assaying," "detecting," or "detection" may be used to refer to all measuring or measurements described herein.

[0115] The term "mucosal healing" as used herein refers to the improvement of one or more characteristics that indicate damage to the mucosal layer. Such characteristics are usually determined by colonoscopy and include, but are not limited to, redness, loss of vascular image, fragility, bleeding, erosion and ulceration. In some circumstances, mucosal healing refers to the complete improvement of the adverse effects that characterize the damage to the mucosal layer. Alternatively, mucosal healing may refer to the reduction or improvement of one or more negative effects that characterize the damage to the mucosal layer.

[0116] As used herein, the term "pharmaceutical composition" refers to an active agent in combination with a pharma- ceutically acceptable carrier (e.g., a carrier commonly used in the pharmaceutical industry). The phrase "pharmaceutically acceptable" is used herein to refer to compounds, materials, compositions, and / or dosage forms that are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and animals without undue toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit / risk ratio. In some embodiments of any aspect, the pharma- ceutically acceptable carrier can be a carrier other than water. In some embodiments of any aspect, the pharma- ceutically acceptable carrier can be a cream, emulsion, gel, liposome, nanoparticle, and / or ointment. In some embodiments of any aspect, the pharma- ceutically acceptable carrier can be an artificial or engineered carrier (e.g., a carrier in which the active ingredient is not found to occur naturally or in nature).

[0117] The term "phylogenetic tree" refers to a graphical representation of the evolutionary relationships of one genetic sequence to another, generated using a defined set of phylogenetic tree reconstruction algorithms (e.g., parsimony, maximum likelihood, Bayesian). The nodes in the tree represent different ancestral sequences, and the reliability of any node is provided by bootstrap or Bayesian posterior probabilities, which measure the uncertainty of the branches.

[0118] In some embodiments, the term "strain" refers to a terminal leaf in a phylogenetic tree and is defined by a specific gene sequence, which may be a concatenated alignment of 120 ubiquitous single-copy proteins (Parks et al. 2018) extracted from a genome assembly using GTDB-tk (Chaumeil et al. 2020) or other tools known in the art.

[0119] The term "clade" refers to a set of phylogenetic tree members downstream of a stable node (bootstrap value >90%) in the phylogenetic tree. A clade is a group of related organisms that represent all phylogenetic descendants of a common ancestor. A clade contains a set of terminal leaves that are separate monophyletic evolutionary units in the phylogenetic tree.

[0120] As used herein, "prebiotics" is understood to mean ingredients that allow certain changes in both composition and / or activity in the gastrointestinal microflora that may (or may not) benefit the host. Preferred prebiotics are those that promote the growth or beneficial function of the probiotic composition, but do not promote the growth of pathogens or genes associated with virulence (e.g., toxins).

[0121] As used herein, "probiotics" is understood to mean "live microorganisms that, when administered in adequate amounts, confer a beneficial health effect on the host," as currently defined by the World Health Organization.

[0122] The term "species" is defined as a collection of closely related organisms that have greater than 97% 16S ribosomal RNA (rRNA) sequence homology and greater than 70% genomic hybridization and are sufficiently distinct from all other organisms to be recognized as a separate unit. Species and other phylogenetic identifications follow classifications known to those skilled in the art of microbiology.

[0123] As used herein, "subject" refers to a human or an animal. Typically, an animal is a vertebrate, such as a primate, a rodent, a livestock or a game animal. Primates include chimpanzees, cynomolgus monkeys, spider monkeys, and macaques (e.g., rhesus monkeys). Rodents include mice, rats, woodchucks, ferrets, rabbits, and hamsters. Livestock and game animals include cows, horses, pigs, deer, bison, buffalo, feline species (e.g., house cats), canine species (e.g., dogs, foxes, wolves), avian species (e.g., chickens, emus, ostriches), and fish (e.g., trout, catfish, and salmon). In some embodiments, the subject is a mammal (e.g., a primate (e.g., a human)). The terms "individual," "patient," and "subject" are used interchangeably herein.

[0124] Preferably, the subject is a mammal. The mammal may be, but is not limited to, a human, a non-human primate, a mouse, a rat, a dog, a cat, a horse, or a cow. Non-human mammals can be advantageously used as subjects representing animal models of inflammatory and autoimmune disorders (e.g., models of intestinal barrier function). The subject may be male or female.

[0125] As used herein, the terms "treat", "treatment", "treating" and the like refer to therapeutic treatments whose purpose is to reverse, alleviate, ameliorate, inhibit, slow down, or stop the progression or severity of a condition associated with a disease or disorder (e.g., an inflammatory or autoimmune disorder). The term "treating" includes reducing or alleviating at least one adverse effect or symptom of a condition, disease or disorder associated with an inflammatory or autoimmune disorder. A treatment is generally "effective" if one or more symptoms or clinical markers are reduced. Alternatively, a treatment is "effective" if the progression of the disease is reduced or stopped. That is, "treatment" includes not only the improvement of symptoms or markers, but also the halting or at least slowing of the progression or worsening of symptoms compared to that expected in the absence of treatment. Beneficial or desired clinical outcomes include, but are not limited to, alleviation of one or more symptoms, reduction in the extent of the disease, stabilization (i.e., not worsening) of the disease state, delay or slowing of disease progression, improvement or alleviation of the disease state, remission (whether partial or total), and / or reduced mortality (whether detectable or undetectable). The term "treatment" of a disease also includes providing relief from the symptoms or side effects of the disease (including palliative treatment). Treatment does not need to cure the disorder (i.e., complete reversal or absence of the disease) to be considered effective.

[0126] In some embodiments, sequencing includes 16S rRNA gene sequencing, which may also be referred to as "16S ribosomal RNA sequencing," "16S rDNA sequencing," or "16S rRNA sequencing." Sequencing of the 16S rRNA gene can be used for genetic research because it is highly conserved among different bacterial species, but absent in eukaryotic species. In addition to the highly conserved regions, the 16S rRNA gene also contains nine hypervariable regions (V1-V9) that differ between species. 16S rRNA gene sequencing typically involves PCR amplification of a bacterial 16S rRNA gene region (including the hypervariable region) using multiple universal primers that bind to conserved regions of the 16S rRNA gene, and sequencing the amplified 16S rRNA gene with next-generation sequencing techniques as described herein (see, e.g., U.S. Pat. Nos. 5,654,418, 6,344,316, and 8,889,358, as well as U.S. Patent Publication Nos. 2013 / 157,265 and 2018 / 195,111, each of which is incorporated by reference in its entirety).

[0127] Each embodiment described in this specification applies mutatis mutandis to all embodiments unless otherwise specified.

[0128] 2. Bacterial Strains The compositions of the present invention comprise a bacterial strain of the genus Intestinicoccus. The examples show that bacteria of this genus are useful for the treatment or prevention of diseases associated with impaired intestinal barrier function. A preferred bacterial strain is of the I. colisanans species.

[0129] Intestinicoccus is a genus of bacteria in the class firmicutes. The scientific classification is: Bacteria (kingdom); Firmicutes (phylum); Clostridia (class); Oscillospirales (order); Acutalibacteraceae (family); Intestinicoccus (genus). Bacteria within the genus Intestinicoccus are gram-variable, have a coccus-like shape, and are obligate anaerobes. These criteria are important because they can inform the phylogenetic classification of bacterial strains.

[0130] The species I. colisanans has not been previously described. It was isolated from a human fecal sample using the methods described in the Examples below.

[0131] The scope of the genus Intestinicoccus and the species I. colisanans may be defined by the Genome Taxonomy Database reference tree, a classification system described in Parks et al., 2018.

[0132] The I. colisanans bacterium (i.e., I. colisanans MH27-1) deposited under the accession number V21 / 015887 is tested in the examples and is one of the preferred strains of the present invention. I. colisanans strain MH27-1 was deposited by Microba IP Pty Ltd (388 Queen Street, Brisbane, Queensland 4000, Australia) on August 6, 2021 with the international depository authority National Measurement Institute (NMI, 1 / 153 Bertie Street, Port Melbourne, Victoria, 3207, Australia) as "Intestinicoccus colisanans MH27-1" and assigned the accession number deposited under the accession number V21 / 015887.

[0133] An exemplary 16S rRNA sequence for the tested I. colisanans strain MH27-1 is set forth in SEQ ID NO:1. A bacterial strain of the I. colisanans species may contain a single 16S rRNA sequence in its genome, or may contain two or more 16S rRNA sequences in its genome (e.g., 2 copies, 3 copies, 4 copies, 5 copies, 6 copies, 7 copies, 8 copies, or more than 8 copies). In some embodiments, a bacterial strain may be identified as I. colisanans strain MH27-1 by determining whether the strain contains a 16S rRNA sequence corresponding to SEQ ID NO:1 by any method known in the art. The chromosomal sequence of I. colisanans strain MH27-1 is provided in SEQ ID NO:3 and SEQ ID NO:4. These sequences were generated using the Illumina NovSeq6000 platform.

[0134] Bacterial strains closely related to strain MH27-1 are also shown in the Examples to be effective in the treatment or prevention of inflammatory and autoimmune disorders through their beneficial effects on restoring intestinal barrier function.

[0135] For example, the I. colisanans bacterium deposited under accession number V21 / 015888 (i.e., I. colisanans MH27-2) was tested in the Examples and is another of the preferred strains of the present invention. An exemplary 16S rRNA sequence for the tested I. colisanans MH27-2 strain is set forth in SEQ ID NO: 2. In some embodiments, a bacterial strain can be identified as I. colisanans MH27-2 strain by determining whether the strain contains a 16S rRNA sequence corresponding to SEQ ID NO: 2 by any method known in the art. I. colisanans strain MH27-2 was deposited with the international depository authority National Measurement Institute (NMI, 1 / 153 Bertie Street, Port Melbourne, Victoria, 3207, Australia) on August 6, 2021 as "Intestinicoccus colisanans MH27-2" by Microba IP Pty Ltd (388 Queen Street, Brisbane, QLD 4000, Australia) and assigned the accession number V21 / 015888. The genome of I. colisanans strain MH27-2 comprises a chromosome having a sequence set forth in one or both of SEQ ID NOs: 5 or 6.

[0136] In other examples, exemplary 16S rRNA sequences for I. colisanans strains MH27-3, MH27-4, MH27-5, and MH27-6 tested in the Examples are set forth in SEQ ID NOs: 7-10. In some embodiments, a bacterial strain may be identified as I. colisanans strain MH27-3 by determining whether the strain contains a 16S rRNA sequence corresponding to SEQ ID NO: 7, by any method known in the art. In some embodiments, a bacterial strain may be identified as I. colisanans strain MH27-4 by determining whether the strain contains a 16S rRNA sequence corresponding to SEQ ID NO: 8, by any method known in the art. In some embodiments, a bacterial strain may be identified as I. colisanans strain MH27-5 by determining whether the strain contains a 16S rRNA sequence corresponding to SEQ ID NO: 9, by any method known in the art. In some embodiments, a bacterial strain can be identified as I. colisanans strain MH27-6 by determining whether the strain contains a 16S rRNA sequence corresponding to SEQ ID NO:10 by any method known in the art.

[0137] The genome of I. colisanans strain MH27-3 comprises a chromosome having a sequence set forth in one or more of SEQ ID NOs: 11-14. The genome of I. colisanans strain MH27-4 comprises a chromosome having a sequence set forth in one or more of SEQ ID NOs: 15-18. The genome of I. colisanans strain MH27-5 comprises a chromosome having a sequence set forth in one or more of SEQ ID NOs: 19-22.

[0138] In certain embodiments, the bacterial strains of the invention have a 16S rRNA sequence that is at least 97.5%, 98%, 98.5%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to the 16S rRNA sequence of a bacterial strain of I. colisanans. Preferably, the bacterial strains of the invention have a 16S rRNA sequence that is at least 97.5%, 98%, 98.5%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to any one of SEQ ID NOs: 1, 2, or 7-10. Some preferred bacterial strains of the invention have a 16S rRNA sequence as set forth by any one of SEQ ID NOs: 1, 2, or 7-10.

[0139] The genome of the bacterial strain may comprise a 16S rRNA sequence set forth in any one of SEQ ID NOs: 1, 2, or 7-10.

[0140] In certain embodiments, bacterial strains of the invention have a chromosome that has sequence identity to one or both of the sequences set forth in SEQ ID NO: 3 or 4. In preferred embodiments, bacterial strains of the invention have a chromosome that has at least 90% sequence identity (e.g., at least 92%, 94%, 95%, 96%, 97%, 97.5%, 98%, 98.5%, 99%, 99.5% or 100% sequence identity) to one or both of SEQ ID NO: 3 or 4 over at least 60% (e.g., at least 65%, 70%, 75%, 80%, 85%, 95%, 96%, 97%, 98%, 99% or 100%) of SEQ ID NO: 3 or 4. For example, a bacterial strain of the invention may have at least 90% sequence identity to one or both of SEQ ID NOs:3 or 4 across 70% of SEQ ID NOs:3 or 4, or at least 90% sequence identity to one or both of SEQ ID NOs:3 or 4 across 80% of SEQ ID NOs:3 or 4, or at least 90% sequence identity to one or both of SEQ ID NOs:3 or 4 across 90% of SEQ ID NOs:3 or 4, or at least 90% sequence identity to one or both of SEQ ID NOs:3 or 4 across 100% of SEQ ID NOs:3 or 4, or at least 95% sequence identity to one or both of SEQ ID NOs:3 or 4 across 70% of SEQ ID NOs:3 or 4, or at least 95% sequence identity to one or both of SEQ ID NOs:3 or 4 across 80% of SEQ ID NOs:3 or 4, or a chromosome having at least 95% sequence identity to one or both of SEQ ID NOs:3 or 4 across 90% of SEQ ID NO:3 or 4, or at least 95% sequence identity to one or both of SEQ ID NOs:3 or 4 across 100% of SEQ ID NO:3 or 4, or at least 98% sequence identity to one or both of SEQ ID NOs:3 or 4 across 70% of SEQ ID NO:3 or 4, or at least 98% sequence identity to one or both of SEQ ID NOs:3 or 4 across 80% of SEQ ID NO:3 or 4, or at least 98% sequence identity to one or both of SEQ ID NOs:3 or 4 across 90% of SEQ ID NO:3 or 4, or at least 98% sequence identity to one or both of SEQ ID NOs:3 or 4 across 100% of SEQ ID NO:3 or 4.A particularly preferred strain of the present invention is the I. colisanans strain deposited under accession number V21 / 015887. This is an exemplary strain MH27-1 that has been tested in the DSS mouse model shown in the Examples and has been shown to be effective in treating disease. Thus, the present invention provides cells, e.g., isolated cells, of the I. colisanans strain deposited under accession number V21 / 015887 or a derivative thereof. The present invention also provides compositions comprising cells of the I. colisanans strain deposited under accession number V21 / 015887 or a derivative thereof. The present invention also provides biologically pure cultures of the I. colisanans strain MH27-1 deposited under accession number V21 / 015887.

[0141] In certain embodiments, bacterial strains of the invention have a chromosome with sequence identity to SEQ ID NO: 5 or 6. In preferred embodiments, bacterial strains of the invention have a chromosome with at least 90% sequence identity (e.g., at least 92%, 94%, 95%, 96%, 97%, 97.5%, 98%, 98.5%, 99%, 99.5% or 100% sequence identity) to one or both of SEQ ID NO: 5 or 6 over at least 60% (e.g., at least 65%, 70%, 75%, 80%, 85%, 95%, 96%, 97%, 98%, 99% or 100%) of SEQ ID NO: 5 or 6. For example, a bacterial strain of the invention may have at least 90% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 70% of SEQ ID NOs: 5 or 6, or at least 90% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 80% of SEQ ID NOs: 5 or 6, or at least 90% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 90% of SEQ ID NOs: 5 or 6, or at least 90% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 100% of SEQ ID NOs: 5 or 6, or at least 95% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 70% of SEQ ID NOs: 5 or 6, or at least 95% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 80% of SEQ ID NOs: 5 or 6, or a chromosome having at least 95% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 90% of SEQ ID NO: 5 or 6, or at least 95% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 100% of SEQ ID NO: 5 or 6, or at least 98% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 70% of SEQ ID NO: 5 or 6, or at least 98% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 80% of SEQ ID NO: 5 or 6, or at least 98% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 90% of SEQ ID NO: 5 or 6, or at least 98% sequence identity to one or both of SEQ ID NOs: 5 or 6 across 100% of SEQ ID NO: 5 or 6.A particularly preferred strain of the present invention is the I. colisanans strain deposited under accession number V21 / 015888. This is an exemplary MH27-2 strain that has been tested in the DSS mouse model shown in the Examples and has been shown to be effective in treating disease. Thus, the present invention provides cells, e.g., isolated cells, of the I. colisanans strain deposited under accession number V21 / 015888 or a derivative thereof. The present invention also provides compositions comprising cells of the I. colisanans strain deposited under accession number V21 / 015888 or a derivative thereof. The present invention also provides biologically pure cultures of the I. colisanans strain MH27-2 deposited under accession number V21 / 015888.

[0142] A derivative of the strain deposited under accession number V21 / 015887 or V21 / 015888 may be a daughter strain (progeny) or a strain cultivated (subcloned) from the original strain. A derivative of the strain of the present invention may be modified, for example at the genetic level, without eliminating biological activity. In particular, a derivative of the present invention is therapeutically active. A derivative has an activity equivalent to the original strain from which it is derived (i.e., the strain deposited under accession number V21 / 015887 or V21 / 015888). In particular, a derivative exerts an equivalent effect in at least one disease model (e.g., colitis), as shown in the examples, which can be identified by using the cultivation and administration protocols described in the examples. A derivative of any one of the V21 / 015887 or V21 / 015888 strains is generally a biotype of the V21 / 015887 or V21 / 015888 strain, respectively.

[0143] Reference to cells of the I. colisanans strain deposited under accession number V21 / 015887 includes any cells having the same safety and therapeutic efficacy characteristics as the strains deposited under any one of accession numbers V21 / 015887 or V21 / 015888, and such cells are encompassed by the present invention.

[0144] 2.1 Bacterial biotypes Bacterial strains that are biotypes of the bacteria deposited under accession numbers V21 / 015887 or V21 / 015888 are also expected to be effective in the treatment or prevention of inflammatory and autoimmune disorders. Biotypes are closely related strains that have identical or very similar physiological and biochemical properties.

[0145] A biotype of the bacteria deposited under accession number V21 / 015887 or V21 / 015888 and suitable for use in the present invention may be identified by sequencing other nucleotide sequences of the bacteria deposited under accession number V21 / 015887 or V21 / 015888. For example, substantially the entire genome may be sequenced, and a biotype strain of the present invention may have at least 95%, 96%, 97%, 98%, 99%, 99.5% or 99.9% sequence identity over at least 80% of its entire genome (e.g., over at least 85%, 90%, 95% or 99%, or over its entire genome). Other sequences suitable for use in identifying biotype strains may include hsp60, or repetitive sequences such as BOX, ERIC, (GTG)5, or REP (Masco et al., 2003; Kim et al., 2019). A biotype strain may have a sequence that has at least 95%, 96%, 97%, 98%, 99%, 99.5% or 99.9% sequence identity to the corresponding sequence of the bacterium deposited under accession number V21 / 015887 or V21 / 015888.

[0146] Alternatively, by using a strain that is a bacterial biotype deposited under accession numbers V21 / 015887 or V21 / 015888, and restriction fragment analysis and / or PCR analysis, such as fluorescent amplified fragment length polymorphism (FAFLP) and repetitive DNA element (rep)-PCR fingerprinting, or protein profiling, or partial 16S or 23s rRNA sequencing. In some preferred embodiments, such techniques can be used to identify other suitable I. colisanans strains.

[0147] In certain embodiments, strains that are biotypes of the bacteria deposited under accession numbers V21 / 015887 or V21 / 015888 and suitable for use in the present invention are those that, when analyzed by amplified ribosomal DNA restriction analysis (ARDRA), for example when using the Sau3AI restriction enzyme (see Srutkova et al., 2011 for exemplary methods and guidance), provide the same pattern as the bacteria deposited under accession numbers V21 / 015887 or V21 / 015888. Alternatively, biotype strains are identified as strains that have the same carbohydrate fermentation pattern as the bacteria deposited under accession numbers V21 / 015887 or V21 / 015888.

[0148] In some embodiments, bacterial strains useful in the present invention can be identified by routine profiling of metabolic product production and consumption by bacterial strains. The bacterial strains described above and elsewhere herein are predicted to result in the production of acetate. Thus, in some embodiments, the bacterial strains of the present invention induce the in vivo production of the metabolic product acetate. Furthermore, in some embodiments, the bacterial strains of the present invention do not produce butyric acid.

[0149] Other Intestinicoccus strains useful in the compositions and methods of the invention, such as the biotypes of bacteria deposited under accession numbers V21 / 015887 or V21 / 015888, may be identified using any suitable method or strategy, including the assays described in the Examples. For example, strains for use in the invention may be identified by culturing in anaerobic TY or PYG medium and / or administering the bacteria to a DSS-induced intestinal barrier function model and then assessing cytokine / chemokine levels, as described in the Examples. In particular, bacterial strains with similar growth patterns, metabolic types and / or surface antigens to the bacteria deposited under accession numbers V21 / 015887 or V21 / 015888 may be useful in the present invention. Useful strains have immunomodulatory activity comparable to that of the V21 / 015887 or V21 / 015888 strains. In particular, biotype strains exert comparable effects on the intestinal function of the host. Additionally, biotypes are expected to have similar effects in disease models (e.g., colitis, asthma, arthritis, multiple sclerosis and uveitis disease models) and comparable effects on cytokine / chemokine levels to those shown in the Examples, which can be identified by using the culture and administration protocols described in the Examples.

[0150] 2.2 Viability of bacterial strains. In a preferred embodiment, the bacterial strain in the composition of the present invention is viable. In a preferred embodiment, the bacterial strain in the composition of the present invention is viable and can partially or completely colonize the intestine. In some preferred embodiments, the bacterial strain in the composition of the present invention is alive. As an example, the bacterial strain in the composition of the present invention is not heat-killed. The bacteria of the present invention may have an immunomodulatory effect that cannot be exhibited by non-viable bacteria, for example, because non-viable bacteria cannot produce metabolic products and interact with the immune system in a different manner. The cell surface of viable bacteria is also likely to be significantly different from dead bacteria, especially heat-killed bacteria.

[0151] In some alternative embodiments, the bacteria is non-viable, for example, in some embodiments the bacteria is heat killed.

[0152] In some preferred embodiments, the bacterial strains used in the present invention are naturally occurring, for example, the bacterial strains are isolated from the digestive tract of a mammal.

[0153] In some preferred embodiments, the bacterial strains used in the present invention are not genetically engineered, e.g., they have not been transformed with recombinant DNA.

[0154] 3. Composition Provided herein are compositions comprising, consisting of, or consisting essentially of a therapeutically effective amount of the bacterial strain(s) described above and / or elsewhere herein. In some embodiments, the bacteria in the composition may be identified by strain, species, operational taxonomic unit (OTU), whole genome sequence, 16S rRNA sequence, or other methods known in the art for defining different types of bacteria.

[0155] 3.1 Most Recent Common Ancestor (MRCA) In some embodiments, the composition comprises an effective amount of a bacterial strain that is a phylogenetic descendant of the MRCA of I. colisanans and I. sp002305575 (see FIG. 1B). Preferably, the phylogenetic classification is as defined by the GTDB (Parks et al., 2018). In some embodiments, the phylogenetic classification is as defined in release 89 (r89) of the GTDB.

[0156] In some embodiments, the determination of whether a bacterial strain is a descendant of the MRCA of I. colisanans and I. sp002305575 can be performed using phylogenetic grouping procedures known in the art. In some embodiments, a rooted phylogenetic tree including I. colisanans and I. sp002305575 and a third taxon of interest (e.g., the taxon to be classified) can be used, and the following analytical packages are applied to determine whether the taxon of interest is useful for the compositions of the present invention: Analyses of Phylogenetics and Evolution ("ape"; https: / / cran.r-project.org / web / packages / ape / index) and Phylogenetic Tool for Comparative Biology ("phytools"; http: / / cran.r-project.org / web / packages / phytools / index.html). Both ape and phytools are packages written in the R language used to study molecular evolution and phylogeny. The ape and phytools packages provide methods for phylogenetic and evolutionary analysis and their use is known to those of skill in the art. In some embodiments, the following scripts may be used: library("ape") library("phytools") input.tree = read.tree(file=”tree_file”) intest = c(“s__Intestinicoccus colisanans”, “s__Intestinicoccus sp002305575”) intest.node = getMRCA(input.tree, intest) intest.tree = extract.clade(input.tree, intest.node) print(intest.tree$tip.label)

[0157] In some embodiments, after running this script, if the taxon of interest is in the printed list, it is a descendant of the MRCA of the two species.

[0158] In other embodiments, various phylogenetic grouping methods known in the art can be used to determine whether a bacterial strain is a descendant of the MRCA of I. colisanans and (see FIG. 1B), including methods based on different programming languages ​​using different analysis packages.

[0159] In some other embodiments, the bacterial strain is a phylogenetic descendant of the MRCA of I. colisanans and I. sp002305575, together with a pharmaceutically acceptable carrier, diluent or excipient. Suitably, the MRCA is defined at node 23596 of the bac120 phylogenetic tree from GTDB. In some embodiments, the phylogenetic tree is generated by release 89 of the GTDB, although any suitable subsequent release is believed to provide equally applicable results.

[0160] 3.2 16S rRNA sequence identity. In some embodiments, a 16S rRNA sequence is obtained or determined for the bacterial species to be classified. The query 16S rRNA sequence is compared to 16S rRNA sequences from bacterial species already classified as members of the genus Intestinicoccus. In some embodiments, the query 16S rRNA sequence is compared to the 16S rRNA sequence set forth in SEQ ID NO: 1. In some embodiments, the query 16S rRNA sequence is compared to all known 16S rRNA sequences for bacterial species already classified as members of the genus Intestinicoccus. In other embodiments, the query 16S rRNA sequence is compared to a subset of all known 16S rRNA sequences for bacterial species already classified as members of the genus Intestinicoccus. The percent identity between the query sequence and the comparison sequence is determined. If the percent identity of the query sequence is determined to be above a defined threshold, the bacterial species to be classified is classified as a member of the genus Intestinicoccus.

[0161] In some embodiments, the threshold sequence identity is 95%. In some other embodiments, the threshold sequence identity is 97.5%. In some other embodiments, the threshold sequence identity is 99.0%. In some embodiments, the threshold sequence identity is 94.5%, 94.6%, 94.7%, 94.8%, 94.9%, 95.0%, 95.1%, 95.2%, 95.3%, 95.4%, 95.5%, 95.6%, 95.7%, 95.8%, 95.9%, 96.0%, 96.1%, 96.2%, 96.3%, 96.4%, 96.5%, 96.6%, 96.7%, 96.8%, 96.9%, 97.0%, 97.1%, 97.2%, 97.3%, 97.4%, 97.5%, 97.6%, 97.7%, 97.8%, 97.9%, 98.0%, 98.1%, 98.2%, 98.3%, 98.4%, 98.5%, 98.6%, 98.7%, 98.8%, 98 ...5%, 98.6%, 98.7%, 98.8%, 98. .1%, 97.2%, 97.3%, 97.4%, 97.5%, 97.6%, 97.7%, 97.8%, 97.9%, 98.0%, 98.1%, 98.2%, 98.3%, 98.4%, 98.5%, 98.6%, 98.7%, 98.8%, 98.9%99.0%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%.99.6%, 99.7%, 99.8%, 99.9% or 100%.

[0162] In some embodiments, a 16S rRNA sequence is obtained or determined for the bacterial species to be classified. The query 16S rRNA sequence is compared to 16S rRNA sequences from bacterial species already classified as members of the Acutalibacteraceae family (including those set forth in any one of SEQ ID NOs: 1, 2, or 7-10). In some embodiments, the query 16S rRNA sequence is compared to all known 16S rRNA sequences for bacterial species already classified as members of the Acutalibacteraceae family. In other embodiments, the query 16S rRNA sequence is compared to a subset of all known 16S rRNA sequences for bacterial species already classified as members of the Acutalibacteraceae family. The percent identity between the query sequence and the comparison sequence is determined. If the percent identity of the query sequence is determined to be above a defined threshold, the bacterial species to be classified is classified as a member of that family.

[0163] In some embodiments, the threshold sequence identity is 95%. In some embodiments, the threshold sequence identity is 98.7%. In some embodiments, the threshold sequence identity is 94.8%. In some embodiments, the threshold sequence identity is 94.5%, 94.6%, 94.7%, 94.8%, 94.9%, 95.0%, 95.1%, 95.2%, 95.3%, 95.4%, 95.5%, 95.6%, 95.7%, 95.8%, 95.9%, 96.0%, 96.1%, 96.2%, 96.3%, 96.4%, 96.5%, 96.6%, 96.7%, 96.8%, 96.9%, 97.0%, 97.1%, 97.2%, 97.3%, 97.4%, 97.5%, 97.6%, 97.7%, 97.8%, 97.9%, 98.0%, 98.1%, 98.2%, 98.3%, 98.4%, 98.5%, 98.6%, 98.7%, 98.8%, 98 ... .1%, 97.2%, 97.3%, 97.4%, 97.5%, 97.6%, 97.7%, 97.8%, 97.9%, 98.0%, 98.1%, 98.2%, 98.3%, 98.4%, 98.5%, 98.6%, 98.7%, 98.8%, 98.9%99.0%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% or 100%.

[0164] In some embodiments, the composition comprises an at least partially isolated bacterial strain of I. colisanans as described above and / or elsewhere herein.

[0165] In certain embodiments, the bacterial strain of the invention has a 16S rRNA sequence that is at least 97.5%, 98%, 98.5%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to the 16S rRNA sequence of a bacterial strain of I. colisanans. Preferably, the bacterial strain of the invention has a 16S rRNA sequence that is at least 97.5%, 98%, 98.5%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to any one of SEQ ID NOs: 1 or 2. In some preferred embodiments, the bacterial strain of the invention has a 16S rRNA sequence represented by any one of SEQ ID NOs: 1 or 2. In some other preferred embodiments, the bacterial strain of the invention has a 16S rRNA sequence represented by any one of SEQ ID NOs: 7-10.

[0166] The genome of the bacterial strain may comprise a 16S rRNA sequence set forth in any one of SEQ ID NOs: 1, 2, or 7-10.

[0167] 3.3 Genomic sequence identity. In certain embodiments, the bacterial strain of the invention has a chromosome having sequence identity to any one of SEQ ID NOs: 3 or 4. In preferred embodiments, the bacterial strain of the invention has a chromosome having at least 90% sequence identity (e.g., at least 92%, 94%, 95%, 96%, 97%, 97.5%, 98%, 98.5%, 99%, 99.5% or 100% sequence identity) to any one of SEQ ID NOs: 3 or 4 over at least 60% (e.g., at least 65%, 70%, 75%, 80%, 85%, 95%, 96%, 97%, 98%, 99% or 100%) of SEQ ID NOs: 3 or 4. For example, a bacterial strain of the invention may have at least 90% sequence identity to any one of SEQ ID NO:3 or 4 across 70% of SEQ ID NO:3 or 4, or at least 90% sequence identity to any one of SEQ ID NO:3 or 4 across 80% of SEQ ID NO:3 or 4, or at least 90% sequence identity to any one of SEQ ID NO:3 or 4 across 90% of SEQ ID NO:3 or 4, or at least 90% sequence identity to any one of SEQ ID NO:3 or 4 across 100% of SEQ ID NO:3 or 4, or at least 95% sequence identity to any one of SEQ ID NO:3 or 4 across 70% of SEQ ID NO:3 or 4, or at least 95% sequence identity to any one of SEQ ID NO:3 or 4 across 80% of SEQ ID NO:3 or 4, or a chromosome having at least 95% sequence identity with any one of SEQ ID NO:3 or 4 across 90% of SEQ ID NO:3 or 4, or at least 95% sequence identity with any one of SEQ ID NO:3 or 4 across 100% of SEQ ID NO:3 or 4, or at least 98% sequence identity with any one of SEQ ID NO:3 or 4 across 70% of SEQ ID NO:3 or 4, or at least 98% sequence identity with any one of SEQ ID NO:3 or 4 across 80% of SEQ ID NO:3 or 4, or at least 98% sequence identity with any one of SEQ ID NO:3 or 4 across 90% of SEQ ID NO:3 or 4, or at least 98% sequence identity with any one of SEQ ID NO:3 or 4 across 100% of SEQ ID NO:3 or 4. A particularly preferred strain of the present invention is the I. colisanans strain deposited under accession number V21 / 015887.This is an exemplary I. colisanans MH27-1 strain that has been tested in the DSS mouse model shown in the Examples and has been shown to be effective in treating the disease. Thus, the present invention provides cells, e.g., isolated cells, of the I. colisanans strain deposited under Accession No. V21 / 015887 or a derivative thereof. The present invention also provides compositions comprising cells of the I. colisanans strain deposited under Accession No. V21 / 015887 or a derivative thereof. The present invention also provides biologically pure cultures of the I. colisanans MH27-1 strain deposited under Accession No. V21 / 015887.

[0168] In certain embodiments, the bacterial strain of the invention has a chromosome having sequence identity to any one of SEQ ID NOs: 5 or 6. In preferred embodiments, the bacterial strain of the invention has a chromosome having at least 90% sequence identity (e.g., at least 92%, 94%, 95%, 96%, 97%, 97.5%, 98%, 98.5%, 99%, 99.5% or 100% sequence identity) to any one of SEQ ID NOs: 5 or 6 over at least 60% (e.g., at least 65%, 70%, 75%, 80%, 85%, 95%, 96%, 97%, 98%, 99% or 100%) of SEQ ID NOs: 5 or 6. For example, a bacterial strain of the invention may have at least 90% sequence identity to any one of SEQ ID NOs: 5 or 6 across 70% of SEQ ID NOs: 5 or 6, or at least 90% sequence identity to any one of SEQ ID NOs: 5 or 6 across 80% of SEQ ID NOs: 5 or 6, or at least 90% sequence identity to any one of SEQ ID NOs: 5 or 6 across 90% of SEQ ID NOs: 5 or 6, or at least 90% sequence identity to any one of SEQ ID NOs: 5 or 6 across 100% of SEQ ID NOs: 5 or 6, or at least 95% sequence identity to any one of SEQ ID NOs: 5 or 6 across 70% of SEQ ID NOs: 5 or 6, or at least 95% sequence identity to any one of SEQ ID NOs: 5 or 6 across 80% of SEQ ID NOs: 5 or 6, or a chromosome having at least 95% sequence identity with any one of SEQ ID NO:5 or 6 across 90% of SEQ ID NO:5 or 6, or at least 95% sequence identity with any one of SEQ ID NO:5 or 6 across 100% of SEQ ID NO:5 or 6, or at least 98% sequence identity with any one of SEQ ID NO:5 or 6 across 70% of SEQ ID NO:5 or 6, or at least 98% sequence identity with any one of SEQ ID NO:5 or 6 across 80% of SEQ ID NO:5 or 6, or at least 98% sequence identity with any one of SEQ ID NO:5 or 6 across 90% of SEQ ID NO:5 or 6, or at least 98% sequence identity with any one of SEQ ID NO:5 or 6 across 100% of SEQ ID NO:5 or 6. A particularly preferred strain of the present invention is the I. colisanans strain deposited under accession number V21 / 015887.This is an exemplary I. colisanans MH27-1 strain that has been tested in the DSS mouse model shown in the Examples and has been shown to be effective in treating the disease. Thus, the present invention provides cells, e.g., isolated cells, of the I. colisanans strain deposited under Accession No. V21 / 015888 or a derivative thereof. The present invention also provides compositions comprising cells of the I. colisanans strain deposited under Accession No. V21 / 015888 or a derivative thereof. The present invention also provides a biologically pure culture of the I. colisanans MH27-2 strain deposited under Accession No. V21 / 015888.

[0169] 4. Functional characterization of bacterial strains Intestinal barrier dysregulation is an important pathway leading to systemic inflammation. As shown in the examples, the bacterial strains of the present invention and compositions comprising the strains are effective in enhancing intestinal barrier function.

[0170] All inflammatory or autoimmune disorders mediated by intestinal barrier dysregulation that cause systemic inflammation in a subject are amenable to treatment with the bacterial strains described above and / or elsewhere herein.

[0171] 4.1 Intestinal barrier function. Intestinal barrier (also known as intestinal barrier) function regulates transport and host defense mechanisms at the mucosal interface with the outside world. Transcellular and paracellular fluxes are tightly controlled by membrane pumps, ion channels and tight junctions, adapting permeability according to physiological needs.

[0172] The translocation of foreign (i.e., non-host) substances, such as lipopolysaccharide (LPS) and other inflammatory compounds, from the luminal side of the intestine to the circulatory system is inhibited by the epithelial barrier. One of the functions of this epithelial barrier is performed by tight junctions. Tight junctions, or zonula occludens, are closely associated regions of two epithelial cells whose membranes join together to form a barrier that is substantially impermeable to fluids, thereby separating the vasculature from the lumen of the digestive tract. Disruption at any level, particularly bacterial translocation due to increased permeability, and disruption of oral immune tolerance due to impaired epithelial and T-cell interactions, can result in inflammation and tissue damage. Thus, a reduction in tight junction barrier function has been shown to increase the translocation of undesirable substances, such as LPS, from the intestinal lumen to the circulatory system.

[0173] The present invention provides a method of restoring or improving intestinal barrier function in a subject, comprising administering to the subject a composition comprising a bacterial strain of I. colisanans, thereby restoring or improving intestinal barrier function in the subject. As used herein, intestinal barrier integrity refers to a measure of intestinal barrier function. High intestinal barrier integrity can be associated with a lack of intestinal or intestinal permeability, with a high level of intestinal permeability indicating low intestinal barrier integrity. In related embodiments, the present invention also provides a method of maintaining healthy or normal intestinal barrier function. Such methods can be used to prevent intestinal barrier dysregulation in subjects considered to be at high risk for intestinal barrier dysregulation (e.g., subjects in remission of IBD).

[0174] In some embodiments, at least one biomarker measured in a sample (particularly a biological sample) is used to assess a change, particularly an improvement, in the intestinal barrier integrity of a subject.

[0175] In some embodiments of the methods and uses provided herein, a composition comprising a bacterial strain of I. colisanans may increase or decrease the level of one or more biomarkers of intestinal barrier integrity in a sample from a subject. In some embodiments, depending on the particular biomarker, either an increase or decrease in the level of the marker indicates increased intestinal barrier integrity and / or decreased intestinal permeability. In some embodiments, the biomarker is selected from a cytokine, a chemokine, a growth factor, an angiogenic factor, an enzyme, a protease, an adhesion molecule, a cell signaling molecule, a hormone, or a sugar. In some embodiments, the biomarker comprises a cytokine. In some embodiments, the marker comprises a chemokine. In some embodiments, the marker comprises a growth factor. In some embodiments, the marker comprises an angiogenic factor. In some embodiments, the marker comprises an enzyme. In some embodiments, the marker comprises a protease. In some embodiments, the marker comprises an adhesion molecule. In some embodiments, the marker comprises a cell signaling molecule. In some embodiments, the marker comprises a hormone. In some embodiments, the marker comprises a sugar.

[0176] The present specification provides an assay for biomarkers of intestinal permeability. A biological sample from a subject, such as blood (plasma or serum) or tissue, can be used to measure the level of any suitable biomarker, including, but not limited to, one or more of LPS, lipopolysaccharide binding protein (LPSBP), intestinal-type fatty acid binding protein (IFABP), zonulin, bacteria, and / or 16S rRNA. LPS, I-FABP, and zonulin can be measured by enzyme-linked immunosorbent assay ("ELISA"). Techniques and kits for ELISA are well known to those skilled in the art. In some embodiments, an increase in LPS, I-FABP, and / or zonulin compared to a control in blood, serum, saliva, urine, and / or plasma is used as an indicator of increased intestinal permeability and therefore reduced intestinal barrier integrity.

[0177] LPSBP can also be measured by ELISA. In some embodiments, a significant change in LPSBP, either higher or lower, compared to a control can be used as an indicator of increased intestinal permeability and can confirm decreased intestinal barrier integrity.

[0178] In some embodiments, an increase in bacterial 16S rRNA is used as an indicator of increased intestinal permeability and thus decreased intestinal barrier integrity. Bacterial 16S rRNA can be purified from blood, serum, organ tissue or urine using standard nucleic acid isolation protocols. These are, for example, commercially available. The isolated nucleic acid can be detected by qPCR amplification using primers specific for bacterial 16S rRNA sequences, or amplification using primers specific for bacterial 16S rRNA and sequencing the resulting amplicon.

[0179] Tight junction proteins expressed by intestinal epithelial cells and regulating intestinal permeability can also be used as biomarkers of intestinal permeability. In some embodiments, tight junction proteins are assayed to determine changes in intestinal permeability and intestinal barrier integrity. In some embodiments, the proteins measured can include, but are not limited to, claudins, occludins, ZO-1, and E-cadherin (adherens junction) proteins. Other tight junction proteins can also be assayed. In some embodiments, tight junction proteins are measured using immunohistochemical staining. In some embodiments, tight junction proteins are measured using ELISA.

[0180] In some embodiments, plasma citrulline is assayed to determine changes in intestinal permeability and intestinal barrier integrity. A decrease in plasma citrulline levels corresponds to a decrease in epithelial cell mass and indicates increased intestinal barrier permeability.

[0181] In some embodiments, the method includes oral administration of an insoluble sugar, such as sucralose, collecting a bodily fluid, such as urine or blood, after one or more defined periods of time, and measuring the insoluble sugar content in the bodily fluid by standard clinical analytical techniques. The insoluble sugar may include, but is not limited to, mannitol, lactulose, sucrose, sucralose, and combinations of any of the foregoing.

[0182] In some embodiments, intestinal barrier integrity is measured using an in vitro assay. A particularly preferred in vitro assay suitable for measuring intestinal barrier function is by transepithelial electrical resistance (TEER). Such assays are well known in the art (e.g., Srinivasan, 2015; and Lea, 2015).

[0183] 4.2 Mucosal healing Mucosal healing has become an important endpoint for evaluating the efficacy of treatment in inflammatory and autoimmune disorders. The definition of complete mucosal healing currently used in IBD (e.g., CD and UC) clinical trials is "complete absence of all inflammatory and ulcerative lesions," but this definition lacks validation and does not include grading of mucosal improvement and mucosal healing.

[0184] Mucosal healing is primarily defined by the endoscopic assessment of intestinal inflammation. Various endoscopic scoring systems have been developed to assess the presence or absence of mucosal healing in endoscopy. These indices make it possible to determine the improvement of endoscopic lesions even if the rather strict endpoint of mucosal healing and therefore complete disappearance of all mucosal ulcers is not achieved. The endoscopic component of the clinical Mayo score, introduced in 1987, is currently the most used score of the mucosal layer in clinical practice (see Schroeder et al., 1987). It includes the variables of redness, loss of vascular image, friability, bleeding, erosion and ulceration and ranges from 0 to 3. Mucosal healing is classically considered to be a score of 0 (normal mucosa) or 1 (mucosal redness, loss of vascular image, mild friability) (D'Haens, 2007).

[0185] In some other embodiments, mucosal healing is determined to have occurred when a patient is determined to have an endoscopic subscore, as assessed by flexible sigmoidoscopy, of 0 or 1. In certain such embodiments, a patient who experiences mucosal healing is determined to have an endoscopic subscore of 0.

[0186] Both corticosteroids and aminosalicylates have been used for decades and are among the most commonly prescribed drugs to repair the mucosal layer (e.g., in UC patients) (Carvalho and Cotter, 2017). The mechanisms by which they reduce mucosal inflammation include the control of nuclear factor (NF)-kB expression and inflammatory cytokines (directly modulating cell migration and proliferation of epithelial cell lines). Anti-TNF drugs (e.g., infliximab, adalimumab, and golimumab) act at several stages of mucosal injury, limiting inflammatory infiltration and T-cell proliferation within the lamina propria (Baert, 1999) and downregulating the expression of metalloproteases and proinflammatory molecules (Baert, 1999). They also act on regenerative processes, restoring the protective capacity of the mucosa by enhancing intestinal permeability and mucosal secretion, activating fibroblasts, and maintaining epithelial regeneration (Suenaert, 2002).

[0187] Other measures for assessing mucosal healing are well known in the art, including measuring biomarkers C-reactive protein and calprotectin.The advantage of using in vitro biomarker assays for assessing mucosal healing is that such assays are typically much less invasive for subjects.Histopathology is another measure of inflammation and has been cited as being particularly informative for mucosal healing.

[0188] 4.3 STAT3 signal transduction pathway Cytokine pathways mediate a wide range of biological functions, including many aspects of inflammation and immunity. Janus kinases (JAKs), including JAK1, JAK2, JAK3, and tyrosine kinase 2 (TYK2), are cytoplasmic tyrosine kinases that associate with type I and type II cytokine receptors and regulate cytokine signaling. Binding of cytokines to their cognate receptors triggers activation of receptor-associated JAKs, which leads to JAK-mediated tyrosine phosphorylation of signal transduction and activator of transcription (STAT) proteins and ultimately transcriptional activation of a specific set of genes (Schindler et al., 2007, J. Biol. Chem. 282:20059-63). Cytokine receptors typically function as heterodimers, such that two or more JAK kinases are usually associated with a cytokine receptor complex. The specific JAKs associated with different cytokine receptor complexes are often determined by genetic studies and supported by other experimental evidence.

[0189] STAT3 plays an important role in the activation of several autoimmune and inflammatory disorders, including IBD. The bacterial strains of the present invention significantly suppress IL-23-mediated STAT3 activation. Thus, the present invention provides a method of suppressing or inhibiting STAT3 signaling (i.e., IL-23-mediated STAT3 signaling) in a subject, comprising administering to the subject a composition comprising a bacterial strain described above and / or elsewhere herein. Thus, in some embodiments, the bacterial strains described herein directly or indirectly suppress STAT3 activity. In some embodiments, a strain of I. colisanans produces a bioactive molecule that directly binds to a STAT3 polypeptide. In some alternative embodiments, the bacterial strain is an indirect inhibitor of STAT3 activation, for example, by binding to a molecule upstream of STAT3 in the IL-23-mediated STAT3 signaling pathway or by binding to a molecule that modulates STAT3 activity (e.g., ubiquitination). As an illustrative example, the bioactive agent may directly bind to or antagonize any one of IL23, JAK2, or TYK2 to suppress the IL-23-mediated STAT3 signaling pathway.

[0190] I. colisanans strains reduce the activation of inflammatory cytokines such as IL-6. Chronic inflammation induced by IL-6 can ultimately lead to cell death. Thus, the bacterial strains of the present invention are particularly useful in the treatment or prevention of inflammatory or autoimmune disorders. In some embodiments, the bacterial strains are useful for the treatment of inflammatory or autoimmune disorders characterized by enhanced activation of IL-6.

[0191] 4.4 Th17 inflammatory response Some bacterial compositions of the present invention are effective in reducing Th17 inflammatory responses. In particular, treatment with the compositions described above and elsewhere herein can modulate Th17 pathway cytokines (including TNF, IL-22, IL-21, and IL-17) and can result in clinical improvement in animal models of pathologies mediated by the Th17 pathway. Thus, the compositions of the present invention can be useful for treating or preventing inflammatory and autoimmune disorders, and in some embodiments, diseases or conditions mediated by Th17. In particular, the compositions of the present invention can be useful for reducing or preventing the elevation of Th17 inflammatory responses.

[0192] Th17 cells are a subset of T helper cells that produce IL17A, IL17F, IL-21 and IL-22, among other cytokines. Th17 cell differentiation can be driven by IL23. These cytokines and others form an important part of the Th17 pathway, a well-established inflammatory signaling pathway that contributes to and underlies many inflammatory and autoimmune disorders (e.g., as described in Ye, 2015; Fabro, 2015; Yin, 2014; Cheluvappa, 2014; Schieck, 2014; Balato, 2014). Some diseases mediated by Th17 can be improved or alleviated by suppressing the Th17 pathway, which can be by reducing the differentiation of Th17 cells, or reducing their activity, or reducing the levels of Th17 pathway cytokines. Diseases mediated by the Th17 pathway may be characterized by increased levels of cytokines produced by Th17 cells, such as IL-17A, IL-17F, IL-21, IL-22, IL-26, IL-9 (reviewed in Monteleone, 2011). Diseases mediated by the Th17 pathway may be characterized by increased expression of Th17-associated genes, such as STAT3 or IL-23 receptor. Diseases mediated by the Th17 pathway may be associated with increased levels of Th17 cells.

[0193] IL-17 is a key cytokine that links T cell activation to neutrophil activation and recruitment, and thus IL-17 plays a central role in innate immunity. However, due to its role in neutrophil activation, it may contribute to inflammatory autoimmune diseases such as inflammatory bowel disease, psoriasis, and rheumatoid arthritis. As used herein, IL-17 may refer to any member of the IL-17 family, including IL-17A, IL-17B, IL-17C, IL-17D, IL-17E, and IL-17F. IL-17-mediated diseases and conditions are characterized by high expression of IL-17 and / or accumulation or presence of IL-17 positive cells in tissues affected by the disease or condition. Similarly, IL-17-mediated diseases and conditions are diseases and conditions that are exacerbated by high or elevated IL-17 levels and ameliorated by low or reduced IL-17 levels. The IL-17 inflammatory response can be local or systemic.

[0194] Examples of diseases and conditions that may be mediated by the Th17 pathway include (but are not limited to) inflammatory bowel disease (such as Crohn's disease and ulcerative colitis), multiple sclerosis; arthritis (such as rheumatoid arthritis, osteoarthritis, psoriatic arthritis, and juvenile idiopathic arthritis); neuromyelitis optica (Devic's disease); ankylosing spondylitis; spondyloarthritis; psoriasis; systemic lupus erythematosus; celiac disease; asthma (such as allergic asthma or neutrophilic asthma); chronic obstructive pulmonary disease (COPD); cancer (such as breast cancer, colon cancer, lung cancer, or ovarian cancer); uveitis; scleritis; vasculitis; Behcet's disease; atherosclerosis; atopic dermatitis; emphysema; periodontitis; allergic rhinitis; and allograft rejection. Thus, in some embodiments, the present invention provides a method of treating or preventing one or more of these conditions or diseases by administering a composition as described above and / or elsewhere herein. In further preferred embodiments, these pathologies or diseases are mediated by the STAT3 signaling pathway. In further preferred embodiments, these pathologies or diseases are mediated via the Th17 pathway.

[0195] In certain embodiments, the present invention provides a method composition of the present invention for use in a method of reducing Th17 cell differentiation in the treatment or prevention of a disease or condition mediated by the Th17 pathway. In certain embodiments, the composition of the present invention is for use in treating or preventing an inflammatory or autoimmune disorder, where the treatment or prevention is achieved by reducing or preventing the elevation of a Th17 inflammatory response. In certain embodiments, the composition of the present invention is for use in treating a patient with an inflammatory or autoimmune disorder, where the patient has elevated IL-17 levels or elevated Th17 cells, or exhibits a Th17 inflammatory response. In certain embodiments, the patient may be diagnosed with a chronic inflammatory or autoimmune disorder or condition, or the composition of the present invention may be for use in preventing an inflammatory or autoimmune disorder or condition from progressing to a chronic inflammatory or autoimmune disorder or condition. In certain embodiments, the disease or condition may not respond to treatment with a TNF inhibitor. These uses of the present invention may be applied to any of the specific diseases or conditions listed in the previous paragraph.

[0196] The Th17 pathway is often associated with chronic inflammatory and autoimmune disorders, and therefore the compositions of the present invention may be particularly useful for treating or preventing the chronic diseases or conditions listed above. In certain embodiments, the compositions are for use in patients with chronic diseases. In certain embodiments, the compositions are for use in preventing the onset of chronic diseases.

[0197] The compositions of the present invention may be useful for treating diseases and conditions mediated by the Th17 pathway and for combating Th17 inflammatory responses, and therefore may be particularly useful for treating or preventing chronic diseases, treating or preventing diseases in patients who have not responded to other therapies (such as treatment with TNF inhibitors), and / or treating or preventing tissue damage and symptoms associated with Th17 cells.For example, IL-17 is known to activate matrix destruction in cartilage and bone tissue, and since IL-17 has an inhibitory effect on matrix production in chondrocytes and osteoblasts, the compositions of the present invention may be useful for treating or preventing bone erosion or cartilage damage.

[0198] In certain embodiments, treatment with the compositions of the invention results in a reduction or prevents an increase in IL-17 levels, particularly IL-17A levels. In certain embodiments, treatment with the compositions of the invention results in a reduction or prevents an increase in IFN-γ or IL-6 levels. Such reduction or prevention of an increase in the levels of these cytokines may be useful in treating or preventing inflammatory and autoimmune disorders and conditions, particularly those mediated by the Th17 pathway.

[0199] 4.5 Th1 inflammatory response CD4 + T cells play a key role in the pathogenesis of inflammatory diseases / disorders and CD4 + Many subsets of T cells have been identified as drivers that sustain chronic intestinal inflammation (see Imam et al., 2018). For example, T helper type 1 (Th1) cells accumulate in the intestinal tract of individuals with IBD and are directly linked to the disease. Interferon-γ (IFN-γ) is the defining cytokine produced by Th1 cells. During intestinal inflammation, IFN-γ and TNF have been proposed to cooperate to drive intestinal epithelial cell β-catenin signaling and limit their differentiation and proliferation (Imam et al., 2018).

[0200] 5.Treatment method In some embodiments, the invention provides a method of treating or preventing an inflammatory or autoimmune disorder in a subject, comprising administering to the subject a bacterial strain described above and / or elsewhere herein.

[0201] Suitably, the inflammatory or autoimmune disorder is selected from the group consisting of inflammatory bowel disease (such as Crohn's disease or ulcerative colitis); asthma (such as allergic asthma or neutrophilic asthma); arthritis (such as rheumatoid arthritis, osteoarthritis, psoriatic arthritis, or juvenile idiopathic arthritis); fatty liver disease (such as non-alcoholic fatty liver disease (NAFLD)); ankylosing spondylitis; psoriasis; systemic lupus erythematosus (SLE); scleroderma; Sjogren's syndrome; vasculitis; and type 1 diabetes.

[0202] 5.1 Inflammatory bowel disease (IBD) The examples demonstrate that the compositions of the invention have a beneficial restorative effect on intestinal barrier function and that they also have anti-inflammatory properties and therefore may be useful in the treatment of IBD. Thus, in some embodiments, the invention provides a composition comprising a bacterial strain of the genus Intestinicoccus for use in a method for treating or preventing inflammatory bowel disease. The inventors have identified that treatment with an Intestinicoccus strain reduces the severity of colitis in a mouse disease model. Thus, the compositions of the invention may be useful in the treatment of inflammatory diseases. In some embodiments, the compositions of the invention are for use in the treatment or prevention of IBD. In some embodiments, the invention provides a method for treating or preventing ulcerative colitis. In some embodiments, the invention provides a method for treating or preventing Crohn's disease. In certain embodiments, the invention provides a method for treating or preventing ulceration and / or bleeding in the treatment of IBD, particularly in the treatment of colitis and ulcerative colitis. In a preferred embodiment, the invention provides a method for treating or preventing IBD in a subject, comprising administering to the subject a composition comprising a bacterial strain of the species I. colisanans. In a further preferred embodiment, the present invention provides a method of treating or preventing colitis (particularly ulcerative colitis) in a subject, comprising administering to the subject a composition comprising a bacterial strain of the I. colisanans species. In a further preferred embodiment, the present invention provides a method of reducing at least one side effect of colitis (particularly ulcerative colitis), including ulceration and / or bleeding.

[0203] IBD is a complex disease that can be caused by multiple environmental and genetic factors. Factors that contribute to the development of IBD include diet, microbiota, intestinal permeability, and genetic susceptibility to increased inflammatory response to intestinal infection. Symptoms of inflammatory bowel disease include abdominal pain, vomiting, diarrhea, rectal bleeding, severe internal cramps / spasms in the pelvic region, weight loss, and anemia. In certain embodiments, the composition is for use in alleviating one or more symptoms associated with IBD. In certain embodiments, the composition of the present invention is for use in preventing one or more symptoms of IBD.

[0204] IBD may be associated with other diseases or conditions, such as cardiovascular disease, neuropsychological disorders, and metabolic syndrome. In certain embodiments, the compositions of the invention are for use in the treatment or prevention of one or more diseases or conditions associated with IBD.

[0205] IBD is generally diagnosed by biopsy or colonoscopy. Measurement of fecal calprotectin is useful for preliminary diagnosis of IBD. Other laboratory tests for the diagnosis of IBD include complete blood count, erythrocyte sedimentation rate, comprehensive metabolic panel, fecal occult blood test or C-reactive protein test. Typically, a combination of laboratory tests and biopsy / colonoscopy is used to confirm the diagnosis of IBD. In certain embodiments, the composition of the present invention is for use in subjects diagnosed with IBD.

[0206] In certain embodiments, the IBD is Crohn's disease and / or ulcerative colitis.As broadly described above, research has shown that some inflammatory cytokines, including but not limited to STAT3 signaling and NFκB signaling pathway-mediated cytokines (e.g., IL-17, TNF, IL-21, IL-22), are upregulated in the inflamed mucosa of patients with Crohn's disease and ulcerative colitis.Therefore, inhibition of cytokine activity via STAT3 signaling pathway and / or cytokine via NFκB signaling pathway can be useful for treating Crohn's disease and ulcerative colitis.In certain embodiments, the composition of the present invention is for use in treating or preventing Crohn's disease and / or ulcerative colitis.

[0207] Crohn's disease and ulcerative colitis are complex diseases with many putative causes, including genetic risk factors, diet, other lifestyle factors such as smoking and alcohol consumption, and microbiome composition. Crohn's disease can appear anywhere along the gastrointestinal tract, whereas ulcerative colitis typically affects the large intestine and colon.

[0208] Gastrointestinal symptoms of IBD range from mild to severe and include abdominal pain, diarrhea, bloody stool, ileitis, excessive bowel movements, increased flatulence, intestinal narrowing, vomiting, and perianal discomfort. The compositions of the invention may be for use in treating or preventing one or more gastrointestinal symptoms of Crohn's disease and / or ulcerative colitis.

[0209] Systemic symptoms of Crohn's disease and ulcerative colitis include failure to maintain pubertal growth, loss of appetite, fever and weight loss, and other growth disorders. Extraintestinal features of Crohn's disease include uveitis, photobia, episcleritis, gallstones, seronegative spondyloarthropathy, arthritis, enthesitis, erythema nodosum, pyoderma gangrenosum, deep vein thrombosis, pulmonary embolism, autoimmune hemolytic anemia, clubbing and osteoporosis. Extraintestinal features are additional pathologies associated with Crohn's disease and / or ulcerative colitis that are manifested outside the gastrointestinal tract. Subjects with Crohn's disease also show increased susceptibility to neurological complications, such as seizures, stroke, myopathy, peripheral neuropathy, headaches and depression. In certain embodiments, the compositions of the present invention are for use in treating or preventing one or more systemic symptoms of Crohn's disease and / or ulcerative colitis. In certain embodiments, the compositions of the invention are for use in the treatment or prevention of one or more extraintestinal features of Crohn's disease and / or ulcerative colitis.

[0210] Diagnosis of Crohn's disease and ulcerative colitis usually involves performing several tests and surgical procedures, such as gastroscopy and / or colonoscopy, and biopsy, typically ileal biopsy, radiology, complete blood count, C-reactive protein test and erythrocyte sedimentation rate.In certain embodiments, the compositions of the present invention are for use in subjects diagnosed with Crohn's disease or ulcerative colitis.In some embodiments, the compositions of the present invention are for use in treating subjects diagnosed with Crohn's disease or ulcerative colitis.

[0211] Crohn's disease and ulcerative colitis are classified according to the extent of the gastrointestinal tract region affected (Gasche et al., 2000). Crohn's disease of both the ileum and colon is classified as ileocolonic Crohn's disease. In some embodiments, the composition is for use in the treatment or prevention of ileocolonic Crohn's disease. In some embodiments, the composition is for use in a subject diagnosed with ileocolonic Crohn's disease / Crohn's ileitis is classified when only the ileum is affected. Crohn's colitis is classified when only the colon is affected. In certain embodiments, the composition is for use in the treatment or prevention of Crohn's ileitis. In some embodiments, the composition is for use in a subject diagnosed with Crohn's ileitis. In certain embodiments, the composition is for use in the treatment or prevention of Crohn's colitis. In some embodiments, the composition is for use in a subject diagnosed with Crohn's colitis.

[0212] Crohn's disease and ulcerative colitis can be treated with several therapeutic agents, such as corticosteroids, such as prednisone, immunosuppressants, such as azathioprine, or biologics, such as infliximab, adalimumab and golimumab, vedolizumab and etrolizumab. In certain embodiments, the compositions of the present invention are for use in the treatment or prevention of Crohn's disease or ulcerative colitis in combination with an additional therapeutic agent, including but not limited to those listed above. In certain embodiments, the additional therapeutic agent is for use in the treatment or prevention of Crohn's disease and / or ulcerative colitis.

[0213] 5.2 Autoimmune disorders In humans, signs of intestinal inflammation are detected before the clinical onset of many autoimmune disorders, such as type 1 diabetes (T1D) (Bosi, 2006). Similarly, diabetes-prone rats display enhanced intestinal permeability before the onset of insulitis compared to diabetes-resistant rats (Meddings, 1999; Neu, 2005). These findings indicate that disruption of intestinal barrier integrity and the associated increased antigen transport and development of low-grade intestinal inflammation precede the onset of T1D and are directly linked to its pathogenesis, rather than being secondary to diabetes-induced metabolic changes (i.e., hyperglycemia). The gastrointestinal barrier is a fundamental gatekeeper to prevent contact between luminal contents and the human body. The barrier is composed of the mucus layer and the intestinal epithelial barrier (IEB), both of which are important in preventing the passage of commensal bacteria, pathogens, and food antigens from the lumen into the intestinal tissue and systemic circulation. The IEB is a single layer of epithelial cells held together by a complex junctional system composed of tight junction adhesion molecules (JAMs), tricellulin, and angulin, whose interactions among themselves and with intracellular scaffolding proteins, namely, tight junction proteins (ZOs), are fundamental for maintaining the integrity of tight junctions and controlling paracellular transport. Alterations in the IEB have been reported in association with intestinal inflammation in patients and rat models of T1D (Meddings, 1999; Sapone, 2006). Moreover, the importance of the intestinal mucus layer, a key intestinal barrier that contains antimicrobial peptides and immune-modulating molecules such as mucins, has been recently reported (see Sorini et al., 2019).

[0214] In some embodiments, bacterial strains from the I. colisanans species may provide therapeutic benefits in the treatment or prevention of asthma, such as allergic asthma or neutrophilic asthma. In certain embodiments, the compositions of the invention are for use in the treatment or prevention of asthma in a subject. In certain embodiments, the invention provides compositions comprising a bacterial strain of the I. colisanans species for use in the treatment or prevention of asthma.

[0215] In some embodiments, bacterial strains from the I. colisanans species may provide therapeutic benefits in the treatment or prevention of GVHD. In certain embodiments, the compositions of the invention are for use in the treatment or prevention of GVHD in a subject. In a preferred embodiment, the invention provides a composition comprising a bacterial strain of the I. colisanans species for use in the treatment or prevention of GVHD.

[0216] In some embodiments, bacterial strains from the I. colisanans species may provide therapeutic benefits in the treatment or prevention of arthritis, such as rheumatoid arthritis, osteoarthritis, psoriatic arthritis, or juvenile idiopathic arthritis. In certain embodiments, the compositions of the invention are for use in treating or preventing arthritis in a subject. In certain embodiments, the invention provides compositions comprising bacterial strains of the I. colisanans species for use in treating or preventing arthritis.

[0217] In some embodiments, bacterial strains from the I. colisanans species may provide therapeutic benefits in the treatment or prevention of multiple sclerosis. In certain embodiments, the compositions of the invention are for use in the treatment or prevention of multiple sclerosis in a subject. In certain embodiments, the invention provides compositions comprising a bacterial strain of the I. colisanans species for use in the treatment or prevention of multiple sclerosis.

[0218] In some embodiments, bacterial strains from the I. colisanans species may provide therapeutic benefits in the treatment or prevention of psoriasis. In certain embodiments, the compositions of the invention are for use in the treatment or prevention of psoriasis in a subject. In certain embodiments, the invention provides compositions comprising a bacterial strain from the I. colisanans species for use in the treatment or prevention of psoriasis.

[0219] In some embodiments, bacterial strains from the I. colisanans species may provide therapeutic benefit in the treatment or prevention of systemic lupus erythematosus (SLE). In certain embodiments, the compositions of the invention are for use in the treatment or prevention of SLE in a subject. In certain embodiments, the invention provides compositions comprising a bacterial strain of the I. colisanans species for use in the treatment or prevention of SLE.

[0220] In some embodiments, bacterial strains from the I. colisanans species may provide therapeutic benefit in the treatment or prevention of allograft rejection. In certain embodiments, the compositions of the invention are for use in the treatment or prevention of allograft rejection in a subject. In certain embodiments, the invention provides compositions comprising a bacterial strain of the I. colisanans species for use in the treatment or prevention of allograft rejection.

[0221] 6. Preparation In some embodiments, the compositions of the present invention comprise fewer than 40 different bacterial strains. In some embodiments, the compositions comprise fewer than 30 different bacterial strains. In some embodiments, the compositions comprise fewer than 20 different bacterial strains. In some embodiments, the compositions comprise fewer than 10 different bacterial strains. In some embodiments, the compositions comprise fewer than 5 different bacterial strains. In some preferred embodiments, the compositions comprise fewer than 3 different bacterial strains. In some preferred embodiments, the compositions comprise a single bacterial strain. In some embodiments, the compositions do not include bacteria of the genus Clostidium.

[0222] The compositions of the invention comprise bacteria (i.e. live and / or dead bacteria). In a preferred embodiment of the invention, the compositions are formulated in a dry form (e.g. freeze-dried form). The compositions of the invention may comprise granules or gelatin capsules, e.g. hard gelatin capsules, comprising the bacterial strains of the invention. Preferably, the compositions of the invention comprise freeze-dried bacteria. Freeze-drying of bacteria is a well-established procedure and relevant guidance is available, for example, in references (Miyamoto-Shinohara, 2008; and Day & Stacey, 2007).

[0223] The compositions of the invention may include live and active bacterial cultures. The examples show that the bacterial cultures of the invention are therapeutically effective.

[0224] In some embodiments, the bacterial strains in the compositions of the invention are not inactivated, e.g., not heat inactivated. In some embodiments, the bacterial strains in the compositions of the invention are not killed, e.g., not heat killed. In some embodiments, the bacterial strains in the compositions of the invention are not attenuated, e.g., not heat attenuated. For example, in some embodiments, the bacterial strains in the compositions of the invention are not killed, inactivated and / or attenuated. For example, in some embodiments, the bacterial strains in the compositions of the invention are live. For example, in some embodiments, the bacterial strains in the compositions of the invention are viable. For example, in some embodiments, the bacterial strains in the compositions of the invention are capable of partially or fully colonizing the intestine. For example, in some embodiments, the bacterial strains in the compositions of the invention are viable and capable of partially or fully colonizing the intestine.

[0225] In some embodiments, the composition comprises a mixture of live and killed bacterial strains. In a preferred embodiment, the composition of the present invention is encapsulated to allow delivery of the bacterial strain to the intestine. Encapsulation protects the composition from degradation until delivery at the target location, for example, by disruption using chemical or physical stimuli such as pressure, enzymatic activity, or physical disintegration, which may be caused by a change in pH. Any suitable encapsulation method can be used. Exemplary encapsulation techniques include entrapment in a porous matrix, attachment or adsorption to a solid support surface, soft flocculation or self-aggregation by a crosslinking agent, and mechanical containment inside a microporous membrane or microcapsule. Guidance on encapsulation that may be useful in preparing the compositions of the present invention is widely available in the art (e.g., Mitropoulou, 2013; and Kailasapathy, 2002).

[0226] The compositions may be administered orally and may be in the form of tablets, capsules or powders. Encapsulated products are preferred, as bacteria of the genus Intestinicoccus are obligate anaerobes.

[0227] The compositions of the invention comprise a therapeutically effective amount of the bacterial strain of the invention. The therapeutically effective amount of the bacterial strain is sufficient to exert a beneficial effect on the patient. The therapeutically effective amount of the bacterial strain may be sufficient to effect delivery to and / or partial or total colonization of the intestine of the patient.

[0228] A suitable daily dose of bacteria, for example, for an adult is about 1×10 3 ~Approx. 1×10 11 Colony forming units (CFU); e.g., approximately 1 x 10 7 ~Approx. 1×10 10 CFU; in another example, approximately 1 x 10 6 ~Approx. 1×10 10 CFU; in another example, approximately 1 x 10 7 ~Approx. 1×10 11 CFU; in another example, approximately 1 x 10 8 ~Approx. 1×10 10 CFU; in another example, approximately 1 x 10 8 ~Approx. 1×1011 It may be CFU.

[0229] In certain embodiments, the dose of bacteria is at least 10 9 cells / day, e.g., at least 10 10 , at least 10 11 , or at least 10 12 cells / day.

[0230] In certain embodiments, the dosage of the composition is about 1×10 6 ~Approx. 1×10 11 The bacterial strain may be included in an amount of colony forming units (CFU) / g. The dose may be suitable for an adult. For example, the composition may contain about 1×10 3 ~Approx. 1×10 11 CFU / g; e.g., about 1 x 10 7 ~Approx. 1×10 10 CFU / g; in another example, approximately 1 × 10 6 ~Approx. 1×10 10 CFU / g; in another example, approximately 1 × 10 7 ~Approx. 1×10 11 CFU / g; in another example, approximately 1 × 10 8 ~Approx. 1×10 10 CFU / g; in another example, approximately 1 × 10 8 ~Approx. 1×10 11 CFU / g, approximately 1 x 10 8 ~Approx. 1×10 10 CFU / g of the bacterial strain. For example, about 1×10 8 ~Approx. 1×10 10 CFU / g. Doses may be, for example, 1 g, 3 g, 5 g, and up to 10 g or more.

[0231] In some embodiments, the compositions described above and / or elsewhere herein have a concentration of about 1×10 per gram by weight of the composition. 3 ~Approx. 1×10 11 It comprises, consists of, or consists essentially of a colony forming unit amount of a bacterial strain.

[0232] In some embodiments, the compositions described above and / or elsewhere herein comprise the bacterial strain in a dose of 500 mg to 1000 mg, 600 mg to 900 mg, 700 mg to 800 mg, 500 mg to 750 mg, or 750 mg to 1000 mg. In certain embodiments, the invention provides such pharmaceutical compositions, wherein the dry bacteria in the pharmaceutical composition is administered in a dose of 500 mg to 1000 mg, 600 mg to 900 mg, 700 mg to 800 mg, 500 mg to 750 mg, or 750 mg to 1000 mg.

[0233] The composition may be formulated as a probiotic, which is defined by the FAO / WHO as a live microorganism that, when administered in adequate amounts, confers a beneficial health effect on the host.

[0234] Typically, probiotics such as the composition of the present invention is optionally combined with at least one suitable prebiotic compound.Prebiotic compounds are usually indigestible carbohydrates, such as oligosaccharides or polysaccharides, or sugar alcohols, which are not broken down or absorbed in the upper gastrointestinal tract.Known prebiotics include commercial products such as inulin and transgalactooligosaccharides.

[0235] Other prebiotic compounds (such as, for example, vitamin C) may be included as oxygen scavengers and to improve in vivo delivery and / or partial or total colonization and survival. Alternatively, the probiotic compositions of the invention may be administered orally as a food or nutritional product, such as a milk or whey-based fermented dairy product, or as a pharmaceutical product.

[0236] In certain embodiments, the probiotic composition of the present invention comprises a prebiotic compound in an amount of about 1 to about 30% by weight (e.g., 5 to 20% by weight) based on the total weight of the composition. Known prebiotics include commercial products such as inulin and transgalactooligosaccharides.

[0237] In some embodiments, the prebiotic is a carbohydrate selected from the group consisting of or including fructooligosaccharides (or FOS), short chain fructooligosaccharides, inulin, isomaltooligosaccharides, pectin, xylooligosaccharides (or XOS), chitosan oligosaccharides (or COS), β-glucan, gum arabic modified and resistant starch, polydextrose, tagatose, acacia fiber, carob, oat, and citrus fiber. In one aspect, the prebiotic is a short chain fructooligosaccharide. Short chain FOS is a resistant carbohydrate, generally obtained by conversion of beet sugar, and contains a saccharose molecule with three glucose molecules attached.

[0238] The compositions of the present invention may include pharma- ceutically acceptable excipients or carriers, such as those described in the Handbook of Pharmaceutical Excipients. Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical arts and are described, for example, in Remington's Pharmaceutical Sciences. Examples of suitable carriers include lactose, starch, glucose, methylcellulose, magnesium stearate, mannitol, sorbitol, and the like. Examples of suitable diluents include ethanol, glycerol, and water. The choice of pharmaceutical carrier, excipient, or diluent can be selected with respect to the intended route of administration and standard pharmaceutical practice. The pharmaceutical compositions may include one or more suitable binders, lubricants, suspending agents, coating agents, and / or solubilizing agents as, or in addition to, the carrier, excipient, or diluent. Examples of suitable binders include starch, gelatin, natural sugars, such as glucose, anhydrous lactose, free-flowing lactose, beta-lactose, corn sweeteners, natural and synthetic gums, such as acacia, tragacanth, or sodium alginate, carboxymethylcellulose, and polyethylene glycol. Examples of suitable lubricants include sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride, and the like. Preservatives, stabilizers, dyes, and even flavorings may be provided in the pharmaceutical composition. Examples of preservatives include sodium benzoate, sorbic acid, cysteine, and esters of 4-hydroxybenzoic acid, for example, in some embodiments, the preservative is selected from sodium benzoate, sorbic acid, and esters of 4-hydroxybenzoic acid. Antioxidants and suspending agents may also be used. A further example of a suitable carrier is sucrose. A further example of a suitable preservative is cysteine.

[0239] The composition of the present invention may be formulated as a food product. For example, the food product may provide nutritional benefits in addition to the therapeutic effects of the present invention, such as in a nutritional supplement. Similarly, the food product may be formulated to enhance the taste of the composition of the present invention, or to make the composition more attractive to consume by resembling a common food item rather than a pharmaceutical composition. In certain embodiments, the composition of the present invention is formulated as a milk-based product. The term "milk-based product" refers to any liquid or semi-solid milk-based or whey-based product with various fat contents. The milk-based product may be, for example, cow's milk, goat's milk, sheep's milk, skim milk, whole milk, milk powder and milk reconstituted from whey without any processing, or processed products such as yogurt, curdled milk, curd, sour milk, sour whole milk, buttermilk and other sour milk products. Alternatively, the milk may be a vegetable milk, such as soy milk, oat milk, almond milk, coconut milk, or macadamia milk. Another important group includes milk drinks, such as whey drinks, fermented milk, concentrated milk, infant or baby milk, flavoured milk, ice cream, sweeteners and other milk-containing foods.

[0240] In some embodiments, the compositions disclosed herein comprise one or more bacterial strains of the genus Intestinicoccus, and no bacteria from any other species, or only low or biologically irrelevant amounts of bacteria from another species. Thus, in some embodiments, the present invention provides compositions comprising one or more bacterial strains of the genus Intestinicoccus (e.g., Intestinicoccus colisanans), and no bacteria from any other species, or only low or biologically irrelevant amounts of bacteria from another species, for use in therapy.

[0241] In some embodiments, a composition comprises one or more bacterial strains of the genus Intestinicoccus and no bacteria from any other genera, or only low or biologically irrelevant amounts of bacteria from another genus. In some embodiments, a composition comprises one or more bacterial strains of the genus Intestinicoccus (e.g., Intestinicoccus colisanans) and no bacteria from any other genera, or only low or biologically irrelevant amounts of bacteria from another genus.

[0242] In certain embodiments, the compositions disclosed herein comprise a single bacterial species and no other bacterial species. In certain embodiments, the compositions disclosed herein comprise a single bacterial strain and no other bacterial strains. For example, the compositions of the present invention may comprise only strains of I. colisanans bacteria. Such compositions may contain only trace or biologically irrelevant amounts of other bacterial strains or species. Such compositions may be cultures that are substantially free of other biological species. In some embodiments, such compositions may be in a dry form and may be substantially free of other biological species.

[0243] In some embodiments, the present invention provides compositions comprising a single bacterial strain of the genus Intestinicoccus, free of bacteria from any other strain, or containing only minor or biologically irrelevant amounts of bacteria from another strain, for use in therapy.

[0244] In some embodiments, the present invention provides compositions comprising a single bacterial strain of the species Intestinicoccus colisanans (e.g., Intestinicoccus colisanans MH27-1, Intestinicoccus colisanans MH27-2, or Intestinicoccus colisanans MH27-3), free of bacteria from any other strain or containing only minor or biologically irrelevant amounts of bacteria from another strain, for use in therapy.

[0245] In certain embodiments, the compositions of the invention comprise a single bacterial strain or species and are free of any other bacterial strains or species. Such compositions may contain only trace or biologically irrelevant amounts of other bacterial strains or species. Such compositions may be cultures that are substantially free of other biological species.

[0246] 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 1-10, preferably 1-5, bacterial strains or species. In some embodiments, the compositions disclosed herein comprise two or more strains from the same species (e.g., more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, or 45 strains), optionally not including bacteria from any other species. In some embodiments, the compositions disclosed herein comprise less than 50 strains from the same species (e.g., less than 45, 40, 35, 30, 25, 20, 15, 12, 10, 9, 8, 7, 6, 5, 4, or 3 strains), optionally not including bacteria from any other species. In some embodiments, the compositions disclosed herein comprise 1-40, 1-30, 1-20, 1-19, 1-18, 1-15, 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, 2-50, 2-40, 2-30, 2-20, 2-15, 2-10, 2-5, 6-30, 6-15, 16-25, or 31-50 strains from the same species, optionally not including bacteria from any other species. In some embodiments, the compositions disclosed herein comprise more than one species (e.g., more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 17, 20, 23, 25, 30, 35, or 40 species) from the same genus, optionally not including bacteria from any other genus. In some embodiments, the compositions disclosed herein comprise less than 50 species (e.g., less than 50, 45, 40, 35, 30, 25, 20, 15, 12, 10, 8, 7, 6, 5, 4, or 3 species) from within the same genus, optionally not including bacteria from any other genus. In some embodiments, the compositions disclosed herein comprise 1-50, 1-40, 1-30, 1-20, 1-15, 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, 2-50, 2-40, 2-30, 2-20, 2-15, 2-10, 2-5, 6-30, 6-15, 16-25, or 31-50 species from within the same genus, optionally not including bacteria from any other genus. The present invention includes any combination of the above.

[0247] In some embodiments, the compositions of the invention comprise two or more bacterial strains or species. For example, in some embodiments, the compositions of the invention comprise two or more strains from the same species (e.g., more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, or 45 strains), optionally not including bacteria from any other species. In some embodiments, the compositions of the invention comprise less than 50 strains from the same species (e.g., less than 45, 40, 35, 30, 25, 20, 15, 12, 10, 9, 8, 7, 6, 5, 4, or 3 strains), optionally not including bacteria from any other species. In some embodiments, the compositions of the invention comprise 1-40, 1-30, 1-20, 1-19, 1-18, 1-15, 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, 2-50, 2-40, 2-30, 2-20, 2-15, 2-10, 2-5, 6-30, 6-15, 16-25, or 31-50 strains from the same species, optionally excluding bacteria from any other species. In some embodiments, the compositions of the invention comprise more than one species (e.g., more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 17, 20, 23, 25, 30, 35, or 40 species) from the same genus, optionally excluding bacteria from any other genus. In some embodiments, the compositions of the invention comprise less than 50 species (e.g., less than 50, 45, 40, 35, 30, 25, 20, 15, 12, 10, 8, 7, 6, 5, 4, or 3 species) from within the same genus, optionally not including bacteria from any other genus. In some embodiments, the compositions of the invention comprise 1-50, 1-40, 1-30, 1-20, 1-15, 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, 2-50, 2-40, 2-30, 2-20, 2-15, 2-10, 2-5, 6-30, 6-15, 16-25, or 31-50 strains from within the same genus, optionally not including bacteria from any other genus. The invention includes any combination of the above.

[0248] In certain embodiments, the pharmaceutical composition of the invention comprises 1 to 50 distinct bacterial strains, such as 1 to 50, 1 to 40, 1 to 30, 1 to 20, 1 to 19, 1 to 18, 1 to 17, 1 to 16, 1 to 15, 1 to 14, 1 to 13, 1 to 12, 1 to 11, 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3 or 2 distinct bacterial strains. In certain embodiments, the pharmaceutical composition of the invention comprises 1 to 50 distinct bacterial strains, such as 1 to 50, 1 to 40, 1 to 30, 1 to 20, 1 to 19, 1 to 18, 1 to 17, 1 to 16, 1 to 15, 1 to 14, 1 to 13, 1 to 12, 1 to 11, 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3 or 2 distinct bacterial strains.

[0249] In some embodiments, the compositions of the invention further comprise a bacterial strain that has the same safety and therapeutic efficacy characteristics as the strains deposited with the NMI (Australia) under accession numbers V21 / 015887 and / or V21 / 015888.

[0250] In some embodiments, in which the composition of the present invention comprises two or more bacterial strains, species or genera, the individual bacterial strains, species or genera may be for administration separately, simultaneously or sequentially.For example, the composition may comprise all of the two or more bacterial strains, species or genera, or the bacterial strains, species or genera may be stored separately and administered separately, simultaneously or sequentially.In some embodiments, the two or more bacterial strains, species or genera are stored separately but mixed together before use.

[0251] Preferably, the compositions disclosed herein are administered to the gastrointestinal (GI) tract to allow delivery to the intestine and / or partial or total colonization of the intestine by the bacterial strain of the present invention. In other words, the bacteria may colonize part or all of the GI tract, and such colonization may be temporary or permanent. More specifically, the phrase "total colonization of the intestine" means that the bacteria have colonized all parts of the intestine (i.e., the small intestine, the large intestine, and the rectum). Additionally or alternatively, the term "total colonization" means that the bacteria are permanently colonized in some or all parts of the intestine.

[0252] Similarly, the phrase "partial colonization of the intestine" means that the bacteria have colonized some, but not all, parts of the intestine. Additionally or alternatively, the term "partial colonization" means that the bacteria are temporarily colonized in some or all parts of the intestine.

[0253] Transience of bacterial engraftment can be determined by periodically (e.g., daily or weekly) assessing the abundance of the bacterial strain of the present invention (e.g., in a fecal sample) after the end of the dosing interval to determine the washout period, i.e., the period from the end of the dosing interval until there are no detectable levels of the bacterial strain of the present invention. In some embodiments, the washout period is 14 days or less, 12 days or less, 10 days or less, 7 days or less, 4 days or less, 3 days or less, 2 days or less, or 1 day or less.

[0254] In some embodiments, the bacteria described above or elsewhere herein are transiently colonized in the large intestine.

[0255] In some embodiments, the bacterial strains of the present invention are obtained from human adult feces. In some embodiments in which the composition of the present invention comprises more than one bacterial strain, all of the bacterial strains are obtained from human adult feces, or if other bacterial strains are present, they are present only in minor amounts. The bacteria can be obtained from these human adult feces and cultured after being used in the composition of the present invention.

[0256] In some embodiments, the one or more Intestinicoccus bacterial strains are the only therapeutically active agents in the compositions of the invention. In some embodiments, the bacterial strains in the composition are the only therapeutically active agents in the compositions of the invention.

[0257] Compositions for use in accordance with the present invention may or may not require marketing approval.

[0258] In certain embodiments, the present invention provides the above pharmaceutical composition, wherein the bacterial strain is in a dried form. Optionally, the bacterial strain is reconstituted prior to administration. Optionally, the reconstitution is by use of a diluent as described herein. In certain embodiments, the present invention provides the above pharmaceutical composition, wherein the bacterial strain is spray dried. In certain embodiments, the present invention provides the above pharmaceutical composition, wherein the bacterial strain is freeze-dried or spray-dried and live. In certain embodiments, the present invention provides the above pharmaceutical composition, wherein the bacterial strain is freeze-dried or spray-dried and viable. In certain embodiments, the present invention provides the above pharmaceutical composition, wherein the bacterial strain is freeze-dried or spray-dried and capable of partially or fully colonizing the intestine. In certain embodiments, the present invention provides the above pharmaceutical composition, wherein the bacterial strain is dried (e.g., freeze-dried or spray-dried), viable, and capable of partially or fully colonizing the intestine. In some of the same embodiments and in some alternative embodiments, the bacterial strain transiently colonizes the intestine.

[0259] In some cases, the freeze-dried or spray-dried bacterial strains are reconstituted prior to administration. In some cases, reconstitution is by use of a diluent as described herein.

[0260] The compositions of the present invention may include a pharma- ceutically acceptable excipient, diluent or carrier.

[0261] In certain embodiments, the present invention provides a pharmaceutical composition comprising a bacterial strain of the present invention and a pharma- ceutically acceptable excipient, carrier, or diluent, the bacterial strain being in an amount sufficient to treat or prevent an inflammatory or autoimmune disorder when administered to a subject in need thereof. In some preferred embodiments, the inflammatory or autoimmune disorder is selected from the group consisting of inflammatory bowel disease (such as Crohn's disease or ulcerative colitis); asthma (such as allergic asthma or neutrophilic asthma); arthritis (such as rheumatoid arthritis, osteoarthritis, psoriatic arthritis, or juvenile idiopathic arthritis); fatty liver disease (such as nonalcoholic fatty liver disease (NAFLD)); ankylosing spondylitis; psoriasis; systemic lupus erythematosus (SLE); scleroderma; Sjogren's syndrome; vasculitis; and type 1 diabetes.

[0262] In certain embodiments, the present invention provides a pharmaceutical composition comprising the bacterial strain of the present invention and a pharma- ceutical acceptable excipient, carrier, or diluent, in an amount sufficient to treat or prevent an inflammatory or autoimmune disorder mediated by the STAT3 signaling pathway. In some preferred embodiments, the disorder is selected from the group consisting of inflammatory bowel disease (such as Crohn's disease or ulcerative colitis); asthma (such as allergic asthma or neutrophilic asthma); arthritis (such as rheumatoid arthritis, osteoarthritis, psoriatic arthritis, or juvenile idiopathic arthritis); fatty liver disease (such as nonalcoholic fatty liver disease (NAFLD)); ankylosing spondylitis; psoriasis; systemic lupus erythematosus (SLE); scleroderma; Sjogren's syndrome; vasculitis; and type 1 diabetes.

[0263] In certain embodiments, the present invention relates to the aforementioned pharmaceutical composition, wherein the amount of the bacterial strain is about 1×10 per gram by weight of the composition. 3 ~Approx. 1×10 11 A pharmaceutical composition is provided that is a colony forming unit (CFU).

[0264] In certain embodiments, the present invention provides a pharmaceutical composition as described above, wherein said composition is administered in a dose of up to or greater than 1 g, 3 g, 5 g, or 10 g.

[0265] In certain embodiments, the present invention provides a pharmaceutical composition as described above, wherein said composition is administered by a method selected from the group consisting of oral, rectal, subcutaneous, nasal, buccal, and sublingual.

[0266] In certain embodiments, the present invention provides a pharmaceutical composition as described above, comprising a carrier selected from the group consisting of lactose, starch, glucose, methylcellulose, magnesium stearate, mannitol and sorbitol.

[0267] In certain embodiments, the present invention provides a pharmaceutical composition as described above, comprising a diluent selected from the group consisting of ethanol, glycerol and water.

[0268] In certain embodiments, the present invention provides the above pharmaceutical composition, comprising an excipient selected from the group consisting of starch, gelatin, glucose, anhydrous lactose, free flowing lactose, beta-lactose, corn sweeteners, acacia, tragacanth, sodium alginate, carboxymethylcellulose, polyethylene glycol, sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, and sodium chloride.

[0269] In certain embodiments, the present invention provides a pharmaceutical composition as described above, further comprising at least one of a preservative, an antioxidant, and a stabilizer.

[0270] In certain embodiments, the present invention provides the aforementioned pharmaceutical composition, further comprising a preservative selected from the group consisting of sodium benzoate, sorbic acid, and esters of 4-hydroxybenzoic acid.

[0271] In certain embodiments, the present invention provides a pharmaceutical composition as described above, wherein the bacterial strain is in a dried form (e.g., freeze-dried, spray-dried, fluid-bed dried, etc.).

[0272] In certain embodiments, the present invention provides a pharmaceutical composition as described above, 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 a relative humidity of 50%, at least 80% of the bacterial strain as measured by colony forming units survives 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.

[0273] In some embodiments, the compositions of the present invention are provided in a sealed container comprising a composition described herein. In some embodiments, the sealed container is a sachet or a bottle. In some embodiments, the compositions of the present invention are provided in a syringe comprising a composition described herein.

[0274] The composition of the present invention may be provided as a pharmaceutical formulation in some embodiments. For example, the composition may be provided as a tablet or capsule. In some embodiments, the capsule is a gelatin capsule ("gel-cap"). The capsule may be a hard or soft capsule. In some embodiments, the formulation is a soft capsule. A soft capsule is a capsule that may have a certain degree of elasticity and flexibility due to the addition of softeners present in the capsule shell, such as glycerol, sorbitol, maltitol and polyethylene glycol. Soft capsules may be made, for example, based on gelatin or starch. Gelatin-based soft capsules are commercially available from various suppliers. Depending on the method of administration, such as oral or rectal, soft capsules may have various shapes, for example, round, oval, oblong, or torpedo-shaped. Soft capsules may be made by conventional methods, such as, for example, the Scherer method, the Accogel method, or the dropping or blowing method.

[0275] In some embodiments, the compositions disclosed herein are administered orally, which may include swallowing so that the compound enters the gastrointestinal tract.

[0276] Pharmaceutical formulations suitable for oral administration include solid plugs, solid particulates, semi-solids and liquids (including multiphase or dispersions), such as tablets; soft or hard capsules containing multiparticulates or nanoparticles, liquids (e.g., aqueous solutions), emulsions, or powders; lozenges (including liquid-filled); chews; gels; fast dispersing dosage forms; films; ovules; sprays; and buccal / mucoadhesive patches.

[0277] In some embodiments, the pharmaceutical formulation is an enteric formulation, i.e., a gastro-resistant formulation (e.g., resistant to the pH of the stomach) suitable for delivery of the composition of the invention to the intestine by oral administration. Enteric formulations may be particularly useful when the bacteria, or another component of the composition, is acid-sensitive (e.g., susceptible to degradation under gastric conditions).

[0278] In some embodiments, the enteric formulation comprises an enteric coating. In some embodiments, the formulation is in an enteric coated dosage form. For example, the formulation can be an enteric coated tablet or an enteric coated capsule, etc. The enteric coating can be a conventional enteric coating, for example, a conventional coating for tablets, capsules, etc. for oral delivery. The formulation can comprise a film coating, for example, a thin layer of an enteric polymer (e.g., an acid-insoluble polymer).

[0279] In some embodiments, the enteric formulation is essentially enteric, e.g., gastroresistant without the need for an enteric coating. Thus, in some embodiments, the formulation is an enteric formulation that does not include an enteric coating. In some embodiments, the formulation is a capsule made from a thermogelling material. In some embodiments, the thermogelling material is a cellulosic material, such as methylcellulose, hydroxymethylcellulose, or hydroxypropylmethylcellulose (HPMC). In some embodiments, the capsule includes a shell that does not include a film-forming polymer. In some embodiments, the capsule includes a shell, the shell includes hydroxypropylmethylcellulose, and does not include a film-forming polymer (as described in U.S. Patent Publication No. 2016 / 0067188). In some embodiments, the formulation is an essentially enteric capsule (e.g., VCAPS® from Capsugel).

[0280] In some embodiments, the composition is a probiotic or medical food comprising a bacterial strain of I. colisanans. The bacteria can be administered, for example, as a probiotic, in capsules, tablets, caplets, pills, troches, lozenges, powders, and / or granules. The strain can also be formulated as a nutraceutical, conventional food, medical food, or drug. The bacteria can also be administered as part of a fecal transplant or via a suppository. In some embodiments, the composition is formulated for delivery to the intestinal tract, as further described herein, with some embodiments having compositions further comprising a prebiotic.

[0281] 6.1 Concomitant administration of additional medications In some embodiments, the methods described herein can further include co-administering a second agent and / or treatment to the subject (e.g., as part of a treatment regimen). Combination therapy, when used, can be tailored to the particular indication. For example, when administering a strain of I. colisanans species to treat an inflammatory disorder (e.g., inflammatory bowel disease), it can be administered in combination with an anti-inflammatory agent or treatment known in the art that is approved for the clinical treatment of inflammatory disorders. Other indications can be treated similarly, for example, by combining the strains of I. colisanans species described herein with agents known in the art or approved for the clinical treatment of these indications.

[0282] Suitable anti-inflammatory agents that may be used in the treatment of inflammatory bowel disease include, but are not necessarily limited to, the group including 5-aminosalicylates, corticosteroids, azathioprine, infliximab, and adalimumab.

[0283] The present invention also includes compositions as described above further comprising an anti-inflammatory agent. Such compositions may optionally be in the form of a single composition or alternatively may be in the form of two or more separate compositions.

[0284] 7. Screening Method The present invention also includes a method for identifying a bacterial strain suitable for use in the method of the present invention. Such a method typically involves screening bacterial strains with a particular functional activity. Suitable assays include those described in the examples below, but any assay for measuring intestinal barrier function, mucosal healing, modulation of NF-κB activity, or modulation of STAT3 signaling is equally applicable.

[0285] In some embodiments, the screening method identifies the ability of a bacterial strain of Intestinicoccus to modulate the STAT3 signaling pathway. As an illustrative example, the present invention provides a method of blocking or inhibiting activation of STAT3 signaling in a target cell, comprising contacting the target cell with at least a soluble component of a bacterial cell preparation of the species Intestinicoccus colisanans to block or inhibit activation of STAT3 signaling in the target cell.

[0286] In some embodiments of this type, the target cells are selected from the group including screening bacterial strains for functional reporter cells (e.g., HEK cells), immune cells (e.g., Th17 immune cells), epithelial cells, and endothelial cells.

[0287] In some embodiments, the bacterial cell preparation comprises a bacterial cell culture. Suitably, the soluble components may comprise the supernatant of the bacterial cell culture. In some embodiments of this type, the soluble components are substantially depleted of bacterial cells.

[0288] In some alternative embodiments, the bacterial cell preparation comprises a bacterial cell pellet. Preferably, the bacterial cells of the cell pellet are lysed by any means known in the art. After cell lysis, the soluble fraction of the cell lysate is typically separated from the insoluble fraction. The cell lysate may be subjected to further processing (e.g., diluted in a buffer) or exposed to a processing reagent before being present in the screening assay.

[0289] 8. Mode of Administration Preferably, the compositions of the present invention are administered to the gastrointestinal tract to allow delivery to the intestine by the bacterial strains of the present invention. Preferably, the compositions of the present invention are formulated to be administered to the gastrointestinal tract to allow delivery to the intestine by the bacterial strains of the present invention. In some embodiments, the compositions of the present invention are formulated to be administered to the gastrointestinal tract to allow delivery to the intestine and partial or total colonization of the intestine by the bacterial strains of the present invention.

[0290] In certain embodiments, the compositions of the present invention may be administered as a foam, as a spray, or as a gel.

[0291] In certain embodiments, the compositions of the present invention may be administered as a suppository, such as a rectal suppository, for example, in the form of theobroma oil (cocoa butter), synthetic hard fats (e.g., SUPPOCIRE®, WITEPSOL), glycerogelatin, polyethylene glycol, or soap glycerin compositions.

[0292] In certain embodiments, compositions of the invention are administered to the gastrointestinal tract via a tube, e.g., a nasogastric tube, an orogastric tube, a stomach tube, a jejunostomy tube (J-tube), a percutaneous endoscopic gastrostomy (PEG), or a port, e.g., a chest wall port, providing access to the stomach, jejunum, and other suitable access ports.

[0293] The compositions of the present invention may be administered once or sequentially as part of a treatment regimen. In certain embodiments, the compositions of the present invention are administered daily (either once or several times). In certain embodiments, the compositions disclosed herein are administered periodically, for example, daily, every two days, or weekly, for an extended period of time, such as at least one week, two weeks, one month, two months, six months, or one year.

[0294] In some embodiments, the compositions disclosed herein are administered for 7 days, 14 days, 16 days, 21 days, or 28 days, or for no more than 7 days, 14 days, 16 days, 21 days, or 28 days. For example, in some embodiments, the compositions disclosed herein are administered for 16 days.

[0295] In a particular embodiment of the invention, treatment according to the invention is accompanied by an assessment of the patient's gut microbiota. If delivery and / or partial or total colonization with the strains of the invention is not achieved and, as a result, efficacy is not observed, treatment may be repeated, or if delivery and / or partial or total colonization is successful and efficacy is observed, treatment may be discontinued.

[0296] In certain embodiments, the compositions of the invention may be administered to a pregnant animal, e.g., a mammal such as a human, to prevent inflammatory or autoimmune disorders (such as those disclosed herein) that develop in the utero and / or in the offspring after birth.

[0297] The compositions of the invention may be administered to patients who have been diagnosed with a disease or condition mediated by dysregulation of intestinal barrier function or who have been identified as being at risk for a disease or condition mediated by intestinal barrier dysregulation, to patients who have been diagnosed with a disease or condition mediated by the STAT3 signaling pathway or who have been identified as being at risk for a disease or condition mediated by the STAT3 signaling pathway, or to patients who have been diagnosed with an inflammatory or autoimmune disorder (such as those disclosed herein). The compositions may also be administered as a prophylactic measure to prevent the onset of a disease or condition mediated by the STAT3 signaling pathway in healthy patients.

[0298] The compositions disclosed herein may be administered to patients who have been diagnosed with an inflammatory or autoimmune disorder, particularly an inflammatory or autoimmune disorder mediated by the microbiota-gut axis, or who have been identified as at risk for an inflammatory or autoimmune disorder, particularly an inflammatory or autoimmune disorder mediated by the microbiota-gut axis. The compositions may also be administered as a prophylactic measure to prevent the onset of an inflammatory or autoimmune disorder, particularly an inflammatory or autoimmune disorder mediated by the microbiota-gut axis, in healthy patients.

[0299] The compositions of the invention may be administered to a patient who has been identified as having an abnormal gut microbiome, for example, the patient may have reduced or absent colonization by bacteria of the genus Intestinicoccus, particularly I. colisanans.

[0300] The compositions of the present invention may be administered as a food product, such as a nutritional supplement.

[0301] Generally, the compositions of the present invention are intended for the prevention or treatment of human diseases, but may also be used to treat animals, including monogastric mammals such as poultry, pigs, cats, dogs, horses, or rabbits. The compositions of the present invention may be useful for enhancing the growth and performance of animals. When administering to animals, oral gavage may be used.

[0302] In some embodiments, the subject to which the composition is administered is an adult. In some embodiments, the subject to which the composition is administered is a human infant.

[0303] 9.Culture method Bacterial strains for use in the present invention may be cultured using standard microbiology techniques detailed in references such as those taught in McSweeney, 2005.

[0304] The solid or liquid medium used for the cultivation can be selected from, for example, TY or PYG medium.

[0305] Exemplary medium compositions suitable for use in the present invention include those provided in Table 1. [Table 2]

[0306] So that the invention may be readily understood and put into practice, certain preferred embodiments are illustrated by the following non-limiting examples. EXAMPLES

[0307] Relevance of Intestinicoccus colisanans to health and disease Inflammatory bowel disease is characterized by structure-function alterations in the microbiome, where both the prevalence and abundance of select gut bacteria are significantly decreased in the IBD gut when compared to the healthy gut. Several studies have shown that these bacteria may modulate the pathogenesis of IBD (Mallone et al., 2011; and Sokol et al., 2008), but the main obstacle to using these bacteria to develop new therapeutics is that low-resolution 16S rRNA-based profiling does not provide sufficient resolution to accurately discriminate between healthy and IBD-associated strains at low taxonomic levels (i.e., genus, species, strains).

[0308] We used the Microba Disease Database (MDD), which contains high-resolution fecal intestinal metagenomic data and associated host metadata from 6,020 adults, to study the prevalence of I. colisanans in inflammatory and autoimmune diseases. Metagenomic sequence reads were analyzed using Microba Community Profiler (MCP) (Parks et al., 2021).

[0309] I. colisanans was thought to be predominant in healthy humans, but was less commonly detected in inflammatory and autoimmune diseases (Figure 1A). The strongest impact was observed in IBD, including both major subtypes of ulcerative colitis and Crohn's disease (Figure 2A and Table 2). This observation was replicated in an independent IBD cohort previously published by Harvard (Franzosa et al., 2018, Figure 1B, and Table 3). [Table 3] [Table 4]

[0310] Isolation and genome-scale analysis of I. colisanans To better understand the role that I. colisanans plays in health and the pathogenesis of IBD, we isolated two new isolates, designated I. colisanans MH27-1 and MH27-2, from healthy human donors by limiting dilution-to-extinction enrichment followed by plating to obtain single colonies. I. colisanans MH27-1 and MH27-2 were grown on TY- and PYG-based media and were typically observed as Gram-variant stained coccus-like cells (Figure 2A).

[0311] Phylogenetic reconstruction of the genus Intestinicoccus using NCBI and high-quality GenBank and RefSeq genomes from I. colisanans MH27-1 and MH27-2 revealed that these isolates were placed with high confidence within the I. colisanans clade, close to several uncultured species, and sister to the genus Acutalibacter (Figure 2B). I. colisanans MH27-1 and I. colisanans MH27-2 are sugar fermenters and are predicted to utilize a wide range of carbohydrate sources, particularly starch, galactose, and mannose. Complete or nearly complete biosynthetic pathways were identified for most amino acids, except tryptophan, glycine, histidine, phenylalanine, and tyrosine. Several pathways for the uptake and fermentation of amino acids (Arg, Asp, Cys, Met, Glu, Gln, Met, Ser, and Thr) were also identified, but are likely not the primary energy source. Metabolic modeling of I. colisanans MH27-1 and I. colisanans MH 27-2 isolates revealed that when fed glucose and other hexose sugars, the main by-product of fermentation was acetic acid. AntiSmash identified BGCs for two RiPP sactipeptides in both strains, but without close homology to BGCs in public databases. DeepBGC identified the same sactipeptide RiPP and seven additional putative BGCs with >1 coding region and deepBGC score >0.75.

[0312] I. colisanans enhances intestinal barrier function To evaluate the role of I. colisanans in the healthy intestine, naïve C57Bl / 6 SPF mice were treated with I. colisanans MH27-1 for 8 days (Figure 3A). During this treatment period, no pathology or changes in general appearance, behavior, posture, mobility, or neurological behavior were observed. Similarly, there was no significant change in body weight, and colon length and weight / length ratio were unaffected in I. colisanans MH27-1 treated animals compared to vehicle controls (Figure 3B-D). I. colisanans MH27-1 did not result in any significant histological changes in the colon compared to vehicle, as determined by assessing epithelial damage, inflammation, and hypervascularization, either alone or combined, as histopathological scores (Figure 3E-H).

[0313] We hypothesized that big data approaches could be used to identify novel candidate live bacterial formulations for inflammatory bowel disease. We therefore tested the therapeutic efficacy of I. colisanans MH27-1 in an acute model of DSS-induced murine colitis, a well-documented model of epithelial damage and repair (Figure 4A). DSS treatment resulted in significant disease activity compared to vehicle controls. A significant reduction in body weight was observed (Figure 4B), which has been shown to be an accurate and reliable indicator of colitis (Britto, 2019). As expected, prednisone exacerbated DSS-induced weight loss (Yamamoto, 2013), but DSS-induced weight loss was ameliorated by treatment with I. colisanans MH27-1 or F. prausnitzii A2-165 (Figure 4B). Endoscopic analysis revealed a progressive increase in disease activity in all treatment groups, with F. prausnitzii A2-165 and I. colisanans MH27-1, but not prednisone, resulting in lower disease activity compared to the vehicle-treated group on day 6 (Figure 4C).

[0314] Histological analysis of DSS-treated mice revealed significant intestinal damage characterized by crypt loss, epithelial erosion, and ulceration. Notably, treatment with I. colisanans MH27-1 led to significant amelioration of pathology characterized by crypt re-formation and re-epithelialization (Figure 4D), as evidenced by improved histopathological healing (Figure 4E) and epithelial damage (Figure 4F). As expected, prednisone and F. prausnitzii A2-165 also led to significant amelioration of disease pathology.

[0315] The therapeutic efficacy of I. colisanans MH27-2 in an acute mouse model of DSS colitis was examined with prednisone acting as a positive control drug. DSS treatment resulted in significant colitis as evidenced by histopathological scoring of colonic tissue damage and inflammation.

[0316] The histological findings of colitis were ameliorated by daily treatment with I. colisanans MH27-2 or the positive control drug prednisone. Notably, the total histological score of DSS-treated mice treated daily with I. colisanans MH27-2 was significantly lower compared to DSS control mice (Figure 4G). This effect was also observed for each of the histological subscores, demonstrating that treatment with I. colisanans MH27-2 reduced both epithelial damage (Figure 4H) and inflammation (Figure 4I) in DSS-treated mice.

[0317] The therapeutic efficacy of I. colisanans MH27-2 drug substance (DS) in an acute mouse model of DSS colitis was investigated using minocycline and prednisone as positive controls. DSS treatment resulted in significant colitis as evidenced by both in vivo colitis measures (disease activity index, body weight, fecal occult blood) and histopathological damage to colonic tissue (histology score and subscores).

[0318] The disease activity index was significantly improved by daily treatment with I. colisanans MH27-2 DS at a dose of 2×10^6 cells per day (Fig. 4J) or by the positive control minocycline (p<0.05). In particular, the disease activity index subscores of body weight change (Fig. 4K) and fecal occult blood (Fig. 4L) were improved by daily treatment with I. colisanans DS or minocycline. The total histopathological score was significantly improved in DSS-treated mice treated daily with either minocycline or I. colisanans MH27-2 DS at a dose of 2×10^8 cells per day (Fig. 4M). This therapeutic effect was characterized by improvements in mucosal structure score (Fig. 4N), erosion / ulceration score (Fig. 4O) and percent lesion score (Fig. 4P).

[0319] The IL-23-Th17 cell immune axis is central to the pathogenesis of inflammatory bowel disease and is a validated therapeutic target (Friedrich, 2019). Because the DSS model of murine colitis is primarily based on Th1 polarized immunity (Yang, 2017), we also tested the therapeutic efficacy of I. colisanans MH27-1 in the murine SKG model. SKG mice carry a mutation in the ZAP-70 gene and develop IL-23-driven Crohn's disease-like ileitis and autoimmune inflammatory arthritis after disease onset with curdlan treatment (Figure 5A) (see Benham, 2014). Histological analysis of vehicle-treated mice revealed significant intestinal damage characterized by inflammatory cell infiltration and granuloma formation 7 days after curdlan treatment. As expected, treatment with anti-IL-23 monoclonal antibodies resulted in a significant reduction in histological damage. Treatment with I. colisanans MH27-1 also resulted in a significant improvement in pathology, as evidenced by improved histopathological scores (Figure 5B).Similarly, treatment with I. colisanans MH27-1 also resulted in a significant decrease in the production of cytokines central to disease pathogenesis, including IL-6 and IL-12 (IL-12p70) (Figures 5C,D).

[0320] The therapeutic efficacy of I. colisanans MH27-2 in an acute mouse model of TNBS-induced colitis was also examined using cyclosporine A as a positive control (Figure 5E). The TNBS model is widely used because it shares immunopathology with Crohn's disease. TNBS treatment resulted in significant macroscopic damage that was ameliorated by treatment with cyclosporine A or I. colisanans MH27-2 (Figure 5F). Notably, I. colisanans MH27-2 showed a significant (p<0.05) improvement in ulcer / inflammation scores (Figure 5G). TNBS treatment resulted in significant histological damage that was ameliorated by treatment with cyclosporine A or I. colisanans MH27-2 (Figure 5H). Colitis lesions, including diffuse mucosal architectural abnormalities, ulceration, crypt dilation, aberrant crypts, crypt loss, mucosal gland distortion, goblet cell loss, and focal to multifocal inflammatory cell infiltration, were less pronounced in I. colisanans MH27-2 compared to the vehicle group, and lesion scores were significantly (p<0.05) reduced in the treatment groups, as reflected by improvements in the degree of individual inflammation, erosion or ulceration, epithelial regeneration, and percent lesion scores (Figure 5I-L). Treatment with I. colisanans MH27-2 resulted in a significant reduction in IL-6 concentrations when compared to vehicle-treated TNBS controls (Figure 5M).

[0321] Taken together, these data demonstrated that I. colisanans MH27-1 did not cause any adverse effects in DSS-treated or untreated mice, and that I. colisanans MH27-1 and 2 promoted mucosal healing in DSS- or TNBS-treated C57Bl / 6 and SKG mice.

[0322] I. colisanans inhibits IL-6-mediated activation of STAT3. Elevated levels of the proinflammatory cytokine IL-6 and signaling through its receptor IL-6R are associated with the pathogenesis of IBD. In particular, IL-6 contributes to chronic inflammation in the intestinal tract due to its proinflammatory and anti-apoptotic effects on immune cells. These effects are mediated by IL-6 receptor binding, which triggers JAK kinase activation and STAT3 dimerization in combination with activation of MAPK / ERK and other downstream kinases. Herein, we investigated whether I. colisanans MH27-1 and MH27-2 can suppress IL-6 classical and trans-signaling-mediated STAT3 activation using the HEK-Blue™ IL-6 reporter cell line. The HEK-Blue™ IL-6 reporter cell line constitutively expresses the human IL-6 receptor, and binding of IL-6 to the receptor induces expression of the STAT3-responsive SEAP reporter. Tofacitinib was used as a control, and as expected, IL-6 and IL-6 / IL-6R-mediated STAT3 activation was completely prevented by tofacitinib (Fig. 6). It was shown that raw culture supernatants of I. colisanans MH27-1, MH27-2, and MH27-3 and their <3 kDa filtered fractions significantly suppressed SEAP reporter activity (Fig. 6A-C), and raw culture supernatants of I. colisanans MH27-4 and MH27-5 also suppressed SEAP reporter activity compared to medium (Fig. 6D-E). In contrast, raw culture supernatants of R. bromii MCB950 and their <3 kDa filtered fractions did not significantly suppress SEAP reporter activity (Fig. 6F). Furthermore, I. colisanans MH27-2 suppressed IL-6 trans-signaling-mediated STAT3 activation (Fig. 6G).

[0323] I. colisanans promotes migration of human intestinal epithelial cells. Damage to the intestinal barrier is common in IBD. Rapid migration of intestinal epithelial cells is a key component of the wound healing process to re-establish homeostasis. To determine whether I. colisanans MH27-1 or MH27-2 could affect the motility of intestinal epithelial cells, a Transwell® migration assay was used. HCT116 cells were seeded at the apical end of Transwell® chambers, and the ability of I. colisanans extracts to promote migration to the basolateral side of the chambers was assessed. Untreated cells had a basal level of migration to the basolateral side of the membrane, which was not affected by treatment with TY medium or the enterobacterium Clostridium bolteae BAA-613 (Figure 7A). I. colisanans MH27-1 and MH27-2 significantly promoted migration of HCT116 cells to the basolateral side (Figure 7A).

[0324] The migration-promoting effect of I. colisanans was further confirmed using an IncuCyte scratch wound assay. After induction of scratch wounding, HCT116 cells showed an accelerated rate of wound closure in the presence of extract from I. colisanans MH27-2 compared to control cells treated with medium (Figure 7B).

[0325] I. colisanans MH27 inhibits IL-23-mediated STAT3 activation. We next sought to investigate whether bacterial products naturally produced by the gut bacterium I. colisanans MH27 could modulate IL-23-mediated STAT3 activation. The JAK-STAT immune axis is a recognized and validated drug target for IBD (Salas et al., 2020) and other diseases (McLornan et al., 2021), with JAK-STAT pathway signaling targeted by several approved IBD therapeutics, including anti-IL-23 antibodies (e.g., ustekinumab) and small molecule inhibitors (e.g., tofacitinib) (Hu et al., 2021). Because STAT3 inhibition can reduce harmful inflammation, I. colisanans MH27 and / or its bioactive substances could potentially be used as novel immunomodulatory therapies for IBD and other diseases. Therefore, we investigated whether I. colisanans MH27 could suppress IL-23-mediated STAT3 activation using the HEK-Blue™ IL-23 reporter cell line. The HEK-Blue™ IL-23 reporter cell line constitutively expresses the human IL-23 receptor, and binding of IL-23 to the receptor induces expression of the STAT3-responsive SEAP reporter. Tofacitinib, a pharmacological JAK-STAT inhibitor, was used as a control.

[0326] As expected, IL-23-mediated STAT3 activation was completely prevented by tofacitinib (Figure 8). I. colisanans MH27 cell-free and <3 kDa filtered culture supernatants significantly suppressed SEAP reporter activity compared to TY medium controls. In contrast, neither raw nor <3 kDa filtered supernatants prepared from Ruminococcus bromii MCB950 suppressed SEAP reporter activity compared to MCM medium controls (Figure 8, right graph).

[0327] These data indicate that the secretome of I. colisanans MH27, but not R. bromii MCB950, is able to suppress the IL-23 / STAT3 signaling axis in vitro. Based on fractionation of culture supernatants, the inhibitory effect on STAT3 activation appears to be mediated by one or more secreted low molecular weight bioactive substances.

[0328] I. colisanans ameliorates IFNγ-driven decline in intestinal barrier integrity. The ability of I. colisanans MH27 culture supernatant to modulate barrier function was examined using T84 cells. To disrupt barrier function, basolateral treatment with IFNγ was used. After 48 h of IFNγ addition to T84 cells, there was a large decrease in resistance indicating an increase in barrier permeability. Treatment with <3 kDa fractionated culture supernatant from I. colisanans MH27 ameliorated the decrease in TEER most significantly after 168 h compared to YG / V medium control (Figure 9, p<0.05 at 168, 192, 216, 240, 288, 312 and 336 h as assessed by two-way ANOVA).

[0329] I. colisanans ameliorates IL-6-driven decline in intestinal barrier integrity. The ability of I. colisanans MH27-2 to modulate barrier function was investigated by monitoring the TEER of T84 cells during and after induction of loss of barrier integrity with the known barrier disrupting factor IL-6. T84 cells were treated with IL-6 for 96 h and, as expected, a significant decrease in TEER could be observed, indicating an increase in barrier permeability. Co-treatment with I. colisanans MH27-2 culture supernatant extract ameliorated the IL-6-mediated TEER decrease in a dose-dependent manner (Figure 10).

[0330] I. colisanans ameliorates IFNγ-mediated reduction of ZO1 expression. Tight junctions (TJs) form a continuous barrier between epithelial cells and act to control paracellular permeability. ZO1 plays a key role in the assembly of tight junctions, and therefore we evaluated the ability of I. colisanans MH27 supernatant extract to alleviate IFNγ-mediated ZO1 expression loss in T84 cells. Stimulation with IFNγ caused a marked decrease in ZO1 expression (Figure 11). Pretreatment with YG / V extract did not significantly affect the decrease in ZO1 expression (Figure 11). In contrast, pretreatment with I. colisanans MH27-1, MH27-2 and MH27-3 supernatant extracts ameliorated the IFNγ-induced decrease in ZO1 expression (Figure 11).

[0331] I. colisanans produces metabolites that regulate intestinal barrier integrity. Based on the ability of I. colisanans supernatant extracts to regulate ZO1 expression, we next investigated the ability of Strata X-100-derived fractions of I. colisanans MH27-2 culture supernatants to regulate ZO1 expression. By this approach, we determined that the ability to regulate ZO1 expression was fractionable and localized to the 15% and 30% fractions (Figures 12A-C).

[0332] Metabolites produced by I. colisanans MH27 ameliorate IFNγ-mediated decrease in ZO1 expression. Based on these data, we hypothesized that I. colisanans produces metabolites that regulate inflammatory responses and barrier integrity in intestinal epithelial cells. Thirty metabolites (classified as level 1 or 2a) were identified in the cell-free culture supernatant and were increased by more than 1.5-fold compared to the YG / V medium control (Table 4). These included metabolites previously reported to regulate inflammation, immune cell infiltration, oxidative stress, and barrier function (e.g., ornithine, indole-3-lactic acid, allopurinol, propionylcarnitine, pyrogallol, 3-(2-hydroxyethyl)indole, and N-acetyl-cysteine). Furthermore, 29 and 48 metabolites were increased by more than 1.5-fold in the 15% and 30% fractions, respectively, compared to the YG / V medium control (Table 4). These included metabolites previously shown to regulate inflammation and barrier integrity (e.g., tryptophol, indole-3-lactic acid, indole-3-propionic acid, cyclo(-Phe-Pro)). The immunomodulatory metabolite indole-3-acrylic acid was also identified in the 60% fraction. Note that some identified metabolites were not present in the control samples, and therefore fold changes could not be calculated.

[0333] Having identified candidate intestinal barrier-modulating metabolites, we next evaluated the ability of selected metabolites to modulate IFNγ-mediated ZO1 expression loss in T84 cells. To this end, T84 cells were pretreated with ornithine, indole-3-acrylic acid (IAyA), or indole-3-propionic acid (IPA) for 18 h, followed by stimulation with IFNγ for 48 h. As previously observed, stimulation with IFNγ caused a marked decrease in ZO1 expression (Fig. 13A, B). Pretreatment with ornithine, IAyA, and IPA all significantly improved the IFNγ-induced decrease in ZO1 expression (Fig. 13A, B). Separately, we also confirmed that cyclo(-Phe-Pro) suppressed IL-23-mediated STAT3 activation (Fig. 13C). [Table 5-1] [Table 5-2] [Table 5-3]

[0334] I. colisanans exhibits an anti-inflammatory IL-10 / IL-12 cytokine ratio Previous studies have shown that the ability of bacteria to induce IL-10 and IL-12 secretion from PBMCs in vitro correlates with their in vivo immunomodulatory potential (Foligne et al., 2007; and Sokol et al., 2008). In particular, the IL-10:IL-12 ratio is widely used to distinguish strains that exhibit anti-inflammatory (high IL-10:IL-12 ratio) or pro-inflammatory (low IL-10:IL-12 ratio), and a mean IL-10:IL-12 ratio above 5 correlates with protection against TNBS-induced experimental colitis. Therefore, the ability of I. colisanans to induce cytokine production from PBMCs was evaluated.

[0335] Treatment with I. colisanans resulted in an IL-10:IL-12 ratio of 30 (FIG. 14), further demonstrating the strong anti-inflammatory activity observed in the above data.

[0336] I. colisanans exhibits NF-κB inhibitory activity The NF-κB signaling axis plays a key role in the pathogenesis of inflammatory bowel disease (IBD) and is a recognized and validated therapeutic target. We show that I. colisanans MH27-2, MH27-3, and MH27-5 cell-free and <3 kDa filtered culture supernatants significantly suppressed luciferase reporter activity compared to the medium control. In contrast, raw supernatant prepared from R. bromii MCB950 suppressed reporter activity compared to the medium control (Figure 15A, D).

[0337] Materials and Methods Bacterial strains, culture conditions, and analyses. Fecal samples were collected from healthy adults with no history of gastrointestinal disorders and mixed with equal weight / volume of sterile, oxygen-free glycerol solution (McSweeney et al., 2005). Donors had not taken antibiotics for 3 months prior to fecal sample collection. All samples were collected with informed consent and in accordance with ethical guidelines approved by Bellberry Limited (HREC2018-05-400-A-6). I. colisanans and Faecalibacterium prausnitzii were routinely processed in Coy vinyl anaerobic chambers with an oxygen-free atmosphere (85% N2:10% CO2:5% H2). I. colisanans were routinely cultured in TY or YG / V medium (Table 1) and F. prausnitzii in TY medium (Table 1). All isolates were stored by mixing 3 mL of actively growing culture with an equal volume of glycerol solution and storing at −80°C.

[0338] Isolation of I. colisanans. Isolates of I. colisanans were generated by inoculating donor fecal samples, in which I. colisanans was present at a relative abundance of 0.37%, into custom medium (trehalose 1 g / L, alanine 400 mg / L, tryptophan 80 mg / L, methionine 200 mg / L, phenylalanine 200 mg / L, tyrosine 200 mg / L, butyric acid 400 μL / L, salt 2 75 ml / L, salt 3 75 ml / L, sodium bicarbonate 8 g / L, resazurin 1 ml / L, cysteine ​​hydrochloride 1 ml / L, vitamin solution 1 ml / L) followed by serial dilution to limiting. The limiting dilution culture series was sequenced and a low diversity enrichment culture with 77% I. colisanans relative abundance was identified. This enrichment culture was then used to establish a further limiting dilution culture series and a low diversity enrichment with >79% I. colisanans was identified. Colonies were harvested on PYG agar and subsequently picked into PYG broth. From this, a biculture consisting of I. colisanans and Ruthenibacterium lactatiformans was identified. To produce a pure culture of I. colisanans, the biculture was inoculated into YCFAmod broth and the enrichment culture was then streaked onto YCFAmod agar. Two distinct colony types were observed after several days and were purified. This approach identified a Gram-variant staining coccus-like isolate, which was designated I. colisanans MH27-1 after whole genome sequencing.

[0339] Isolates of I. colisanans MH27-2 were generated by inoculating a donor fecal sample, in which I. colisanans was present at a relative abundance of 0.38%, into custom medium (1 g / L maltose, 400 mg / L alanine, 80 mg / L tryptophan, 200 mg / L methionine, 200 mg / L phenylalanine, 200 mg / L tyrosine, 125 mg / L histidine, 75 ml / L salt 2, 75 ml / L salt 3, 8 g / L sodium bicarbonate, 1 ml / L resazurin, 1 ml / L cysteine ​​hydrochloride, and 1 ml / L vitamin solution) and then serially diluting to the limit. The limiting dilution culture series was sequenced and an enrichment with an I. colisanans relative abundance of 72.6% was identified. The enrichment was streaked onto PYG plates and isolates with coccus-like cell morphology were identified. After purification, a Gram-variant staining coccus-like isolate was identified and named I. colisanans MH27-2 after whole genome sequencing.

[0340] Isolates of I. colisanans MH27-3 were generated by inoculating a donor fecal sample, in which I. colisanans was present at a relative abundance of 0.38%, into custom medium (maltose 1 g / L, alanine 400 mg / L, tryptophan 80 mg / L, methionine 200 mg / L, phenylalanine 200 mg / L, tyrosine 200 mg / L, histidine 125 mg / L, salt 2 75 ml / L, salt 3 75 ml / L, sodium bicarbonate 8 g / L, resazurin 1 ml / L, cysteine ​​hydrochloride 1 ml / L, vitamin solution 1 ml / L) followed by serial dilution to limiting. Limiting dilution culture series were sequenced and an enrichment with an I. colisanans relative abundance of 14.5% was identified. This enrichment was used to inoculate a second limiting dilution experiment in the same GDI medium, yielding a new 28% enrichment of I. colisanans with other bacterial species at less than 27% relative abundance. The enrichment was plated on YG / V and a single colony was identified consisting of Gram-variant stained coccus-like cells. The colony was picked and streaked two more times on YG / V agar. After whole genome sequencing, the pure isolate was designated I. colisanans MH27-3.

[0341] I. colisanans MH27-4, MH27-5, and MH27-6 were produced from donor fecal samples using a microbe-based single-cell sorting approach. For I. colisanans MH27-4, approximately 1 g of fecal sample containing I. colisanans at a relative abundance of 0.3% was mixed with 1 mL of anaerobic buffer dilution solution and vortexed for 10 seconds to separate the bacteria from the fecal debris. For I. colisanans MH27-5, approximately 1 g of fecal sample containing I. colisanans at a relative abundance of 0.67% was mixed with 1 mL of anaerobic buffer dilution solution and vortexed for 10 seconds to separate the bacteria from the fecal debris. For I. colisanans MH27-6, approximately 1 g of fecal sample containing I. colisanans at a relative abundance of 2.5% was mixed with 1 mL of anaerobic buffer diluent and vortexed for 10 seconds to separate the bacteria from the fecal debris. Ruminococcus bromii MCB950 was similarly generated from donor fecal samples using a microbe-based single-cell sorting approach and used for comparative analysis. For R. bromii MCB950, approximately 1 g of fecal sample containing R. bromii at a relative abundance of 5.5% was mixed with 1 mL of anaerobic buffer diluent and vortexed for 10 seconds to separate the bacteria from the fecal debris. Bacterial cells were sorted using a BD FACSAria™ Fusion Flow Cytometer equipped with a 100 μm nozzle and a small particle detector according to the manufacturer's instructions. The system was pressurized at 20 psi and events were triggered based on scattering, with a threshold set using 0.2 μm filtered PBS to allow few events above the noise floor. Bacterial cells were also sorted using a CytoFLEX SRT Benchtop cell sorter in a COY anaerobic chamber. The instrument was set up and quality controlled according to the manufacturer's instructions. Dry ice was placed in the anaerobic chamber to keep the instrument within the set temperature range. The Fusion and SRT sheaths were sparged with nitrogen gas for 1 hour before sorting.To select the bacterial cells, an aliquot was filtered through a 40 μm filter followed by dilution of 10 ml of the filtrate using 0.2 μm filtered anaerobic buffer dilution solution (i.e., 38 ml / L each of salt solutions 2 and 3 (McSweeney et al., 2005)). -3 Dilutions were prepared. The diluted filtrate was run to determine the dilution resulting in 500-1200 events per second. Targets were gated based on scatter and doublets were excluded (Figure 16). Single cells were plated on TY agar plates and incubated at 37°C for up to 3 weeks. Isolates were identified by whole genome sequencing after growth in TY broth. This approach tentatively identified isolates belonging to I. colisanans and R. bromii. I. colisanans isolates were purified by repeatedly streaking single colonies on YG / V agar and R. bromii was purified by repeatedly streaking single colonies on TY agar. The final purified isolates were glycerol stocked and subjected to whole genome sequencing, and this approach generated isolates designated I. colisanans MH27-4 and MH27-5.

[0342] For I. colisanans MH27-6, an enrichment containing I. colisanans MH27-6 at 10.6% relative abundance was identified following growth of the cell-sorted isolate in TY broth. From a glycerol stock of this enrichment, 200 μl was used to inoculate YG / V medium, enriching I. colisanans to 71.5% relative abundance. I. colisanans colonies were generated and subsequently purified by streaking on YG / V agar. The final purified isolate was stocked in glycerol and subjected to whole genome sequencing, and this approach generated an isolate designated I. colisanans MH27-6.

[0343] Metabolic restructuring. Protein coding sequences were predicted and annotated using the annotate function of enrichM (0.6.2). Briefly, enrichM uses prodigal (version) in -p meta mode to identify protein coding sequences. Amino acid sequences were then searched against the UniRef100 database (version) using DIAMOND (version), with EC, TCDB and eggnog classifications taken from the id mapping files distributed with UniRef. Functional domains, key metabolic markers and carbohydrate active (CAZy) enzymes were annotated using Hmmer hmmsearches (version 3.1b2) against Pfam (release 33.0), TIGRFAM (release 15.0), and dbCAN2 (downloaded in September 2019), respectively. Metabolic pathways were identified using the classify function of enrichM, which evaluates annotations and their genomic locations against manually defined metabolic pathway definitions. A pathway was considered to be present in the genome if it encoded more than 80% of the required proteins and passed all required synteny checks. These automatically predicted pathways were then manually assessed. Furthermore, gutSMASH (version 1.0.0) was applied to identify common functions mediated by the gut microbiome.

[0344] Phylogenetic tree. Clade 23560 in the species representation tree of GTDB r89 was visualized using the R libraries phytools (v0.7.70), ape (v5.4) and ggtree (v2.2.4). Separate genome trees were constructed from high-quality genomes (>90% contamination and <5% contamination by checkM analysis) within the genus Intestinococcus (NCBI r89) and isolate MH27. For each genome, a set of 122 bacteria-specific conserved marker genes was extracted from each genome using gtdbtk identify. These genes were aligned to the profile HMM and concatenated into a single alignment with gtdbtk align, and a maximum likelihood phylogenetic tree was constructed from the alignments using FastTree (v2.1.10) and gtdbtk infer. Nonparametric bootstrap values ​​were estimated from 1000 replicates using GenomeTreetk (v0.1.6).

[0345] Preparation of bacterial strains for animal experiments. I. colisanans strains were grown to early stationary phase in PYG or YG / V. F. prausnitzii was grown in TY medium. The cell density of the individual cultures was calculated using a Helber counting chamber. To prepare the bacterial gavage solutions, the individual cultures were centrifuged at 5000 g for 10 min under a layer of sterile mineral oil, and then the cell-free supernatant was discarded. The cell pellet was washed with 1.5 ml of sterile anaerobic buffer (salt solutions 2 and 3 (McSweeney et al., 2005) at 38 ml / L, respectively, 1 mL / L of 0.1% (w / v) resazurin solution, and 1 g / L of L-cysteine) and then centrifuged again. Finally, the washed cell pellet was resuspended in half the content of glycerol solution (15% v / v glycerol solution in anoxic buffer diluent) to a final concentration of 1 × 10 9 Cells were made up to cells / ml, aliquoted, and frozen at -80°C until needed. Viability of cell preparations was confirmed by thawing a single aliquot and streaking onto an agar plate. Identity and purity of individual strain preparations were confirmed by whole genome sequencing.

[0346] Acute model of DSS-induced colitis. For the preventative model, 6-week-old C57BL / 6 female mice purchased from Animal Resources Centers (Western Australia, Australia) were randomized and then co-housed for 7 days before the experiment. To induce disease, mice were given 3.5% DSS in drinking water ad libitum for 6 days. Untreated age-matched control mice were treated and given drinking water without DSS. All treatments were started 1 day before the administration of DSS, and all mice were sacrificed 2 days after the last DSS treatment. For treatment, mice were anesthetized with isofluorane and gavaged with 200 μL of bacterial preparation or vehicle control. Prednisone (2 mg / kg) was administered by intraperitoneal injection after anesthesia. Body weight and stool consistency were recorded daily. Fecal samples were collected daily. After sacrifice, colon, liver and spleen were harvested and analyzed. Blood was collected by cardiac puncture.

[0347] For the treatment model, groups of 10 or 20 female C57BL / 6 mice were used. All animals except the healthy group received 2.5% dextran sulfate sodium (DSS) in drinking water for a total of 6 days (days 0-5). DSS was then discontinued and replaced with normal drinking water for an additional 5 days (days 6-10). For treatment, mice were gavaged once daily with 200 μL of I. colisanans MH27-2 at a dose of 2×10^8 viable cells per day or a vehicle consisting of sterile glycerol and phosphate buffered saline. The positive control drug, prednisone, was similarly gavaged at a dose of 2 mg / kg per day. Treatment began on day 4 and was given for 7 consecutive days until day 10. On day 10, animals were sacrificed approximately 4 hours after the final treatment. Colons were harvested, rinsed, weighed, photographed, and sectioned longitudinally. Colon tissue was fixed in 4% formalin and maintained in 70% ethanol for histopathological analysis using the Swiss-roll method.

[0348] Endoscopic and histological scoring. Animals were examined with a small animal gastrointestinal endoscope (Karl Storz Endoskope, Tuttlingen, Germany) on days -1, 2, and 6 to assess the degree of colonic mucosal inflammation (Marks, 2015; and Liu, 2019). Briefly, mice were anesthetized with isoflurane and a colonoscope was inserted rectally. Images captured by high-definition video were examined in a blinded manner to assess the presence and extent of disease pathology (Table 5). Histological scoring was performed essentially as described by Marks et al. (Marks, 2015). Briefly, samples were fixed in 4% formalin, paraffin embedded, and sectioned. Tissue sections were stained with hematoxylin and eosin to assess disease pathology and mucin production with Alcian blue. Slides were imaged using an Aperio digital imaging system (Leica Biosystems, Nuβloch, Germany). To grade the severity of colitis, the degree of inflammation and epithelial damage in tissue sections was semiquantitatively graded using an established scoring system (Table 6). Samples were then randomized and subsequently scored in a blinded fashion by trained gastrointestinal pathologists.

[0349] SKG model of mouse ileitis. Five-week-old SKG female mice (n=3 males; n=3 females) were randomized and then co-housed for 3 weeks before the experiment. To induce disease, mice were administered curdlan (1,3-β-glucan, 3 mg per mouse) intraperitoneally (ip). Untreated age-matched control mice were treated similarly except that saline was administered intraperitoneally. All treatments were started before administration of curdlan, and all mice were sacrificed 7 days after curdlan treatment. For bacterial treatment, mice were gavaged with 200 μl of bacterial preparation or vehicle control starting 2 days before curdlan administration. Anti-mouse IL-23 p19 monoclonal antibody (Thermo Fisher, 30 μg / mouse) was administered by intraperitoneal injection 1 day before curdlan administration. Fecal samples were collected daily. Body weights were measured on days -2, 0, and 7. After sacrifice, the colon, distal small intestine, mesenteric lymph nodes and spleen were harvested and analyzed. Blood was collected by cardiac puncture.

[0350] Clinical and histological scoring. Histological scoring was performed essentially as described by Benham et al. 2014. Briefly, samples were fixed in 4% formalin, paraffin embedded, and sectioned. Tissue sections were stained with hematoxylin and eosin to assess disease pathology and Alcian blue to assess goblet cells. Slides were imaged using an Olympus VS120 slide scanner (Olympus Corporation, Tokyo, Japan). To grade the severity of ileitis, the degree of inflammation and epithelial damage in tissue sections was graded semiquantitatively using an established scoring system (Table 7) (Benham et al., 2014). Samples were then randomized and subsequently scored in a blinded manner by an independent trained pathologist.

[0351] To characterize the cytokines present in the serum, mice were euthanized by CO2 asphyxiation, after which blood was collected by cardiac bleed, and serum was isolated by centrifugation. Serum samples were stored at -80°C. These serum samples were then thawed and the effect on cytokine production (IL-23, IL-1α, IFN-γ, TNF, MCP-1, IL-12p70, IL-1β, IL-10, IL-6, IL-27, IL-17A, IFN-β, GM-CSF) was determined using the LEGENDplex Mouse Inflammation Panel (13-plex) (BioLegend, Cat. 740446). Serum samples were diluted two-fold and then incubated with capture beads conjugated to antibodies against specific analytes. After washing, a biotinylated detection antibody mixture is added to create a "capture bead-analyte-detection antibody" sandwich. Streptavidin-phycoerythrin (SA-PE) is added to bind the biotinylated detection antibody. After a final wash, the mixture is analyzed by flow cytometry, and the beads are differentiated by size and intrinsic fluorescence intensity. Cytokine concentrations are determined by PE fluorescence and comparison to standard curves of known cytokine concentrations using BioLegend's LEGENDplex data analysis software. The unique size and fluorescence properties of the beads allow for the simultaneous measurement of 13 cytokines.

[0352] TNBS model of murine colitis Groups of 5 or 10 male BALB / c mice were used. Mice were fasted overnight (day 1) and then challenged with 2,4,6-trinitrobenzenesulfonic acid solution (TNBS) on day 2. Distal colitis was induced by intracolonic injection of TNBS (1 mg in 0.1 mL of 50% ethanol), after which the animals were maintained in a vertical position for 30 seconds to ensure that the solution remained in the colon. For treatment, mice were gavaged with 200 μl of I. colisanans MH27-2 at 1×10^9 cells / day or vehicle (sterile glycerol and phosphate solution) for a total of 5 consecutive days (days 1–5), starting from day 1 (i.e., 1 day before TNBS) until day 5. The positive control cyclosporine A was given by oral gavage at 75 mg / kg once daily from day 1 (i.e., 1 day before TNBS) to day 4 for a total of 4 consecutive days (days 1–4). On the day of TNBS challenge, vehicle, I. colisanans MH27-2 and cyclosporine A were given 2 h before TNBS. Animals were sacrificed on day 5 and blood was collected by cardiac puncture from all animals. Colon tissue was also collected and snap frozen in liquid nitrogen for cytokine measurements. On day 5, mice were euthanized by CO2 asphyxiation. Each colon was removed, rinsed and then cut 4 cm from the anus. Tissue sections were fixed in 10% formalin and maintained in 70% ethanol for histopathological structure.

[0353] Macroscopic scoring of TNBS colitis On day 5, the mice were euthanized by CO2 asphyxiation, the colons were weighed, and their lengths were measured. Furthermore, adhesions between the colon and other organs were noted when the abdominal cavity was opened prior to colectomy, and the presence of colonic ulcers was noted after resection and weighing of each colon. A gross score was performed (Table 8) and photographs of intact colons were taken.

[0354] Histopathological scoring of TNBS colitis Each colon was removed, rinsed, grossly scored, photographed, weighed, its length was measured, and then cut into two parts 4 cm from the anus. One part was fixed in 10% formalin and kept in 70% ethanol to obtain histopathological structure, and the other part was snap frozen in liquid nitrogen for cytokine measurement (IL-6). For histological analysis (colitis scoring; essentially as described by Dieleman LA et al., 1998), 4-micrometer tissue sections were cut and stained with hematoxylin and eosin (H&E) under a light microscope (LEICA DM2700 M, USA). Histological criteria included abnormalities of mucosal architecture, degree of inflammation, erosion or ulceration, epithelial regeneration, and percent lesions due to disease process. Scoring was based on observer findings by examining two sections from each colon per animal. A total colitis score (total colitis index) was added, resulting in a combined histological score ranging from 0 to 40 (Table 9). Cytokines were measured using Millipore ELISA kits and protocols adapted from the product information and manual. Two sections were scored between 0 and 20 and added together for a total score ranging from 0 to 40.

[0355] Cell migration analysis. The TRANSWELL migration assay was used to evaluate the migration of HCT116 cells during exposure to I. colisanans culture supernatant extracts. These bacterial extracts were prepared using Amberlite XAD-7 resin essentially as previously described by Colosimo et al. (Colosimo, 2019). Briefly, a single colony was inoculated and grown to early stationary phase. This "seed" broth was used to inoculate 600 mL of TY broth and the culture was incubated to early stationary phase. Culture supernatant was prepared by centrifuging the culture at 4000 g for 30 min and then passing the cell-free supernatant through a 3 kDa filter (Sartorius Vivaflow® 50 Ultrafiltration Unit 3 kDa MWCO PES) according to the manufacturer's instructions. Activated Amberlite XAD-7 resin was added to 400 mL of 3 kDa filtered cell-free supernatant (10% w / v) and the slurry was gently shaken overnight at 4 °C. The resin was collected, washed with 400 mL of deionized water, and then mixed with 120 mL of 100% methanol. After 2 hours of incubation with gentle shaking, the methanol eluate was collected. A second elution in 120 mL of 100% methanol was performed as above, and the two eluates were finally combined and dried under vacuum using a rotary evaporator. The extract was thoroughly resuspended in 100% DMSO (hereafter referred to as 1000x) and stored at -20°C.

[0356] Human HCT116 intestinal epithelial cells were maintained in McCoys 5a medium supplemented with 10% FBS and 1% Pen / Strep. To assess cell migration via the Transwell® assay, 3.5×10 4HCT116 cells were seeded in 100 μL of 10% FBS culture medium in the upper compartment of a 6.5 mm insert with a TC-treated polycarbonate membrane in a 24-well plate (8 μm pore size, Corning Costar). 600 μl of 10% FBS culture medium was added to the lower compartment. The cells were left to rest for 24 hours. After DPBS washing, 100 μL and 600 μL of 0.5% FBS medium were added to the upper and lower compartments, respectively. Then, 0.5-fold concentrated extract from I. colisanans was added to the lower compartment. After 16 hours, the cells were washed with DPBS, and the cells attached to the top of the membrane were carefully removed with a cotton tip. The migrated cells at the bottom of the membrane were then fixed in 70% ethanol for 10 minutes, followed by staining in 0.25% crystal violet for 5 minutes. The Transwell® insert was washed with water, dried, and the membrane was mounted on a glass slide with 50% glycerol in water and immediately imaged. Transwell® experiments were performed in biological and technical triplicates, and for each replicate, two representative images of the membrane were taken at 10x magnification. The number of migrated cells was automatically counted using ImageJ, and the average cell number was displayed. The extent of cell migration was expressed as the average number of migrated cells in two microscopic fields per well from three biological replicates and three technical replicates.

[0357] The IncuCyte® live cell imaging system (Essen BioScience) and transwell migration assay were used to assess migration of HCT116 cells during exposure to sterile culture supernatant from I. colisanans. Human HCT116 intestinal epithelial cells were maintained in McCoys 5a medium supplemented with 10% FBS and 1% Pen / Strep. In the IncuCyte® scratch wound assay, 3.5 × 10 4HCT116 cells were plated on poly-L-ornithine coated IncuCyte® ImageLock 96-well plates (Essen BioScience). After 24 hours, homogenous scratch wounds were induced in the near-confluent cell monolayer using the IncuCyte® WoundMaker tool. Cells were washed twice with DPBS and treated with 0.3x I. colisanas supernatant extract (prepared using Amberlite XAD-7 resin as previously described in the "Preparation of Bacterial Supernatants and Media Extracts" section below) in 200 μL of 0.5% FBS McCoys 5a medium. A similarly prepared bacterial media extract served as a negative control. Immediately after the addition of stimuli, plates were transferred to the IncuCyte® System and cell migration was monitored by imaging each well every 2 hours for 72 hours. Data analysis was performed using integrated analysis software. [Table 6] [Table 7] [Table 8] For the total histology score, the scores from sections 1, 2 and 3 are added and multiplied by the cross-sectional area affected. [Table 9] [Table 10]

[0358] Characterization of IL-6 and IL-6 / IL-6R-mediated STAT3 suppression activity. To evaluate IL-6 and IL-6 / IL-6R-mediated STAT3 suppression activity, three independent colonies were inoculated and grown to early stationary phase. The various culture broths were then used to inoculate two technical replicates, generating six technical replicates from three biological replicates each. The technical replicates were grown to early stationary phase, and then cell-free culture supernatants were harvested as previously described (Giri et al., 2019). Culture supernatants were size-fractionated by passing them through a 3 kDa CENTRICON® column according to the manufacturer's instructions (Merck Millipore).

[0359] IL-6 and IL-6 / IL-6R-mediated STAT3 activity was assessed using the HEK Blue IL-6 cell line (Invivogen). Briefly, 50,000 cells per well were seeded in triplicate in 96-well plates 24 hours before the start of the assay. Bacterial supernatants or sterile bacterial medium were added to the cells at a final concentration of 10% v / v and pretreated for 60 minutes. Recombinant human IL-6 (2 ng / mL) or IL-6 / IL-6R complex (400 ng / mL) (R&D systems) were then added and cells were incubated for 24 hours at 37°C. The ability of the supernatants to suppress IL-6 or IL-6 / IL-6R-mediated STAT3 activation was compared to the Janus kinase inhibitor tofacitinib (10 μM). After 24 hours, STAT3-regulated SEAP reporter activity was assessed using Quanti Blue solution as recommended by the manufacturer (Invivogen). Results are the average of three (IL-6) or one (IL-6 / IL-6R) independent experiments. Cytotoxicity was assessed using the CellTiter-Glo® 2.0 Cell Viability Assay (Promega, Australia) as recommended by the manufacturer.

[0360] Characterization of IL-23-mediated STAT3 suppression activity. I. colisanans MH27-3 supernatant samples were prepared using standard protocols. Briefly, three independent colonies of the bacteria of interest were inoculated and grown to early stationary phase. The various culture broths from the three biological replicates were then used to inoculate two technical replicates, thereby generating six technical replicates. The technical replicates were grown to early stationary phase, and then the raw cell-free culture supernatant was harvested. The culture supernatant was also size fractionated by passing through a 3 kDa CENTRICON® column according to the manufacturer's instructions (Merck Millipore). R. bromii MCB950 supernatant samples were prepared similarly, except that two biological replicates were used to generate four technical replicates.

[0361] IL-23-mediated STAT3 activity was assessed using the HEK Blue IL-23 cell line (Invivogen). Briefly, the HEK-Blue IL-23 reporter cell line is stably transfected with IL23R, STAT3 and secreted embryonic alkaline phosphatase (SEAP) reporter genes. Stimulation with IL-6 results in STAT3-dependent expression of SEAP. SEAP is secreted into the medium and the degree of SEAP expression can be quantified using QUANTI-Blue solution. HEK-Blue IL-23 cells were cultured in DMEM supplemented with 10% FBS according to the manufacturer's instructions.

[0362] For the IL23-STAT3 assay, 50,000 cells of the HEK-Blue™ IL-23 cell line were grown overnight in 96-well plates. Supernatants were initially tested at a final concentration of 10%, 25% or 50% v / v with IL-23 at a final concentration of 5 ng / mL. For all experiments and treatments demonstrated herein, supernatants were tested at a final concentration of 25% (v / v). IL-23 was tested at a final concentration of 5 ng / mL and tofacitinib was tested at a final concentration of 5 μM. IL-23 alone and IL-23 with tofacitinib were included in the assay as positive and negative controls for IL-23 signaling. Treated cells were incubated at 37° C. for 6 hours.

[0363] SEAP production was quantified using QUANTI-Blue™ solution and recorded as optical density (OD) at 630 nm using a PHERAstar FS plate reader (BMG Labtech). The inhibition of STAT3 signaling by bacterial supernatants was compared to the STAT3 signaling activation of their associated medium controls. Of note, although in some cases the medium controls themselves showed a level of STAT3 signaling inhibition, the effect of the associated lead was often more potent than that of the medium.

[0364] All experiments were performed at least in triplicate. All data were generated from at least three technical replicates and at least three biological replicates. T-tests and analysis of variance tests were performed as appropriate using GraphPad Prism 9 software.

[0365] Preparation of bacterial supernatants and medium extracts. Bacterial culture supernatants were prepared by inoculating three independent colonies of I. colisanans MH27-2 and growing the cultures to early stationary phase. The three "seed cultures" were used to inoculate 160 mL of YG / V broth in duplicate, and the cultures were again incubated to early stationary phase. Culture supernatants were harvested and prepared by centrifuging the cultures at 4000 g for 30 min and then passing the cell-free supernatant through an Amicon Ultra-15 3 kDa centrifugal filter.

[0366] Bacterial culture supernatant extracts were prepared using Amberlite XAD-7 resin as previously described by Colosimo et al. (supra). Briefly, activated Amberlite XAD-7 resin was added to 150 mL of 3 kDa filtered cell-free supernatant (10% w / v) and gently shaken overnight at 4°C. The resin was collected, washed with 150 mL of deionized water, and mixed with 50 mL of 100% methanol. After 2 hours of incubation with gentle shaking, the methanol eluate was collected. A second elution in 25 mL of 100% methanol was performed as described above, and the two eluates were combined and dried using a rotary evaporator under vacuum. The dried extract was resuspended at 100x concentration in 100% DMSO and stored at -80°C.

[0367] Solid-phase extract fractions of bacterial culture supernatants were prepared using a Strata-X 33 μM polymeric reversed-phase column. Briefly, after conditioning and equilibration, the column was loaded with 3 kDa filtered cell-free supernatant, washed four times with an equal volume of deionized water, and then eluted with 15, 30, 60, and 100% acetonitrile. Each eluate was dried on a rotary evaporator under vacuum, resuspended at 100x concentration in 100% DMSO, and stored at -80°C.

[0368] LC-MS / MS-based metabolomic analysis. Targeted metabolomics analysis was performed by MS-Omics (Denmark). Briefly, to evaluate the metabolites produced by I. colisanans MH27, six independent colonies were inoculated and grown to early stationary phase. The various culture broths were then used to inoculate two technical replicates of YG / V, generating 12 technical replicates from six biological replicates. The technical replicates were grown to early stationary phase, and then the cell-free culture supernatants were harvested, followed by centrifugation at 12,550 g for 3 min in an anaerobic chamber. The culture supernatants were flash frozen on dry ice and then stored at -80 °C until testing.

[0369] Analysis was performed using a Thermo Scientific Vanquish LC coupled to a Thermo Q Exactive HF MS. An electrospray ionization interface was used as the ionization source. Analysis was performed in negative and positive ionization modes. UPLC was performed using a slightly modified version of the protocol described by Catalin et al. (UPLC / MS Monitoring of Water-Soluble Vitamin Bs in Cell Culture Media in Minutes, Water Application note 2011, 720004042en). Peak areas were extracted using Compound Discoverer 3.1 (Thermo Scientific). Compound identification was performed at four levels: Level 1: identification by retention time (comparison with in-house standards), accurate mass (tolerated deviation 3 ppm), and MS / MS spectrum; Level 2a: identification by retention time (comparison with in-house standards), accurate mass (tolerated deviation 3 ppm); Level 2b: identification by accurate mass (tolerated deviation 3 ppm) and MS / MS spectrum; Level 3: identification by accurate mass only (tolerated deviation 3 ppm).

[0370] Untargeted metabolomic analysis was performed using a Thermo scientific UltiMate 3000 UHPLC coupled to a Thermo Q Exactive Plus MS. A gradient of 3-95% acetonitrile with 0.1% formic acid was run for a total of 85 min at a flow rate of 0.25 μL / min. An electrospray ionization interface was used as the ionization source. MS data were acquired from MS1 surveys spanning m / z 100-1500 at a resolution of 35,000 in data-dependent acquisition mode, and up to 10 MS2 scans per cycle at a resolution of 35,000 in CID / HCD mode with one microscan in positive or negative mode. The maximum injection time was set to 100 ms and the MS2 precursor window was set to 1.2 m / z. The normalized collision energy was set in step energy mode, with normalized collision energies (NCEs) from 20, 30 and 40% combined, and the default charge state was set to z=1. The MS2 experiment was set to be automatically triggered within 5-10 s of the first occurrence at the apex of the peak. The dynamic exclusion time was set to 10 s. Ion species with unassigned charge states and isotopic peaks were excluded. Further metabolic profile analysis and key metabolite identification were performed using the GNPS platform as described by Aron et al. (9).

[0371] Assessment of barrier function. The ability of I. colisanans MH27 to prevent loss of barrier integrity was assessed by measuring the transepithelial electrical resistance (TEER) across a confluent monolayer of T84 intestinal epithelial cells. T84 cells were purchased from CellBank Australia and cultured in Dulbecco's modified Eagle's medium nutrient mixture 12 (DMEM / F12; ThermoFisher Scientific, Waltham, MA, USA) supplemented with 5% fetal bovine serum and 1% penicillin-streptomycin. T84 cells were seeded in 24-well Millicell polycarbonate cell culture inserts with 0.4 μm pore size (PSHT010R5) at a density of 60.000 cells / well in 400 μL medium, and 24 ml of medium was added to a single-well feeder tray. Medium changes in both compartments were performed every 2 days. After 7 days of culture, the top of the plate assembly with cell culture inserts was transferred from the feeder tray to a 24-well receiver tray (PSMW010R5), with each well containing 800 μL of medium. The TEER value of each well was measured daily using a Millicell ERS-2 Voltohmmeter. The experiment was started when the cells in all wells reached a stable TEER reading above 1500Ω.

[0372] In the first experiment, 3 kDa filtered bacterial medium (YG / V) or 3 kDa filtered I. colisanans MH27 bacterial culture supernatant diluted to 10% v / v in T84 medium was added to the apical compartment and pretreated for 1 h. IFNγ (50 ng / ml) was then added to the basal compartment to disrupt barrier integrity. After 48 h of IFNγ treatment, the medium containing IFNγ in the basolateral compartment was removed, the wells were washed twice with warm PBS, and fresh T84 medium was added. Thereafter, the medium in the lower compartment was replaced every 24 h. Similarly, the YG / V and I. colisanans MH27-2 base treatment in the apical compartment was replaced with a fresh one every 24 h, and TEER values ​​were measured immediately before and after treatment. Data from two biological replicates, each measured in duplicate, were presented as the percentage difference in TEER values ​​compared to the control (untreated T84 cells). Statistical significance was determined by unpaired t-test.

[0373] In the second experiment, 2x, 1x and 0.5x concentrations of bacterial medium extract (YG / V) or I. colisanans MH27-2 bacterial extract were added to the apical compartment. IL-6 (10ng / mL) was then added to disrupt barrier integrity and removed after 96 hours of treatment. Every 24 hours, treatment and medium were replaced and TEER values ​​were measured in duplicate. Data from two biological replicates, each measured in duplicate, are presented as the percentage difference in TEER values ​​compared to the control (untreated T84 cells). Statistical significance was determined by unpaired t-test.

[0374] Assessment of tight junction-associated protein expression. The ability of I. colisanans MH27-1, MH27-2, and MH27-3 to prevent IFNγ-mediated loss of zonula occludens 1 (ZO1) expression was assessed by immunofluorescence staining and confocal microscopy. T84 cells were cultured as described above and seeded on microscope slides in 24-well plates at a density of 150.000 cells / well in 800 μL of medium. Cells were grown for 3 weeks, with medium changed every 2 days. For I. colisanans, cells were pretreated with 3 kDa filtered extract control (YG / V) or 3 kDa filtered complete or fractionated I. colisanans MH27 bacterial extract diluted 1x in medium and incubated overnight at 37°C, 5% CO2, after which 100 ng / mL IFNγ was added to selected wells. For metabolites produced by I. colisanans, T84 cells were pretreated with 1 mM ornithine, indole-3-acrylic acid, or indole-3-propionic acid for 18 h and then stimulated with IFNγ for 48 h. Cells were incubated for another 48 h, then fixed with 4% paraformaldehyde for 15 min, washed three times with PBS, and stained protected from light. For this purpose, coverslips were first incubated with 0.1% Triton® X-100 in 5% BSA / PBS for 10 min. Cells were washed three times with PBS and incubated in 5% BSA / PBS for 2 h. They were then washed three times with PBS and incubated with the primary rabbit anti-human ZO1 antibody (5 μg / mL, Invitrogen) in 5% BSA / PBS for 2 h, then washed again three times with PBS. Cells were incubated with Alexa Fluor® 488-conjugated goat anti-rabbit IgG H&L secondary antibody (1:2000, ThermoFisher Scientific) and DAPI (1:1000, ThermoFisher Scientific) in 5% BSA / PBS for 1 h. Coverslips were washed three times with PBS and once with ultrapure water, then mounted with ProLong Gold Antifade Mountant (Invitrogen).Image acquisition was performed using an inverted fully motorized Nikon / Spectral Spinning Disc Confocal microscope (X-1 Yokogawa spinning disc with Borealis modification) equipped with a 60× NA 1.49 Plan Apochromat oil immersion objective (Nikon). Images were acquired across the entire cell using a charge coupled device (CCD) camera (Andow Clara) and Nikon elements imaging software (Nikon, version 4.40). For each condition, four separate images were taken. Maximum projection images were collected and the relative brightness of stained cells was quantified and calculated for each image using Fiji ImageJ (version 1.53t), normalized to unstimulated control cells. Experimental raw data can be found in Appendices 3–5. Statistical significance was determined by one-way ANOVA with Dunnett's correction for multiple comparisons.

[0375] PBMC isolation and stimulation PBMCs were isolated from peripheral blood of healthy donors. Cells were cultured at 2 × 10 in RPMI 1640 supplemented with gentamicin (150 μg / mL), 2 mM L-glutamine and 10% heat-inactivated FBS. 6 The cells were adjusted to a density of 1000 cells / mL and seeded into 24-well tissue culture plates. After overnight incubation at 37°C in a 5% CO2 incubator, 50 μL of live I. colisanans strain MH27-2 was added to obtain a multiplicity of infection of 1:1. The supernatant was collected and stimulated for 24 hours at 37°C in a 5% CO2 incubator before clarification by centrifugation. The supernatant was stored at -80°C until required. IL-10 and IL-12 were quantified using the Ella Automated Immunoassay System according to the manufacturer's instructions (Protein Simple).

[0376] Assessment of NF-κB regulatory activity NF-κB activity was assessed using a custom LS174T goblet cell-like cell line stably transfected with an NF-κB reporter lentivirus carrying firefly luciferase under the control of a minimal (m)CMV promoter and tandem repeats of the NF-kB transcription response element. Stimulation with TNF results in NF-κB-p65-dependent expression of luciferase, which can be quantified using the Pierce Firefly Luc One-Step Glow Assay Kit (Thermo Scientific). LS174T-NF-κB cells were cultured in DMEM supplemented with 10% FBS. For the NF-κB assay, 50,000 cells of the LS174T-NF-κB cell line were grown overnight in 96-well plates. Cells were pretreated with bacterial supernatant at a starting concentration of 25% v / v for 30 min at 37°C. TNF was then added to a final concentration of 50 ng / ml. TNF alone and TNF plus the NF-κB inhibitor indole-3-carbinol (I3C) were included in the assay at a final concentration of 5 mM as positive and negative controls for NF-κB signaling. Treated cells were incubated for 7 hours at 37°C. Luciferase activity was quantified using the Pierce Firefly Luc One-Step Glow assay kit and recorded using a PHERAstar FS plate reader (BMG Labtech). Modulation of NF-κB signaling by bacterial supernatants was compared to NF-κB signaling activation by its associated media control.

[0377] The disclosures of all patents, patent applications, and publications cited herein are hereby incorporated by reference in their entireties.

[0378] The citation of any reference herein should not be construed as an admission that such reference is available as "Prior Art" to the present application.

[0379] Throughout this specification, the objective has been to describe preferred embodiments of the invention without limiting the invention to any one embodiment or particular collection of features. Thus, those skilled in the art will appreciate in light of this disclosure that various modifications and changes can be made in the specific embodiments exemplified without departing from the scope of the invention. All such modifications and changes are intended to be included within the scope of the appended claims. References Arumugam, M. et al., Enterotypes of the human gut microbiome. Nature 473(7346):174-180(2011). Azad et al., Probiotic supplementation during pregnancy or infancy for the prevention of asthma and wheeze: systematic review and meta-analysis. BMJ. (2013)347:f6471. 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Claims

1. A composition comprising a cell or biologically pure culture, The composition, wherein the cell or biologically pure culture is a cell or biologically pure culture of the Intestinicoccus colisanans strain deposited under accession number V21 / 015887 or V21 / 015888 or a derivative thereof.

2. A composition comprising a bacterial strain having a 16S rRNA sequence that is at least about 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to SEQ ID NO: 1 or 2, or a 16S rRNA gene sequence represented by either SEQ ID NO: 1 or 2.

3. A pharmaceutical composition comprising a bacterial strain that is a phylogenetic descendant of the MRCA of I. colisanans and I. sp002305575, together with a pharmaceutically acceptable carrier, diluent, or excipient.

4. (a) prebiotics; and / or (b) one or more additional bacterial strains; The composition of any one of claims 1 to 3, further comprising:

5. The composition of any one of claims 1 to 3, wherein the bacterial strain produces an agent that attenuates or impairs signal transduction of signal transducer and activator of transcription 3 (STAT3) in cells, and / or the bacterial strain produces one or more metabolites selected from cyclo(-Phe-Pro), indole-3-lactic acid, allopurinol, propionylcarnitine, pyrogallol, 3-(2-hydroxyethyl)indole, N-acetyl-cysteine, tryptophol, indole-3-propionic acid, ornithine, acetic acid, and / or combinations thereof.

6. The composition described in claim 5, wherein the active substance specifically binds to any one of STAT3, JAK2, TYK, or IL-23.

7. The composition of claim 1, wherein the bacterial strain is of the I. colisanans species.

8. A composition described in any one of claims 1 to 3 for use in a method for restoring or improving intestinal barrier function in a subject, or a method for inducing or enhancing mucosal healing in a subject.

9. A composition for use as described in claim 8, wherein the restoration or improvement of intestinal barrier function is characterized by at least one of: (i) an increase in the quality and / or quantity of mucin; (ii) an improvement in the integrity of tight junction proteins; (iii) a reduction in the translocation of luminal contents into the systemic circulation; or (iv) a reduction in intestinal ulcers and / or wounds, and optionally, the luminal contents include lipopolysaccharides (LPS).

10. A composition for use as described in claim 8, wherein the restoration or improvement of intestinal barrier dysfunction results in a reduction in systemic inflammation in the subject, and optionally, systemic inflammation is identified in the subject when levels of inflammatory cytokines (e.g., IL-1β, IL-8, IL-6, and TNF) in a sample from the subject exceed a predetermined threshold.

11. Mucosal healing is measured using one or more fecal or serum markers; Optionally, the one or more fecal markers are selected from the group comprising calprotectin, lactoferrin, metalloproteinase (MMP)-9, and lipocalin-2, and / or the mucosal healing is measured using an endoscopic score. A composition for use according to claim 8.

12. A composition according to any one of claims 1 to 3 for use in a method for reducing inflammation in a subject.

13. A composition for use as described in claim 12, wherein the inflammation is local to the intestinal environment or is systemic inflammation.

14. A composition for use as described in claim 12, wherein the bacterial strain attenuates the NFκB pathway (e.g., by reducing or inhibiting NFκB).

15. A composition according to any one of claims 1 to 3 for use in a method for treating or preventing an inflammatory or autoimmune disorder in a subject.

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