CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Provisional Application No. 62/928,232 filed on October 30, 2019 and U.S. Provisional Application No. 62/834,336 filed on April 15, 2019, each of which is herein incorporated by reference in its entirety.

TECHNICAL FIELD

[0002] The present disclosure is related to bacterial strains, and compositions thereof, that can suppress IL-23-induced IL-17 secretion. Such bacterial strains, and compositions thereof, are useful for treating inflammatory diseases in a subject.

BACKGROUND

[0003] Inflammatory diseases represent a substantial problem in the healthcare industry. For example, chronic inflammatory diseases include many common conditions such as inflammatory bowel disease (IBD), rheumatoid arthritis, restenosis, psoriasis, multiple sclerosis, surgical adhesions, tuberculosis, and chronic inflammatory lung diseases. It is estimated that about 3 million people in the United States currently suffer from IBD alone, and the incidence of IBD has dramatically increased in developed countries in recent years. IBD is characterized by chronic inflammation of the gastrointestinal tract and can lead to stenoses, abscesses, fistulas, extraintestinal manifestations, colitis-associated neoplasias, and cancer. Crohn's disease (CD) and ulcerative colitis (UC) are the two main forms of IBD, which have distinct as well as overlapping pathologic and clinical characteristics. It is known that both genetic and environmental factors, including impaired host immune response to the intestinal microbiota, contribute to IBD.

[0004] The microbiome of the gastrointestinal tract comprises a diverse array of microorganisms, primarily prokaryotes, which play a significant role in the health of the host organism. The complexity of the microbiome, in terms of both its population makeup and composite function, has recently become an intense area of study as research increasingly shows that manipulation of the microbiome can provide health benefits and may be effective in treating a number of diseases and disorders. Currently, a number of probiotics are marketed that contain live bacteria and yeast and are believed to augment the benefits of these microbes which naturally occur in the human body. Increasingly, live biotherapeutic products (LBPs) are being developed for controlled clinical studies and regulatory approval in the treatment of disease.

[0005] Finding a microbe-based therapeutic for IBD and other inflammatory diseases has been challenging. In IBD, for example, this is at least partly because it is a heterogeneous disease with a complex diagnosis, as well as multiple etiologies, pathologies, and treatment responses. Furthermore, finding consistent associations between inflammatory diseases and the microbiome has proven difficult. Improved therapies such as microbe-based therapeutics are desirable.

SUMMARY

[0006] Provided herein are methods and compositions for treating a subject in need thereof. For example, methods provided herein can include administering to the subject a composition that includes an effective amount of a bacterial strain. In some embodiments the bacterial strain can suppress IL-23 -induced IL-17 secretion.

[0007] In some embodiments, the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, and a combination thereof (e.g., a combination of two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, twenty- one, twenty-two, or twenty- three strains).

[0008] In some embodiments, the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, and a combination thereof (e.g., a combination of two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, or thirteen strains).

[0009] In some embodiments, the bacterial strain is selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1 , Alistipes shahii WAL 8301, and a combination thereof (e.g., two or three of Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, and Alistipes shahii WAL 8301).

[0010] In some embodiments, the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1 , Alistipes shahii WAL 8301, and a combination thereof.

[0011] In some embodiments, the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, and a combination thereof (e.g., two, three, or four strains).

[0012] In some embodiments, the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, Parabacteroides distasonis C103T12C09, and a combination thereof (e.g., two, three, four, five, six, or seven strains).

[0013] Also provided herein are methods for suppressing IL-23-induced IL-17 secretion in a subject in need thereof that include administering to the subject a composition that includes an effective amount of a bacterial strain selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof (e.g., two or three of Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1 , and Alistipes shahii WAL 8301). In some embodiments, the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1 , Alistipes shahii WAL 8301, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, and a combination thereof (e.g., two, three, or four strains). In some embodiments, the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, Parabacteroides distasonis C103T12C09, and a combination thereof (e.g., two, three, four, five, six, or seven strains).

[0014] In some embodiments, the bacterial strain suppresses IL-23 -induced IL-17 secretion in the intestine of the subject.

[0015] Also provided herein are methods for treating a subject in need thereof that include administering to the subject a composition that includes an effective amount of a bacterial strain selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, and a combination thereof. In some embodiments, the bacterial strain is selected form the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof (e.g., two or three of Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1 , Alistipes shahii WAL 8301). In some embodiments, the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, and a combination thereof (e.g., two, three, or four strains). In some embodiments, the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, Parabacteroides distasonis C103T12C09, and a combination thereof (e.g., two, three, four, five, six, or seven strains).

[0016] In some embodiments, the subject has been diagnosed with an inflammatory disease. For example, the inflammatory disease can be an inflammatory bowel disease (e.g., ulcerative colitis and Crohn's disease), multiple sclerosis, myocarditis, psoriasis, atrophic gastritis, arthritis, atopic dermatitis, pouchitis, inflammatory hemolytic anemia, graft rejection, inflammatory neutropenia, bullous pemphigoid, celiac disease, a demyelinating neuropathy, dermatomyositis, myositis, a nasal polyp, chronic sinusitis, pemphigus vulgaris, primary glomerulonephritis, a surgical adhesion, stenosis or restenosis, scleritis, scleroderma, eczema (e.g., atopic dermatitis, contact dermatitis, irritant dermatitis, or allergic dermatitis), type I diabetes, vasculitis, pancreatitis, primary sclerosing cholangitis, a benign stricture (e.g., a stricture of bile ducts, esophagus, duodenum, small bowel, or colon), a respiratory tract disease (e.g., asthma, hypersensitivity pneumonitis, asbestosis, silicosis and other forms of pneumoconiosis, chronic bronchitis, or chronic obstructive airway disease), a nasolacrimal duct disease, or a eustachean tube disease.

[0017] Also provided herein are methods for treating an inflammatory disease in a subject that include administering to the subject a composition that includes an effective amount of a bacterial strain selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof (e.g., two or three of Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1 , and Alistipes shahii WAL 8301). In some embodiments, the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, and a combination thereof (e.g., two, three, or four strains). In some embodiments, the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, Parabacteroides distasonis C103T12C09, and a combination thereof (e.g., two, three, four, five, six, or seven strains).

[0018] Also provided herein are methods for treating an inflammatory disease in a subject that include (a) detecting a dysbiosis associated with an inflammatory disease in a sample (e.g., a biopsy sample, a colorectal biopsy sample, a fecal sample) from the subject; and (b) administering to the subject an effective amount of a bacterial strain, e.g., a bacterial strain that suppresses IL- 23 -induced IL-17 secretion. For example, the bacterial strain can be selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, and a combination thereof. In some embodiments, the bacterial strain can be selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof (e.g., two or three of Clostridium discporicum DS1, Streptococcus mar imammalium M54/01/1 , and Alistipes shahii WAL 8301). In some embodiments, the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, and a combination thereof (e.g., two, three, or four strains). In some embodiments, the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, Parabacteroides distasonis C103T12C09, and a combination thereof (e.g., two, three, four, five, six, or seven strains).

[0019] In some embodiments, detecting the dysbiosis associated with an inflammatory disease comprises determining bacterial gene expression in the sample from the subject. In some embodiments, detecting the dysbiosis associated with an inflammatory disease comprises detecting bacterial gene expression associated with high IL-23 activation in the sample from the subject. In some embodiments, detecting the dysbiosis associated with an inflammatory disease comprises determining bacterial composition in the sample from the subject. In some embodiments, detecting the dysbiosis associated with an inflammatory disease comprises detecting a bacterial strain associated with high IL-23 activation in the sample from the subject. In some embodiments, detecting the dysbiosis comprises determining that Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, or a combination thereof are reduced in the gastrointestinal tract of the subject. In some embodiments, detecting the dysbiosis comprises determining that Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, or a combination thereof are reduced in the sample from subject. In some embodiments, detecting the dysbiosis comprises determining that Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, or a combination thereof (e.g., two or three of Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1 , and Alistipes shahii WAL 8301 ) are reduced in the sample from subject. In some embodiments, detecting the dysbiosis comprises determining that Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, or a combination thereof are reduced in the sample from subject. In some embodiments, detecting the dysbiosis comprises determining that Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, Parabacteroides distasonis C103T12C09, or a combination thereof are reduced in the sample from subject. In some embodiments, the bacterial strain is reduced in the gastrointestinal tract of the subject.

[0020] In some embodiments, the inflammatory disease is selected from the group consisting of: an inflammatory bowel disease, multiple sclerosis, myocarditis, psoriasis, atrophic gastritis, inflammatory hemolytic anemia, arthritis, atopic dermatitis, graft rejection, inflammatory neutropenia, bullous pemphigoid, celiac disease, a demyelinating neuropathy, dermatomyositis, myositis, nasal polyps, chronic sinusitis, pemphigus vulgaris, primary glomerulonephritis, a surgical adhesion, stenosis or restenosis, scleritis, scleroderma, eczema, type I diabetes, vasculitis, pancreatitis, primary sclerosing cholangitis, benign stricture, a respiratory tract disease, a nasolacrimal duct disease, and a eustachean tube disease. In some embodiments, the inflammatory bowel disease is ulcerative colitis or Crohn's disease.

[0021] In some embodiments, the bacterial strain comprises Clostridium discporicum DS1. In some embodiments, the bacterial strain comprises Streptococcus marimammalium M54/01/1. In some embodiments, the bacterial strain comprises Alistipes shahii WAL 8301. In some embodiments, the bacterial strain comprises Firmicutes bacterium ASF500. In some embodiments, the bacterial strain comprises Eubacterium coprostanoligenes str. HL. In some embodiments, the bacterial strain comprises Howardella ureilytica GPC 589. In some embodiments, the bacterial strain comprises Cupriavidus respiraculi au5353. In some embodiments, the bacterial strain comprises Dialister invisus E7.25. In some embodiments, the bacterial strain comprises Clostridium lituseburense VKM B-2279. In some embodiments, the bacterial strain comprises Coprococcus sp. HPP0074. In some embodiments, the bacterial strain comprises Dialister pneumosintes DSM 11619. In some embodiments, the bacterial strain comprises Clostridium glycyrrhizinilyticum ZM35. In some embodiments, the bacterial strain comprises Lactobacillus rogosae ATCC 27753. In some embodiments, the bacterial strain comprises Intestinibacter bartlettii 2789STDY5834879. In some embodiments, the bacterial strain comprises Clostridium sp. 1 1 41A1FAA. In some embodiments, the bacterial strain comprises Intestinibacter bartlettii BSD2780061688ST1 A9. In some embodiments, the bacterial strain comprises Intestinibacter bartlettii DSM 16795. In some embodiments, the bacterial strain comprises Lachnospira pectinoschiza 2789STDY5834886. In some embodiments, the bacterial strain comprises Butyricicoccus sp. AF15 40. In some embodiments, the bacterial strain comprises Butyricicoccus sp. AM28 25. In some embodiments, the bacterial strain comprises Butyricicoccus sp. AM32 19. In some embodiments, the bacterial strain comprises Roseburia inulinivorans A2- 194. In some embodiments, the bacterial strain comprises Lactobacillus rogosae ATCC 27753. In some embodiments, the bacterial strain comprises Parabacteroides distasonis C103T12C09.

[0022] In some embodiments, Clostridium discporicum DS1 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:2.

[0023] In some embodiments, Streptococcus marimammalium M54/01/1 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:3.

[0024] In some embodiments, Alistipes shahii WAL 8301 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 1.

[0025] In some embodiments, Firmicutes bacterium ASF500 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:4. [0026] In some embodiments, Eubacterium coprostanoligenes str. HL has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:5.

[0027] In some embodiments, Howardella ureilytica GPC 589 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:6.

[0028] In some embodiments, Cupriavidus respiraculi au5353 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:7.

[0029] In some embodiments, Dialister invisus E7.25 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 8.

[0030] In some embodiments, Clostridium lituseburense VKM B-2279 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:9.

[0031] In some embodiments, Coprococcus sp. HPP0074 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 10.

[0032] In some embodiments, Dialister pneumosintes DSM 11619 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: l 1.

[0033] In some embodiments, Clostridium glycyrrhizinilyticum ZM35 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 12.

[0034] In some embodiments, Lactobacillus rogosae ATCC 27753 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 13.

[0035] In some embodiments, Intestinibacter bartlettii 2789STDY5834879 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 14.

[0036] In some embodiments, Clostridium sp. 1 1 41 A1FAA has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 15.

[0037] In some embodiments, Intestinibacter bartlettii BSD2780061688ST1 A9 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 16.

[0038] In some embodiments, Intestinibacter bartlettii DSM 16795 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 17. [0039] In some embodiments, Lachnospira pectinoschiza 2789STDY5834886 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 18.

[0040] In some embodiments, Butyricicoccus sp. AF15 40 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 19.

[0041] In some embodiments, Butyricicoccus sp. AM28 25 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:20.

[0042] In some embodiments, Butyricicoccus sp. AM32 19 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:21.

[0043] In some embodiments, Roseburia inulinivorans A2-194 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:22.

[0044] In some embodiments, Parabacteroides distasonis C103T12C09 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:23.

[0045] In some embodiments, the bacterial strain in the composition is viable. In some embodiments, the bacterial strain in the composition is lyophilized. In some embodiments, the bacterial strain in the composition further comprises one or more crypreservants.

[0046] In some embodiments, the effective amount of the bacterial strain comprises at least about 1 xlO ³ colony forming units (CFU) of the bacterial strain. In some embodiments, the effective amount of the bacterial strain comprises about 1 xlO ⁴ to about 1 xlO ¹⁵ CFU of the bacterial strain. In some embodiments, the effective amount of the bacterial strain comprises about 1 xlO ⁷ to about 1 xlO ¹² CFU of the bacterial strain.

[0047] In some embodiments, the bacterial strain in the composition is non-viable. In some embodiments, the non-viable bacterial strain is heat-killed, irradiated, fixed, or lysed.

[0048] In some embodiments, the method comprises administering the composition to the subject once, twice, or three times per day.

[0049] In some embodiments, the composition further includes one or more excipients. In some embodiments, the composition is formulated for oral administration. In some embodiments, the composition is formulated as a tablet, a capsule, a powder, or a liquid. In some embodiments, the composition is formulated as a tablet. In some embodiments, the tablet is coated. In some embodiments, the coating comprises an enteric coating. In some embodiments, the composition is formulated for topical delivery. In some embodiments, the composition is in the form of a paste, gel, cream, spray, suppository, mousse, emollient, ointment, foam, or suspension.

[0050] In some embodiments, the composition is formulated for rectal administration. In some embodiments, the composition is formulated as a suppository.

[0051] In some embodiments, the method further comprises administering one or more other treatments of an inflammatory disease to the subject. In some embodiments, the other treatment of an inflammatory disease can be included in the composition or can be administered separately. If administered separately, the other treatment of an inflammatory disease can be administered before, after, or at the same time as the composition comprising the bacterial strain. In some embodiments, the other treatment of an inflammatory disease is surgery. In some embodiments, the other treatment of an inflammatory disease is a therapeutic agent.

[0052] In some embodiments, the method further comprises administering an adjunct therapy such as a therapeutic agent to control pain and/or inflammation to the subject. In some embodiments, the adjunct therapy can be included in the composition or can be administered separately. If administered separately, the adjunct therapy can be administered before, after, or at the same time as the composition comprising the bacterial strain.

[0053] In some embodiments, the therapeutic agent comprises an anti-inflammatory agent, an immunosuppressant, an antibiotic, an anti-diarrheal agent, a pain reliever, an iron supplement, or a combination thereof. In some embodiments, the anti-inflammatory agent comprises sulfasalazine, mesalamine, balsalazide, olsalazine, prednisone, hydrocortisone, or a combination thereof. In some embodiments, the immunosuppressant comprises azathioprine, mercaptopurine, cyclosporine, infliximab, adalimumab, golimumab, vedolizumab, or a combination thereof.

[0054] In some embodiments, the treatment for inflammatory disease and/or adjunct therapy comprises a probiotic such as Bifidobacteria (e.g., B. animal is, B. breve , B. lactis , B. longum , B. longum , or . infantis ), Lactobacillus (e.g., L. acidophilus , L. reuteri , L. bulgaricus , L. lactis , L. casei, L. rhamnosus , L. plantarum , L. paracasei, or L. de I breuckii I bulgaricus), Saccharomyces boulardii , L.coli Nissle 1917, or Streptococcus thermophiles.

[0055] Also provided herein are compositions that include: (a) a bacterial strain selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, and a combination thereof; and (b) one or more excipients. In some embodiments, the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, and a combination thereof (e.g., two, three, or four strains). In some embodiments, the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, Parabacteroides distasonis C103T12C09, and a combination thereof (e.g., two, three, four, five, six, or seven strains).

[0056] Also provided herein is the use of a bacterial strain described herein in the manucfacture of a medicament for treating an inflammatory disease. In some embodiments, the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, and a combination thereof. In some embodiments, the medicament includes one or more excipients. In some embodiments, the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, and a combination thereof (e.g., two, three, or four strains). In some embodiments, the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, Parabacteroides distasonis C103T12C09, and a combination thereof (e.g., two, three, four, five, six, or seven strains). In some embodiments, the medicament includes one or more excipients.

[0057] In some embodiments, Clostridium discporicum DS1 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:2.

[0058] In some embodiments, Streptococcus marimammalium M54/01/1 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:3.

[0059] In some embodiments, Alistipes shahii WAL 8301 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 1. [0060] In some embodiments, Firmicutes bacterium ASF500 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:4.

[0061] In some embodiments, Eubacterium coprostanoligenes str. HL has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:5.

[0062] In some embodiments, Howardella ureilytica GPC 589 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:6.

[0063] In some embodiments, Cupriavidus respiraculi au5353 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:7.

[0064] In some embodiments, Dialister invisus E7.25 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 8.

[0065] In some embodiments, Clostridium lituseburense VKM B-2279 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:9.

[0066] In some embodiments, Coprococcus sp. HPP0074 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 10.

[0067] In some embodiments, Dialister pneumosintes DSM 11619 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: l 1.

[0068] In some embodiments, Clostridium glycyrrhizinilyticum ZM35 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 12.

[0069] In some embodiments, Lactobacillus rogosae ATCC 27753 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 13.

[0070] In some embodiments, Intestinibacter bartlettii 2789STDY5834879 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 14.

[0071] In some embodiments, Clostridium sp. 1 1 41 A1FAA has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 15.

[0072] In some embodiments, Intestinibacter bartlettii BSD2780061688ST1 A9 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 16.

[0073] In some embodiments, Intestinibacter bartlettii DSM 16795 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 17. [0074] In some embodiments, Lachnospira pectinoschiza 2789STDY5834886 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 18.

[0075] In some embodiments, Butyricicoccus sp. AF15 40 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO: 19.

[0076] In some embodiments, Butyricicoccus sp. AM28 25 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:20.

[0077] In some embodiments, Butyricicoccus sp. AM32 19 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:21.

[0078] In some embodiments, Roseburia inulinivorans A2-194 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:22.

[0079] In some embodiments, Parabacteroides distasonis C103T12C09 has a 16S RNA gene that is at least 90% identical (e.g., at least 92%, 94%, 96%, or 99% identical) to SEQ ID NO:23.

[0080] In some embodiments, the composition comprises at least about 1 xlO ³ CFU of the bacterial strain. In some embodiments, the composition comprises about 1 xlO ⁴ to about 1 xlO ¹⁵ CFU of the bacterial strain. In some embodiments, the composition comprises about 1 xlO ⁷ to about 1 xlO ¹² CFU of the bacterial strain.

[0081] In some embodiments, the composition is formulated for oral administration. In some embodiments, the composition is formulated as a tablet, a capsule, a powder, or a liquid. In some embodiments, the composition is formulated as a tablet. In some embodiments, the tablet is coated. In some embodiments, the coating comprises an enteric coating. In some embodiments, the composition is formulated for topical delivery. In some embodiments, the composition is in the form of a paste, gel, cream, spray, suppository, mousse, emollient, ointment, foam, or suspension.

[0082] Also provided herein are methods of treating a subject having an inflammatory disease that include administering one or more bacterial strains, or a composition thereof, wherein the one or more bacterial strains suppress IL-23 -induced IL-17 secretion.

[0083] In some embodiments, the one or more bacterial strains are selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, and a combination thereof. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii. In some embodiments, the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof. In some embodiments, the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, and a combination thereof (e.g., two, three, or four strains). In some embodiments, the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, Parabacteroides distasonis C103T12C09, and a combination thereof (e.g., two, three, four, five, six, or seven strains).

[0084] In some embodiments, the one or more bacterial strains suppress IL-23-induced IL- 17 secretion in the intestine of the subject.

[0085] Also provided herein are methods of treating a subject having inflammatory bowel disease that include administering one or more bacterial strains, or a composition thereof, wherein the one or more bacterial strains are selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A 9, and Intestinibacter bartlettii DSM 16795. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, and Parabacteroides distasonis C103T12C09.

[0086] Also provided herein are methods of treating a subject having inflammatory bowel disease that include administering an effective amount of one or more bacterial strains, or a composition thereof, wherein the one or more bacterial strains are selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, and Intestinibacter bartlettii DSM 16795. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, and Parabacteroides distasonis C103T12C09.

[0087] Also provided herein are methods for suppressing IL-23 -induced IL-17 secretion in a subject in need thereof that include administering one or more bacterial strains, or a composition thereof, wherein the one or more bacterial strains are selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A 9, and Intestinibacter bartlettii DSM 16795. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, and Parabacteroides distasonis C103T12C09.

[0088] Also provided herein are methods for treating a subject having inflammatory bowel disease that include detecting a bacterial strain associated with high IL-23 activation; and administering one or more bacterial strains, or a composition thereof, wherein the one or more bacterial strains are selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, Clostridium discporicum DS1, Streptococcus marimammalium , Alistipes shahii , and a combination thereof. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammal nan , and Alistipes shahii. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, and Intestinibacter bartlettii DSM 16795. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, and Parabacteroides distasonis C103T12C09.

[0089] In some embodiments, the method further comprises obtaining a sample from the subject. In some embodiments, the sample is a biopsy sample. In some embodiments, detecting a bacterial strain associated with high IL-23 activation comprises analyzing the biopsy sample for intestinal gene expression and bacterial composition.

[0090] In some embodiments, the Streptococcus marimammalium bacteria is the Streptococcus marimammalium M54/01/1 strain. In some embodiments, the Alistipes shahii bacteria is the Alistipes shahii WAL 8301 strain. In some embodiments, the inflammatory bowel disease is Crohn’s disease. In some embodiments, the inflammatory bowel disease is ulcerative colitis.

[0091] Also provided herein are compositions that include a) a bacterial strains selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium , Alistipes shahii , Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA,

Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, and combinations thereof; and b) one or more excipients. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, and Intestinibacter bartlettii DSM 16795. In some embodiments, the one or more bacterial strains are selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, and Parabacteroides distasonis C103T12C09. In some embodiments, the Streptococcus marimammalium bacteria is the Streptococcus marimammalium M54/01/1 strain. In some embodiments, the Alistipes shahii bacteria is the Alistipes shahii WAL 8301 strain.

[0092] As used herein, the phrase an "effective amount" or a "therapeutically effective amount" of a bacterial strain can refer to an amount of the bacterial strain sufficient enough to reduce or eliminate one or more symptoms of the disorder or in some cases, to effect a cure upon administration. Effective amounts of the bacterial strain will vary with the kind of bacterial strain chosen, the particular condition or conditions being treated, the severity of the condition, the duration of the treatment, the specific components of the composition being used, and like factors. An "effective amount" can also refer to an amount of a combination of two or more bacterial strains or a combination of a bacterial strain and a therapeutic agent sufficient to reduce or eliminate one or more symptoms of the disorder or in some cases, to effect a cure upon administration. For example, an "effective amount" can refer to an amount of a combination of bacterial strains or a combination of a bacterial strain and another treatment (e.g., a therapeutic agent) when an additive or synergistic effect is observed with the combination compared to administration of the bacterial strain(s) and/or therapeutic agent(s) alone.

[0093] As used herein, "subject" or "patient" refers to any subject, particularly a mammalian subject such as a human, for whom diagnosis, prognosis, or therapy is desired.

[0094] As used herein, "treatment" or "treating" of a disease, disorder, or condition encompasses alleviation of at least one symptom thereof, a reduction in the severity thereof, or the delay or inhibition of the progression thereof. Treatment need not mean that the disease, disorder, or condition is totally cured. A useful composition herein needs only to reduce the severity of a disease, disorder, or condition, reduce the severity of one or more symptoms associated therewith, or improve a patient or subject's quality of life.

[0095] The term "preventing" as used herein means the prevention of the onset, recurrence, or spread, in whole or in part, of the disease or condition as described herein, or a symptom thereof.

[0096] The term“administration” or“administering” refers to a method of giving an amount of a bacterial strain or a composition thereof, or other treatment, to a subject. The method of administration can vary depending on various factors, e.g., the components of the composition, the site of the disease, and the severity of the disease.

[0097] “Microbiome” refers to the collection of microorganisms and viruses and/or their genes from a given environment. For example,“microbiome” can refer to the collection of the microorganisms and viruses and/or their genes from the gastrointestinal tract of humans. “Microbiota” refers to the microorganisms in a specific environment.

[0098] “Dysbiosis” refers to a state of the microbiota or microbiome of the gut or other body area (e.g., mucosal or skin surfaces or any other microbiota niche) of a subject (i.e., the host) in which the diversity and/or function of the ecological network is disrupted, e.g., as compared to the state of the microbiota or microbiome of the gut or other body area in a control population. A control population can include individuals that meet one or more qualifications such as individuals that have not been diagnosed with a disease (e.g., the same disease as the subject); individuals that do not have a known genetic predisposition to a disease (e.g., the same disease as the subject); or individuals that do not have a known environmental predisposition to a disease (e.g., the same disease as the subject); or individuals that do not have a known predisposition that would prevent treatment of and/or recovery from a disease (e.g., the same disease as the subject). In some embodiments, the individuals in the control population meet one of the above control population qualifications. In some embodiments, the individuals in the control population meet two of the above control population qualifications. In some embodiments, the individuals in the control population meet three of the above control population qualifications. In some embodiments, the individuals in the control population meet four of the above control population qualifications. In some embodiments, the control population is homogenous with respect to at least one of the qualifications. Any disruption in the microbiota or microbiome of a subject (i.e., host) compared to the microbiota or microbiome of a control population can be considered a dysbiosis, even if such dysbiosis does not result in a detectable decrease in health of the subject. Dysbiosis in a subject can be unhealthy for the subject (e.g., result in a diseased state in the subject), it can be unhealthy for the subject under only certain conditions (e.g., result in diseased state under only certain conditions), or it can prevent the subject from becoming healthier (e.g., can prevent a subject from responding to treatment or recovering from a disease or disorder). Dysbiosis can be due to a decrease in diversity of the microbiota population composition (e.g., a depletion of one or more bacterial strains, an overgrowth of one or more bacterial strains, or a combination thereof), the overgrowth of one or more population of pathogens (e.g., a population of pathogenic bacteria) or pathobionts, the presence of and/or overgrowth of a symbiotic organism able to cause disease only when certain genetic and/or environmental conditions are present in a subject, or a shift to an ecological network that no longer provides a beneficial function to the host and therefore no longer promotes health.

[0099] As used herein the terms“microorganism” or“microbe” should be taken broadly. These terms are used interchangeably and include, but are not limited to, the two prokaryotic domains, Bacteria and Archaea, as well as eukaryotic fungi and protists. In some embodiments, the disclosure refers to a“bacterium” or a“microbe.” This characterization can refer to not only the identified taxonomic bacterial genera of the microbe, but also the identified taxonomic species, as well as the bacterial strains. A“strain” can include descendants of a single isolation in pure culture that is usually made up of a succession of cultures ultimately derived from an initial single colony. In some embodiments, a strain includes an isolate or a group of isolates that can be distinguished from other isolates of the same genus and species by phenotypic characteristics, genotypic characteristics, or both.

[00100] The term“relative abundance” as used herein, is the number or percentage of a microbe present in the gastrointestinal tract or any other microbiota niche of a subject, such as the ocular, placental, lung, cutaneous, urogenital, or oral microbiota niches, relative to the number or percentage of total microbes present in the gastrointestinal tract or the other microbiota niche of the subject. The relative abundance can also be determined for particular types of microbes such as bacteria, fungi, viruses, and/or protozoa, relative to the total number or percentage of bacteria, fungi, viruses, and/or protozoa present. Relative abundance can be determined by a number of methods readily known to the ordinarily skilled artisan, including, but not limited to, array or microarray hybridization, sequencing, quantitative PCR, and culturing and performance of colony forming unit (cfu, CFU) assays or plaque forming unit (pfu, PFU) assays performed on a sample from the gastrointestinal tract or other microbiota niche.

[00101] As used herein, terms such as“isolate” and“isolated” in reference to a microbe, are intended to mean that a microbe has been separated from at least one of the materials with which it is associated in a particular environment (for example, gastrointestinal fluid, gastrointestinal tissue, human digestive fluid, human digestive tissue, etc.). Accordingly, an“isolated microbe” does not exist in its naturally occurring environment. In some embodiments, an isolated microbe, e.g., a bacterial strain, can exist as, for example, a biologically pure culture, or as spores (or other forms of the bacterial strain) in association with a pharmaceutically acceptable excipient suitable for human administration. In some embodiments, more than one microbe can be isolated. For example,“isolated microbes” can refer to a mixture of two or more microbes that have been separated from at least one of the materials with which they are associated in a particular environment.

[00102] In some embodiments, the isolated microbes exist as isolated and biologically pure cultures. As used herein, the term“biologically pure” refers to a composition comprising a species or strains of a microbe, wherein the composition is substantially free from the material from which the microbe was isolated or produced and from other microbes (e.g., other species or strains and other microbes of a different taxonomic classification). In some embodiments,“biologically pure” can refer to a composition that comprises a strain of a bacterial strain that is substantially free from the material from which the bacterial strain was isolated or produced and from other microbes, e.g., other strains of the same bacterial strain, other species of the same bacteria, and other bacteria and/or microbes of a different taxonomic classification). It will be appreciated by one of skill in the art, that an isolated and biologically pure culture of a particular microbe, denotes that said culture is substantially free (within scientific reason) of other living organisms and contains only the individual microbe in question. As used herein,“substantially free” means that a composition comprising a species or strain of a microbe is at least about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% free of the material from which the microbe was isolated or produced and from other microbes. In some embodiments, a biologically pure composition contains no other bacterial strain in quantities that can be detected by typical bacteriological techniques.

[00103] As used herein, the term “mutation” includes a natural or induced mutation comprising at least a single base or amino acid alteration in a DNA or protein sequence. For example, a mutation can include a base substitution, a deletion, an insertion, a transversion, or any other modification known to those skilled in the art, including a genetic modification introduced into a parent nucleotide or an amino acid sequence. [00104] As used herein,“probiotic” refers to a substantially pure microbe (i.e., a single isolate) or a mixture of microbes, and can also include any additional components that can be administered to a subject (e.g., a human), for restoring or altering the microbiota or microbiome in the subject. In some embodiments, a probiotic or microbial inoculant composition can be administered with an agent to allow the microbe(s) to survive the environment of the gastrointestinal tract, i.e., to resist low pH and/or to grow in the gastrointestinal environment. In some embodiments, a composition as described herein includes a probiotic.

[00105] As used herein,“prebiotic” refers to an agent that increases the number and/or activity of one or more microbes. Such microbes can include microbes for restoring or altering the microbiota or microbiome of a subject. Non-limiting examples of a prebiotic include a fructooligosaccharide (e.g., oligofructose, inulin, or an inulin-type fructan), a galactooligosaccharide, an amino acid, an alcohol. See, for example, Ramirez-F arias et al. (2008. Br. J Nutr. 4: 1-10) and Pool-Zobel and Sauer (2007. J Nutr. 137:2580-2584).

[00106] As used herein, a“live biotherapeutic product” or“LBP” refers to a biological product that: 1) contains live organisms, such as bacteria, and 2) is applicable to the prevention, treatment, and/or cure of a disease or condition of a subject.

[00107] A“combination” of two or more bacteria, e.g., bacterial strains, can refer to the physical co-existence of the bacteria, either in the same material or product. In some embodiments, a combination of two or more bacteria can include the temporal co-administration or co localization of the two or more bacteria.

[00108] The terms“percent identity” or“identity” in the context of two or more nucleic acids or polypeptides, refers to the measurement of the similarity between the two or more sequences. The percent identity can be measured by any method known to one of skill in the art including using a sequence comparison software, an algorithm, and by visual inspection.

[00109] In general, the percent identity for two or more sequences (e.g., a nucleic acid or amino acid sequence), also referred to as the“percent sequence identity”, is calculated by determining the number of matched positions in the aligned nucleic acid or amino acid sequences, dividing the number of matched positions by the total number of aligned nucleotides or amino acids, respectively, and multiplying by 100. A matched position refers to a position in which identical nucleotides or amino acids occur at the same position in the aligned sequences. As an example, the total number of aligned nucleotides can refer to the minimum number of the 16S rRNA gene nucleotides that are necessary to align the second sequence, and does not include alignment (e.g., forced alignment) with non-16S rRNA gene sequences. The total number of aligned nucleotides can correspond to the entire 16S rRNA gene sequence or can correspond to fragments of the full-length 16S rRNA gene sequence.

[00110] Sequences can be aligned using an algorithm, for example, the algorithm as described by Altschul et al. (Nucleic Acids Res, 25:3389-3402, 1997) and incorporated into BLAST (basic local alignment search tool) programs, which are available at ncbi.nlm.nih.gov. BLAST searches or alignments can be performed to determine percent sequence identity between a 16S rRNA gene nucleic acid and any other sequence or portion thereof using the Altschul et al. algorithm. BLASTN can be used to align and compare the identity between nucleic acid sequences, while BLASTP can be used to align and compare the identity between amino acid sequences. When utilizing a BLAST program to calculate the percent identity between a 16S rRNA gene sequence and another sequence, the default parameters of the program are used.

[00111] Generally, a bacterial strain genomic sequence will contain multiple copies of 16S rRNA sequences. The 16S rRNA sequences can be used for making distinctions between species and strains. For example, if one or more of the 16S rRNA sequences shares less than 97% sequence identity from a reference sequence, then the two organisms from which the sequences were obtained can be of different species or strains.

[00112] The term "combination therapy" as used herein refers to a dosing regimen of one or more bacterial strains and one or more other treatments of ulcerative colitis and/or adjunct therapies, wherein the bacterial strain and other treatment (e.g., a therapeutic agent) are administered together or separately in a manner prescribed by a medical care taker or according to a regulatory agency. As can be appreciated in the art, a combination therapy can be administered to a patient for a period of time. In some embodiments, the period of time occurs following the administration of one or more of: a different bacterial strain, a different treatment/therapeutic agent, and a different combination of treatments/therapeutic agents to the subject. In some embodiments, the period of time occurs before the administration of one or more of: a different bacterial strain, a different treatment/therapeutic agent, and a different combination of therapeutic treatments/agents to the subject. [00113] The term "fixed combination" means that one or more bacterial strains as described herein, or a composition thereof, and at least one other treatment and/or adjunct therapy (e.g., a prebiotic, a probiotic, an immunosuppressant, an anti-inflammatory agent, an antibiotic, an anti- diarrheal agent, a pain reliever, an iron supplement, or a combination thereof), are both administered to a subject simultaneously in the form of a single composition or dosage.

[00114] The term "non- fixed combination" means that one or more bacterial strains as described herein, or a composition thereof, and at least one other treatment or adjunct therapy (e.g., a prebiotic, a probiotic, an immunosuppressant, an anti-inflammatory agent, an antibiotic, an anti- diarrheal agent, a pain reliever, an iron supplement, or a combination thereof) are formulated as separate compositions or dosages such that they can be administered to a subject simultaneously or sequentially with variable intervening time limits. These also apply to cocktail therapies, e.g., the administration of three or more therapeutic agents.

[00115] Reference to the term "about" has its usual meaning in the context of compositions to allow for reasonable variations in amounts that can achieve the same effect and also refers herein to a value of plus or minus 10% of the provided value. For example, "about 20" means or includes amounts from 18 to and including 22.

[00116] Unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. As used herein, the singular form "a", "an", and "the" include plural references unless indicated otherwise. For example, "an" excipient includes one or more excipients. It is understood that aspects and variations of the invention described herein include "consisting of’ and/or "consisting essentially of’ aspects and variations.

[00117] The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

[00118] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.

DESCRIPTION OF DRAWINGS

[00119] FIGS. 1A and IB are principal coordinate analysis (PCoA) plots based on selected genes.

[00120] FIG. 2A is a PCoA plot showing that the clusters are differentiated on the IL-23 gene plot, and FIG. 2B is a plot showing the cluster differentiation.

[00121] FIG. 3 is a plot showing the differentially abundant sequences between clusters 1 and 2

[00122] FIG. 4 is a plot showing the differentially abundant sequences between clusters 1 and 4.

[00123] FIG. 5 is a plot showing that three strains were significantly associated with low IL- 23 pathway activity. The 14 datasets include multiple platforms (next generation sequencing (NGS), PhyloChip) and multiple contrasts (different levels of IL-23 expressions) from three cohorts. Random effects model was used to identify concordant beneficial (negatively associated with IL-23 pathway activity) strains. Strain 1 is Clostridium discporicum DS1, Strain 2 is Streptococcus marimammalium M54/01/1, and Strain 3 is Alistipes shahii WAL 8301.

[00124] FIG. 6 is a plot showing that the identified strains reduce IL-23 activity. Strain 1 is Clostridium discporicum DS11, Strain 2 is Streptococcus marimammalium M54/01/1, and Strain 3 is Alistipes shahii WAL 8301. **indicates p<0.01.

[00125] FIG. 7 is a representative forest plot showing the strain effect size for each dataset analyzed followed by the meta-analysis effect size at the bottom.

[00126] FIG. 8 is a table that contains the sequences for SEQ ID NOs: 1-39.

DETAILED DESCRIPTION

[00127] This document provides compositions and methods for treating subjects in need thereof (e.g., subjects having an inflammatory disease) and for suppressing IL-23-induced IL-17 secretion using one or more bacterial strains. Also provided herein is the use of one or more bacterial strains described herein in the manucfacture of a medicament for treating an inflammatory disease and/or for suppressing IL-23-induced IL-17 secretion. Inflammation involves the activation of the immune system in response to harmful stimuli, such as a pathogen, an infection, an irritant, or damage to cells. Chronic inflammation is a slow, long-term inflammation lasting for prolonged periods of several months to years, whereas in acute inflammation, the symptoms can last for a few days to weeks. Generally, acute inflammation is related to tissue damage, for example, due to microbial invasion, trauma, or noxious compounds. Inflammatory disorders can involve the immune system attacking the body’s own cells or tissues, which can lead to abnormal inflammation. Common inflammatory diseases include inflammatory bowel disease (IBD), rheumatoid arthritis, restenosis, psoriasis, multiple sclerosis, surgical adhesions, tuberculosis, and chronic inflammatory lung diseases.

[00128] Suppressing the IL-23 pathway has been suggested as a potential therapy for IBD and other inflammatory diseases such as psoriasis, rheumatoid arthritis, and multiple sclerosis (see Neurath. Nat Rev Gastroenterol Hepatol. 2017. 14(5):269-278; and Tang et al. Immunology. 2012. 135(2): 112-124). As described herein, segmenting patients based on molecular phenotypes can identify bacterial strain and bacterial strains associated with molecular pathways such as the IL- 23 pathway. For example, biopsy samples from multiple clinical cohorts can be analyzed for both intestinal gene expression and bacterial composition and can be used to compare direct interactions between the host and microbiome. By separating samples by IL-23 pathway activation, different strains of bacteria can be identified than would have been observed in a simple“healthy” versus “diseased” comparative analysis. These strains can be used for modulating the IL-23 pathway in the host.

[00129] In some embodiments, methods for treating a subject in need thereof are provided herein. In some embodiments, IL-23 -induced IL-17 secretion is suppressed in a subject. In some embodiments, an inflammatory disease is treated in the subject. The methods provided herein can include administering to the subject a composition comprising an effective amount of a bacterial strain. In some embodiments, the bacterial strain suppresses IL-23 -induced IL-17 secretion. Methods for determining whether a bacterical strain suppresses IL-23-induced IL-17 secretion can include an ELISA for IL-17 secretion, see, e.g., the in vitro test described in Example 2. In some embodiments, the bacterial strain can be selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, and a combination thereof (e.g., any two, any three, any four, any five, any six, any seven, any eight, any nine, any ten, any eleven, any twelve, any thirteen, any fourteen, any fifteen, any sixteen, any seventeen, any eighteen, any nineteen, any twenty, any twenty-one, any twenty-two, or twenty- three of the bacterial strains).

[00130] In some embodiments, the bacterial strain in the composition comprises Alistipes shahii. Alistipes shahii is a gram-negative, strictly anaerobic bacterium that has been isolated from human intestinal tissue (see Song et al. Int J Syst Evol Microbiol. 2006. 56, (Pt 8): 1985-90). A complete genomic sequence for Alistipes shahii WAL 8301 is available in the GenBank database as, e.g., Accession No. NC_021030. Alistipes shahii WAL 8301 is also known as Alistipes shahii ATCC BAA 1179, Alistipes. shahii CCUG 48947, Alistipes shahii DSM 19121, and Alistipes shahii JCM 16773. In some embodiments, the Alistipes shahii WAL 8301 included in a composition provided herein can have a genomic sequence with at least about 95% sequence identity to the genomic sequence published as NC 021030. For example, Alistipes shahii WAL 8301 included in a composition provided herein can have a genomic sequence with at least about 96%, about 97%, about 98%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% sequence identity to the genomic sequence published as NC 021030. In some embodiments, Alistipes shahii WAL 8301 included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 1. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 1. [00131] In some embodiments, the bacterial strain in the composition comprises Clostridium discporicum DS1. Bacteria from the genus Clostridium are gram positive obligate anaerobes generally found in soil and animal intestinal tracts including humans. In some embodiments, Clostridium discporicum DS1 included in a composition provided herein has a 16S rRNA gene that is at least 90% identical to SEQ ID NO:2. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO:2.

[00132] In some embodiments, the bacterial strain in the composition comprises Streptococcus marimammalium M54/01/1. Bacteria from the genus Streptococcus are gram positive cocci. Streptococcus marimammalium M54/01/1 is also known as Streptococcus marimammalium CCUG 48494, Streptococcus marimammalium CIP 108309, Streptococcus marimammalium DSM 18627, and Streptococcus marimammalium SAC m54/01/l . In some embodiments, Streptococcus marimammalium M54/01/1 included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO:3. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO:3.

[00133] In some embodiments, the bacterial strain in the composition comprises Intestinibacter bartlettii 2789STDY5834879. In some embodiments, Intestinibacter bartlettii 2789STDY5834879 included in a composition provided herein has a 16S rRNA gene that is at least 90% identical to SEQ ID NO: 14. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 14.

[00134] In some embodiments, the bacterial strain in the composition comprises Clostridium sp. 1 1 41 A1FAA. In some embodiments, Clostridium sp. 1 1 41 A1FAA included in a composition provided herein has a 16S rRNA gene that is at least 90% identical to SEQ ID NO: 15. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 15.

[00135] In some embodiments, the bacterial strain in the composition comprises

Intestinibacter bartlettii BSD2780061688ST1 A9. In some embodiments, Intestinibacter bartlettii BSD2780061688ST1 A9 included in a composition provided herein has a 16S rRNA gene that is at least 90% identical to SEQ ID NO: 16. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 16.

[00136] In some embodiments, the bacterial strain in the composition comprises

Intestinibacter bartlettii DSM 16795. Intestinibacter bartlettii DSM 16795 is also known as Clostridium bartlettii ATCC BAA 827, Clostridium bartlettii CCUG 48263, Clostridium bartlettii CCUG 48940, Clostridium bartlettii DSM 16795, and Clostridium bartlettii WAL 16138. In some embodiments, Intestinibacter bartlettii DSM 16795 included in a composition provided herein has a 16S rRNA gene that is at least 90% identical to SEQ ID NO: 17. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 17.

[00137] In some embodiments, the bacterial strain in the composition comprises Lachnospira pectinoschiza 2789STDY5834886. In some embodiments, Lachnospira pectinoschiza 2789STDY5834886 included in a composition provided herein has a 16S rRNA gene that is at least 90% identical to SEQ ID NO: 18. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 18.

[00138] In some embodiments, the bacterial strain in the composition comprises Butyricicoccus sp. AF15 40. In some embodiments, Butyricicoccus sp. AF15 40 included in a composition provided herein has a 16S rRNA gene that is at least 90% identical to SEQ ID NO: 19. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 19.

[00139] In some embodiments, the bacterial strain in the composition comprises

Butyricicoccus sp. AM28 25. In some embodiments, Butyricicoccus sp. AM28 25 included in a composition provided herein has a 16S rRNA gene that is at least 90% identical to SEQ ID NO:20. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO:20.

[00140] In some embodiments, the bacterial strain in the composition comprises

Butyricicoccus sp. AM32 19. In some embodiments, Butyricicoccus sp. AM32 19 included in a composition provided herein has a 16S rRNA gene that is at least 90% identical to SEQ ID NO:21. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO:21.

[00141] In some embodiments, the bacterial strain in the composition comprises Roseburia inulinivorans A2-194. Roseburia inulinivorans A2-194 is also known as Roseburia inulinivorans CIP 109405, Roseburia inulinivorans DSM 16841, and Roseburia inulovorans NCIMB 14030. In some embodiments, Roseburia inulinivorans A2-194 included in a composition provided herein has a 16S rRNA gene that is at least 90% identical to SEQ ID NO:22. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO:22.

[00142] In some embodiments, the bacterial strain in the composition comprises Parabacteroides distasonis C103T12C09. In some embodiments, Parabacteroides distasonis C103T12C09 included in a composition provided herein has a 16S rRNA gene that is at least 90% identical to SEQ ID NO:23. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO:23.

[00143] In some embodiments, the bacterial strain in the composition comprises Firmicutes bacterium ASF500. In some embodiments, Firmicutes bacterium ASF 500 included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO:4. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO:4.

[00144] In some embodiments, the bacterial strain in the composition comprises Eubacterium coprostanoligenes str. HL. In some embodiments, Eubacterium coprostanoligenes str. HL included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO:5. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO:5. [00145] In some embodiments, the bacterial strain in the composition comprises Howardella ureilytica GPC 589. In some embodiments, Howardella ureilytica GPC 589 included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO:6. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO:6.

[00146] In some embodiments, the bacterial strain in the composition comprises Cupriavidus respiraculi au5353. In some embodiments, Cupriavidus respiraculi au5353 included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO:7. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO:7.

[00147] In some embodiments, the bacterial strain in the composition comprises Dialister invisus E7.25. In some embodiments, Dialister invisus E7.25 included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO:8. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO:8.

[00148] In some embodiments, the bacterial strain in the composition comprises Clostridium lituseburense VKM B-2279. In some embodiments, Clostridium lituseburense VKM B-2279 included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO:9. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 9.

[00149] In some embodiments, the bacterial strain in the composition comprises Coprococcus sp. HPP0074. In some embodiments, Coprococcus sp. HPP0074 included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 10. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 10.

[00150] In some embodiments, the bacterial strain in the composition comprises Firmicutes bacterium ASF500. In some embodiments, Dialister pneumosintes DSM 11619 included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 11. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 11.

[00151] In some embodiments, the bacterial strain in the composition comprises Clostridium glycyrrhizinilyticum ZM35. In some embodiments, Clostridium glycyrrhizinilyticum ZM35 included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 12. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 12.

[00152] In some embodiments, the bacterial strain in the composition comprises Lactobacillus rogosae ATCC 27753. Lactobacillus rogosae ATCC 27753 is also known as Lactobacillus rogosae VPI C37-38. In some embodiments, Lactobacillus rogosae ATCC 27753 included in a composition provided herein has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 13. For example, at least about 91%, about 91.5% about 92%, about 92.5%, about 93%, about 93.5%, about 94%, about 94.5%, about 95%, about 95.5%, about 96%, about 96.5%, about 97%, about 97.5%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, or about 99.9% identical to SEQ ID NO: 13.

[00153] In some embodiments, the composition can include two or more bacterial strains selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, and Parabacteroides distasonis C103T12C09. For example, the bacterial strain can comprise three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, eleven or more, twelve or more, thirteen or more, fourteen or more, fifteen or more, sixteen or more, seventeen or more, eighteen or more, nineteen or more, twenty or more, twenty-one or more, twenty-two or more, or twenty-three or more bacterial strains selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, and Clostridium disporicum DS1.

[00154] In some embodiments, compositions described herein can include A. shahii WAL 8301, Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, or a combination thereof (e.g., any two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, or all fourteen of A. shahii WAL 8301, Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09). In some embodiments, compositions described herein can include d shahii WAL 8301, Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, or a combination thereof (e.g., A. shahii WAL 8301 and Clostridium discporicum DS1; A. shahii WAL 8301 and Streptococcus marimammalium M54/01/1; Clostridium discporicum DS1 and Streptococcus marimammalium M54/01/1; or A. shahii WAL 8301, Clostridium discporicum DS1, and Streptococcus marimammalium M54/01/1). In some embodiments, compositions described herein can include Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, or a combination thereof (e.g., any two, three, or all four of Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, and Intestinibacter bartlettii DSM 16795). In some embodiments, compositions described herein can include Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, Parabacteroides distasonis C103T12C09, or a combination thereof (e.g., any two, three, four, five, six, or all seven or Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, and Parabacteroides distasonis C103T12C09). Identifying characteristics of each strain are described above.

[00155] In some embodiments, the bacterial strain is Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, or Parabacteroides distasonis C103T12C09. In some embodiments, the bacterial strain is a combination of two or more of Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, and Parabacteroides distasonis C103T12C09. In some embodiments, the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, and a combination thereof.

[00156] In some embodiments, a method as described herein can include detecting in a sample from the subject a dysbiosis associated with an inflammatory disease, e.g., before administering to the subject an effective amount of a bacterial strain or a composition containing the bacterial strain. The sample can be a biopsy sample such as an intestinal biopsy sample or a colorectal biopsy sample. In some embodiments, the sample is a fecal sample.

[00157] In some embodiments, detecting the dysbiosis associated with an inflammatory disease can include determining bacterial gene expression in the sample from the subject. In some embodiments, detecting the dysbiosis associated with an inflammatory disease comprises detecting bacterial gene expression associated with high IL-23 activation in the sample from the subject. For example, the bacterial gene expression can be determined in the sample from the subject e.g., before administering to the subject an effective amount of a bacterial strain or a composition containing the bacterial strain and/or after administering to the subject an effective amount of a bacterial strain or a composition containing the bacterial strain. Determining the bacterial gene expression can include performing, for example, RNAseq and/or RT-qPCR. In some embodiments, detecting the dysbiosis associated with an inflammatory disease comprises determining bacterial composition in the sample from the subject (e.g., fecal sample or a biopsy sample such as an intestinal biopsy sample or a colorectal biopsy sample). For example, the bacterial composition can be determined in a sample from the subject, e.g., before administering to the subject an effective amount of a bacterial strain or a composition containing the bacterial strain and/or after administering to the subject an effective amount of a bacterial strain or a composition containing the bacterial strain. Determining the bacterial composition can include, for example, sequencing one or more nucleic acids from the bacteria, e.g., performing RNAseq and/or RT-qPCR. In some embodiments, bacteria can be identified by their 16S rRNA gene sequence. In some embodiments, detecting bacterial gene expression can include performing, for example, RNAseq and/or RT-qPCR.

[00158] In some embodiments, detecting the dysbiosis associated with an inflammatory disease comprises detecting a bacterial strain associated with high IL-23 activation in the sample from the subject. In some embodiments, detecting the dysbiosis comprises determining that Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41 A 1 F A A, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, or a combination thereof, are reduced in the sample from subject. In some embodiments, Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, and Parabacteroides distasonis C103T12C09 are reduced in the gastrointestinal tract of the subject. In some embodiments, Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, and Alistipes shahii WAL 8301 are reduced in the gastrointestinal tract of the subject. In some embodiments, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, and Intestinibacter bartlettii DSM 16795 are reduced in the gastrointestinal tract of the subject. In some embodiments, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, and Parabacteroides distasonis C103T12C09 are reduced in the gastrointestinal tract of the subject.

[00159] In some embodiments, the subject in need thereof has been diagnosed with an inflammatory disease. Non-limiting examples of an inflammatory disease include an inflammatory bowel disease (e.g., ulcerative colitis and Crohn's disease), multiple sclerosis, myocarditis, psoriasis, atrophic gastritis, inflammatory hemolytic anemia, arthritis, atopic dermatitis, pouchitis, graft rejection, inflammatory neutropenia, bullous pemphigoid, celiac disease, a demyelinating neuropathy, dermatomyositis, myositis, a nasal polyp, chronic sinusitis, pemphigus vulgaris, primary glomerulonephritis, a surgical adhesion, stenosis or restenosis, scleritis, scleroderma, eczema (e.g., atopic dermatitis, contact dermatitis, irritant dermatitis, allergic dermatitis), type I diabetes, vasculitis, pancreatitis, primary sclerosing cholangitis, a benign stricture (e.g., a stricture of bile ducts, esophagus, duodenum, small bowel or colon), a respiratory tract disease (e.g., asthma, hypersensitivity pneumonitis, asbestosis, silicosis and other forms of pneumoconiosis, chronic bronchitis, and chronic obstructive airway disease), a nasolacrimal duct disease, and a eustachean tube disease.

[00160] Non-limiting examples of vasculitis include Behcet’s Disease, Buerger’s Disease, Eosinophilic Granulomatosis with Polyangiitis, formerly Churg-Strauss Syndrome (EGPA), Cryoglobulinemia, Giant Cell Arteritis, Henoch- Schonlein Purpura, Microscopic Polyangiitis, Polyarteritis Nodosa, Rheumatoid Vasculitis, Takayasu’s Arteritis, Granulomatosis with Polyangiitis.

[00161] In some embodiments, the inflammatory disease is inflammatory bowel disease. In some embodiments, the inflammatory bowel disease is ulcerative colitis or Crohn’s disease.

[00162] Inflammatory bowel disease (IBD) includes ulcerative colitis (UC) and Crohn's disease (CD). The pathogenesis of inflammatory bowel disease is not well understood. A genetic predisposition has been suggested, and a host of environmental factors, including bacterial, viral and, perhaps, dietary antigens, can trigger an ongoing enteric inflammatory cascade. IBD can cause severe diarrhea, pain, fatigue, and weight loss. IBD can be debilitating and sometimes leads to life- threatening complications. Accordingly, in some embodiments, a method of treatment as described herein reduces, prevents, or eliminates any one or more of the symptoms described above. In some embodiments, the method of treatment results in remission. Collagenous colitis and lymphocytic colitis also are considered inflammatory bowel diseases, but are usually regarded separately from classic inflammatory bowel disease.

[00163] Ulcerative colitis causes long-lasting inflammation and sores (ulcers), in the innermost lining of the large intestine (colon) and rectum. Ulcerative colitis typically presents with shallow, continuous inflammation. This inflammation generally extends from the rectum and can include part of or the entire colon. Subjects with inflammation limited to part of the colon (e.g., proctitis) can have mild but frequently recurrent symptoms, whereas subjects with extensive disease (e.g., pancolitis) more commonly have severe symptoms. See, for example, Botoman et al, Am. Fam. Physician , Vol. 57(l):57-68 (Jan 01, 1998).

[00164] Unlike ulcerative colitis, Crohn's disease can involve the entire intestinal tract, from the mouth to the anus, with discontinuous focal ulceration, fistula formation, and perianal involvement. The terminal ileum is most commonly affected, usually with variable degrees of colonic involvement. Subsets of subjects can have perianal disease with fissures and fistula formation. Only 2 to 3 percent of patients with Crohn’s disease have clinically significant involvement of the upper gastrointestinal tract. See, for example, Botoman et al, Am. Fam. Physician , Vol. 57(l):57-68 (Jan 01, 1998). Inflammation in Crohn’s disease can spread deep into affected tissues.

[00165] Psoriasis can involve the skin and/or joints and can be categorized into plaque psoriasis, guttate psoriasis, inverse psoriasis, pustular psoriasis, erythrodermic psoriasis, and psoriatic arthritis. Psoriasis often causes dry, thick, and raised patches on the skin that can be covered with scale. Subjects with psoriasis can also experience itching and/or soreness around the patches. Many issues such as the autoimmune cause of inflammation, role of external, genetic, cutaneous, and systemic factors that affect the progression and treatment of psoriasis are still unclear. See, e.g., Todke and Shah. Int. J. Dermatol. 2018 Nov;57(l 1): 1387-1402. [00166] In some embodiments, a method as described herein can include administering the composition that includes an effective amount of one or more bacterial strains to the subject at least once per day. For example, the composition can be administered two, three, four, or more times per day. In some embodiments, an effective amount of the bacterial strain is administered in one dose, e.g., once per day. In some embodiments, an effective amount of the bacterial strain is administered in more than one dose, e.g., more than once per day. In some embodiments, the method comprises administering the composition to the subject daily, every other day, every three days, or once a week.

[00167] In some embodiments, a composition comprising a bacterial strain as described herein can be used in combination with one or more additional therapies or therapeutic agents. For example, a composition comprising a bacterial strain as described herein can be used in combination with an immunosuppressant that works by the same or by a different mechanism of action.

[00168] In some embodiments, an effective amount of a bacterial strain (e.g., Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, or a combination thereof) in a composition described herein can include at least about 1 xlO ³ CFUs of the bacterial strain. For example, an effective amount of a bacterial strain can be at least about 1 xlO ³ , about 1 xlO ⁴ , about 1 xlO ⁵ , about 1 xlO ⁶ , about 1 xlO ⁷ , about 1 xlO ⁸ , about 1 xlO ⁹ , about 1 xlO ¹⁰ , about 1 xlO ¹¹ , about 1 xlO ¹² , about 1 xlO ¹³ , or about 1 xlO ¹⁴ CFUs of the bacterial strain. In some embodiments, the effective amount of a bacterial strain in a composition described herein comprises about 1 xlO ³ to about 1 xlO ¹⁵ CFUs of the bacterial strain (e.g., about 1 xlO ³ to about 1 xlO ⁶ , about 1 xlO ³ to about 1 xlO ⁸ , about 1 xlO ³ to about 1 xlO ¹⁰ , about 1 xlO ³ to about 1 xlO ¹² , about 1 xlO ³ to about 1 xlO ¹⁴ , about 1 xlO ⁷ to about 1 xlO ¹² , about 1 xlO ¹³ to about 1 xlO ¹⁵ , about 1 xlO ¹¹ to about 1 xlO ¹⁵ , about 1 xlO ⁹ to about 1 xlO ¹⁵ , about 1 xlO ⁷ to about 1 xlO ¹⁵ , or about 1 xlO ⁵ to about 1 xlO ¹⁵ CFUs of the bacterial strain).

[00169] In some embodiments, methods provided herein can include administering a composition comprising a bacterial strain as described herein in combination with one or more other treatments of an inflammatory disease and/or in combination with adjunct therapies such as a therapeutic agent to control pain and/or inflammation. In some embodiments, the treatment of an inflammatory disease can be surgery (e.g., a proctocolectomy). In some embodiments, the treatment of an inflammatory disease and/or adjunct therapy can be a therapeutic agent such as an anti-inflammatory agent, an immunosuppressant, a corticosteroid, or an antibiotic. In some embodiments, the therapeutic agent is one or more of an anti-inflammatory agent, an immunosuppressant, an antibiotic, an anti-diarrheal agent, a pain reliever, an iron supplement, or a combination thereof. In some embodiments, the anti-inflammatory agent is a JAK inhibitor (e.g., tofacitinib, ruxolitinib, and baricitinib) sulfasalazine, mesalamine, balsalazide, olsalazine, prednisone, hydrocortisone, or a combination thereof). In some embodiments, the immunosuppressant is selected from the group consisting of: azathioprine, mercaptopurine, cyclosporine, infliximab, adalimumab, golimumab, vedolizumab, or a combination thereof.

[00170] The composition comprising a bacterial strain and any other treatments and/or adjunct therapies can be administered together (e.g., in the same formulation), or the composition comprising the bacterial strain can be administered concurrently with, prior to, or subsequent to, the one or more other treatments or adjunct therapies.

[00171] In some embodiments, a treatment of ulcerative colitis and/or an adjunct therapy administered in combination with a composition comprising a bacterial strain as described herein comprises an anti-inflammatory agent, an immunosuppressant, a corticosteroid, an antibiotic, an anti-diarrheal agent, a pain reliever, an iron supplement, a probiotic, a prebiotic, or a combination thereof. In some embodiments, the anti-inflammatory agent comprises a JAK inhibitor (e.g., tofacitinib, ruxolitinib, and/or baricitinib), sulfasalazine, mesalamine, balsalazide, olsalazine, a corticosteroid, or a combination thereof. In some embodiments, the immunosuppressant comprises azathioprine, mercaptopurine, cyclosporine, infliximab, adalimumab, golimumab, vedolizumab, or a combination thereof. In some embodiments, the corticosteroid comprises prednisone, hydrocortisone, rednisone, budesonide, or a combination thereof. See, for example, Kayal and Shah. J Clin Med. 2019 Dec 30;9(1).

[00172] In some embodiments, a prebiotic and/or probiotic can be administered in combination with a composition comprising a bacterial strain as described herein. Non-limiting examples of a probiotic include one of more of Bifidobacteria (e.g., B. animal is, B. breve , B. lactis , B. longum , B. longum , or B. infantis ), Lactobacillus (e.g., L. acidophilus , L. reuteri , L. bulgaricus , L. lactis , . casei, L. rhamnosus , . plantar um, L. paracasei, or . de I breuckii I bulgaricus), Saccharomyces boulardii , E.coli Nissle 1917, and Streptococcus thermophiles. Non-limiting examples of a prebiotic include a fructooligosaccharide (e.g., oligofructose, inulin, or an inulin- type fructan), a galactooligosaccharide, an amino acid, or an alcohol. See, for example, Ramirez- Farias et al. (2008. Br. J Nutr. 4: 1-10) and Pool-Zobel and Sauer (2007. J Nutr. 137:2580-2584).

[00173] In some embodiments, method provided herein can include monitoring the subject after treatment with a composition described herein to determine if one or more symptoms have been alleviated, if the severity of one or more symptoms has been reduced, or if progression of the disease has been delayed or inhibited in the subject. Non-limiting examples of ulcerative colitis symptoms include: diarrhea, abdominal pain, abdominal cramping, rectal pain, rectal bleeding, urgency to defecate, inability to defecate despite urgency (tenesmus), weight loss, fatigue, fever, and failure to grow (in children). There are numerous scores and clinical markers that can be utilized to assess the efficacy of administering a composition that includes bacterial strain as described herein in treating an inflammatory disease.

[00174] As an example, there are two general approaches to evaluating patients with IBD. The first involves the visual examination of the mucosa and relies on the observation of signs of damage to the mucosa. Any procedure that allows an assessment of the mucosa can be used. Non limiting examples include a barium enema, an x-ray, and endoscopy. An endoscopy can be of the esophagus, stomach and duodenum (esophagogastroduodenoscopy), small intestine (enteroscopy), or large intestine/colon (colonoscopy, sigmoidoscopy). These techniques can be used to identify an area of inflammation, an ulcer, and/or an abnormal growth such as a polyp. A scoring system based on the visual examination of the GI tract can be used to determine the status and/or severity of IBD. The scoring systems can help ensure the uniform assessment of different subjects, e.g., even if subjects are assessed by different medical professionals. For example, non-limiting examples of evaluations based on visual examination of UC are described and compared in Daperno et al. J Crohns Colitis. 2011 5:484-98. In some embodiments, findings on endoscopy or other examination of the mucosa can be incorporated into a clinical scoring systems. A clinical scoring system can also incorporate data based on one or more symptoms including stool frequency, rectal bleeding, and a physician's global assessment. Some of these scoring systems also take into account a quantitative assessment of the effect on quality of life.

[00175] An example of a scoring system for UC is the Mayo scoring system (Schroeder et al, N Eng J Med, 1987, 317: 1625-1629). Other non-limiting examples of scoring systems for UC include the Ulcerative Colitis Endoscopic Index of Severity (UCEIS) score (Travis et al, 2012, Gut, 61 :535-542), Baron Score (Baron et al, 1964, BMJ, 1 :89), Ulcerative Colitis Colonoscopic Index of Severity (UCCIS) (Thia et al., 2011, Inflamm Bowel Dis, 17: 1757-1764), Rachmilewitz Endoscopic Index (Rachmilewitz, 1989, BMJ, 298:82-86), Sutherland Index (also known as the UC Disease Activity Index (UCDAI) scoring system; Sutherland et al, 1987, Gastroenterology, 92: 1994-1998), Matts Score (Matts, 1961, QJM, 30:393-407), and Blackstone Index (Blackstone, 1984, Inflammatory bowel disease. In: Blackstone MO (ed.) Endoscopic interpretation: normal and pathologic appearances of the gastrointestinal tract, 1984, pp. 464-494). Also see, for example, Paine, 2014, Gastroenterol Rep 2: 161-168.

[00176] An example of a scoring system for CD is the Crohn's Disease Activity Index (CDAI) (Sands Bet al 2004, N Engl J Med 350 (9): 876-85). Calculation of the CDAI score includes scoring of the number of liquid stools over 7 days, instances and severity of abdominal pain over 7 days, general well-being over 7 days, extra- intestinal complications (e.g., arthritis/arthralgia, iritis/uveitis, erythema nodosum, pyoderma gangrenosum, aphtous stomatitis, anal fissure/fistula/abscess, and/or fever > 37.8°C), use of an antidiarrheal drug over 7 days, present of abdominal mass, hematocrit, and body weight as a ratio of ideal/observed or percentage deviation from standard weight. Based on the CDAI score, the CD can be classified as either asymptomatic remission (0 to 149 points), mildly to moderately active CD (150 to 220 points), moderately to severely active CD (221 to 450 points), or severely active fulminant disease (451 to 1000 points). Further examples of a scoring system for CD include, but are not limited to, the Harvey-Bradshaw index (Harvey et al, 1980, Lancet 1(8178): 1134-1135), the Inflammatory Bowel Disease Questionnaire (IBDQ) (Irvine et al, 1994, Gastroenterology 106: 287-296), CDEIS, and SES CD (see, e.g., Levesque, et al. (2015) Gastroentrol. 148:37 57).

[00177] In some embodiments, treatment of Crohn’s disease or ulcerative colitis in a subject is assessed using one or more indexes or biomarkers selected from the group consisting of: the UC Disease Activity Index, Crohn’s Disease Activity Index, the UC Disease Activity Index, the Mayo Score, Mayo Score, the Harvey-Bradshaw Index, an IBD questionnaire, Manitoba IBD Index, IBD-Control questionnaire, CRP levels, calprotectin levels, fecal lactoferrin levels, an endoscopy, Crohn’s Disease Endoscopic Index of Severity, Simple Endoscopic Score for Crohn’s Disease, Rachmilewitz Endoscopic Index, Ulcerative Colitis Endoscopi Index of Severity, and CD Digestive Damage Score. For example, an improvement in one or more of the above indexes or biomarkers after administering a bacterial strain, or a composition thereof, as described herein to the subject indicates treatment of the Crohn’s disease or ulcerative colitis. In some embodiments, a reduction in the Mayo Score indicates treatment of UC in a subject. The Mayo Score is a combined endoscopic and clinical scale used to assess the severity of UC and has a scale of 1-12. In some embodiments, treatment comprises a reduction in the Mayo Score by at least 1, 2 or 3 points in at least one of: rectal bleeding, blood streaks seen in the stool, endoscopy subscore, and physician's global assessment.

[00178] Diagnosing ulcerative colitis in a subject can include ruling out other possible causes for a subject’s symptoms (e.g., an infection caused by a bacteria, virus, or parasite). In some embodiments, diagnosing ulcerative colitis in a subject can include performing one or more tests or procedures such as a blood test (e.g., a test for anemia or a test for an infection using a blood sample form the subject), a stool sample (e.g., a test for white blood cells in stool sample from the subject), a colonoscopy, a biopsy, a sigmoidoscopy, an X-ray, a computerized tomography (CT) scan, a CT enterography, and a magnetic resonance (MR) enterography. Imaging methods such as a colonoscopy, a sigmoidoscopy, an X-ray, a computerized tomography (CT) scan, a CT enterography, and a magnetic resonance (MR) enterography, can be used to determine the level and location of inflammation in the colon of a subject. In some embodiments, compositions provided herein can include one or more excipients and can be formulated for any of a number of delivery systems suitable for administration to a subject (e.g., probiotic or LBP delivery systems) Non-limiting examples of an excipient include a buffering agent, a diluent, a preservative, a stabilizer, a binding agent, a filler, a lubricant, a dispersion enhancer, a disintegrant, a lubricant, a disintegrant, a wetting agent, a glidant, a flavoring agent, a sweetener, and a coloring agent. For example, in some embodiments, tablets or capsules can be prepared by conventional means with excipients such as binding agents, fillers, lubricants, disintegrants, or wetting agents. Any of the compositions described herein can be administered to a subject to treat or prevent a disease or disorder such as an inflammatory disorder as described herein. In some embodiments, the compositions as described herein can be administered to a subject to treat or prevent a disease or disorder with activated IL-23 -induced IL-17 secretion.

[00179] In some embodiments, a composition as described herein can be formulated for oral delivery. In some embodiments, the composition can be formulated as a tablet, a chewable tablet, a capsule, a stick pack, a powder, effervescent powder, or a liquid. In some embodiments, a composition can include coated beads that contain the bacterial strain. In some embodiments, a powder comprising the bacterial strain can be suspended or dissolved in a drinkable liquid such as water for administration. In some embodiments, the composition is a solid composition.

[00180] In some embodiments, a composition described herein can be formulated for various immediate and controlled release profiles of the bacterial strain. For example, a controlled release formulation can include a controlled release coating disposed over the bacterial strain. In some embodiments, the controlled release coating is an enteric coating, a semi-enteric coating, a delayed release coating, or a pulsed release coating. In some embodiments, a coating can be suitable if it provides an appropriate lag in active release (i.e., release of the bacterial strain). For example, in some embodiments, the composition can be formulated as a tablet that includes a coating (e.g., an enteric coating).

[00181] In some embodiments, the composition can be formulated for topical delivery. In some embodiments, the composition can be in the form of a paste, gel, cream, spray, suppository, mousse, emollient, ointment, foam, or suspension.

[00182] In some embodiments, the bacterial strain in the composition is a culture of a single strain of organism. In some embodiments, the composition comprises a bacterial strain that is isolated. In some embodiments, the bacterial strain is isolated and cultured in vitro to increase the number or concentration of the bacterial strain. Increasing the number or concentration of the bacterial strain can be useful for example, to enhance the therapeutic efficacy of a composition comprising the bacterial strain.

[00183] In some embodiments, an effective amount of the bacterial strain in a composition described herein comprises at least about 1 xlO ³ CFU of the bacterial strain. For example, at least about 1 xlO ³ , about 1 xlO ⁴ , about 1 xlO ⁵ , about 1 xlO ⁶ , about 1 xlO ⁷ , about 1 xlO ⁸ , about 1 xlO ⁹ , about 1 xlO ¹⁰ , about 1 xlO ¹¹ , about 1 xlO ¹² , about 1 xlO ¹³ , or about 1 xlO ¹⁴ CFUs of the bacterial strain. In some embodiments, the effective amount of a bacterial strain in a composition described herein comprises about 1 xlO ³ to about 1 xlO ¹⁵ CFUs of the bacterial strain. For example, about 1 xlO ³ to about 1 xlO ⁶ , about 1 xlO ³ to about 1 xlO ⁸ , about 1 xlO ³ to about 1 xlO ¹⁰ , about 1 xlO ³ to about 1 xlO ¹² , about 1 xlO ³ to about 1 xlO ¹⁴ , about 1 xlO ⁷ to about 1 xlO ¹² , about 1 xlO ¹³ to about 1 xlO ¹⁵ , about 1 xlO ¹¹ to about 1 xlO ¹⁵ , about 1 xlO ⁹ to about 1 xlO ¹⁵ , about 1 xlO ⁷ to about 1 xlO ¹⁵ , or about 1 xlO ⁵ to about 1 xlO ¹⁵ CFUs of the bacterial strain.

[00184] In some embodiments, the composition can include one or more biologically pure strains (e.g., two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, eleven or more, twelve or more, thirteen or more, fourteen or more, fifteen or more, sixteen or more, seventeen or more, eighteen or more, nineteen or more, twenty or more, twenty-one or more, twenty-two or more, or twenty-three bacterial strains). For example, the composition can include biologically pure Firmicutes bacterium ASF500, biologically pure Eubacterium coprostanoligenes str. HL, biologically pure Howardella ureilytica GPC 589, biologically pure Cupriavidus respiraculi au5353, biologically pure Dialister invisus E7.25, biologically pure Clostridium lituseburense VKM B-2279, biologically pure Alistipes shahii WAL 8301, biologically pure Coprococcus sp. HPP0074, biologically pure Dialister pneumosintes DSM 11619, biologically pure Streptococcus marimammalium M54/01/1, biologically pure Clostridium glycyrrhizinilyticum ZM35, biologically pure Lactobacillus rogosae ATCC 27753, biologically pure Clostridium disporicum DS1, biologically pure Intestinibacter bartlettii 2789STDY5834879, biologically pure Clostridium sp. 1 1 41A1FAA, biologically pure Intestinibacter bartlettii BSD2780061688ST1 A9, biologically pure Intestinibacter bartlettii DSM 16795, biologically pure Lachnospira pectinoschiza 2789STDY5834886, biologically pure Butyricicoccus sp. AF15 40, biologically pure Butyricicoccus sp. AM28 25, biologically pure Butyricicoccus sp. AM32 19, biologically pure Roseburia inulinivorans A2-194, biologically pure Lactobacillus rogosae ATCC 27753, biologically pure Parabacteroides distasonis C103T12C09 or any combination thereof.

[00185] In some embodiments, the composition is a solid composition that includes at least 1 xlO ³ CFUs of a bacterial strain (e.g., a biologically pure strain) and one or more excipients. Identifying characteristics of suitable strains, including homology to 16S rRNA sequences are described above.

[00186] In some embodiments, each member of the same bacterial strain has a substantially identical 16S rRNA gene sequence.

[00187] In some embodiments, a bacterial strain in a composition described herein is preserved. Methods for preserving bacterial strains can include lyophilization and cryopreservation, optionally in the presence of a protectant Non-limiting examples of protectants include sucrose, inulin, and glycerol. In some embodiments, a composition can include a lyophilized or cryopreserved bacterial strain such as Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Parabacteroides distasonis C103T12C09, or a combination thereof, and an optional protectant.

[00188] In some embodiments, the composition is a live bacterial product (LBP). In some embodiments, the bacterial strain in the composition is viable. The viable bacterial strain can be, for example, cryopreserved and/or lyophilized. In some embodiments, a composition for delivery of live bacterial strains (e.g., Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, ar abac ter oides distasonis C103T12C09, or a combination thereof), can be formulated to maintain viability of the bacterial strain.

[00189] In some embodiments, wherein the bacterial strain is a combination of two or more of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, and Parabacteroides distasonis C103T12C09 one or more of Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, and Parabacteroides distasonis C103T12C09 VPI 57-31 are viable.

[00190] In some embodiments, the composition comprises elements that protect the bacterial strain from the acidic environment of the stomach (e.g., an enteric coating).

[00191] In some embodiments, the bacterial strain in the composition can be non-viable. In some embodiments, the non-viable bacterial strain is heat-killed, irradiated, or lysed. [00192] In some embodiments, wherein the bacterial strain is a combination of two or more of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, and Parabacteroides distasonis C103T12C09 one or more of Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, and Parabacteroides distasonis C103T12C09 VPI 57-31 are non-viable (e.g., heat-killed, irradiated, or lysed).

[00193] In some embodiments, the bacterial strain as described herein (e.g., Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, or a combination thereof) can be used in prophylactic applications. For example, in a prophylactic application, a bacterial strain or a composition described herein can be administered to a subject susceptible to, or otherwise at risk of, a particular disease in an amount that is sufficient to at least partially reduce the risk of developing a disease. One of ordinary skill in the art will appreciate that the precise amounts of the bacterial strain administered can depend on a number of subject specific factors such as the subject's state of health and/or weight.

[00194] The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES

Example 1. Identification of bacterial strains associated with high or low IL-23 pathway activation

[00195] Paired microbiome (16S) and RNAseq data were screened from biopsy samples collected from IBD and non-IBD patients (Table 1).

Table 1. Samples

*May include inflamed, non-inflamed, active, remission, and/or different time points from the same patient.

** There were 2 studies for each biospecimen type, except there were 2 studies for the ulcerative colitis biopsy and the control biopsy.

[00196] Genes related to the target pathway of interest (e.g., IL-23 and a4b7) were identified through literature review and Qiagen’s Ingenuity Pathway Analysis (IP A). See digitalinsights.qiagen.com/products-overview/discovery-insig hts-portfolio/analysis-and- visualization/qiagen-ipa/. Patient samples were clustered based on gene expression patterns of the selected genes in the RNAseq data (see FIG. 1). These cluster identifiers were assigned to the patient samples (see FIG. 2). The microbiome data was then evaluated to identify differentially abundant microbes between these newly defined clusters. This analysis was repeated for each study dataset independently. Results from each study were evaluated together using a multi technology meta-analysis platform (MTMA) to identify concordant, differentially abundant strains and/or species between RNA-seq derived clusters. See Table 2 and FIGS. 3-5.

Table 2. Comparisons versus Disease Status

*Goes in opposite directions

** ASV refers to amplicon sequence variant

Example 2. Strains associated with low IL-23 activation decrease IL-17 secretion in human primary cells

[00197] Human peripheral blood mononuclear cells (PBMCs) were stimulated with anti-CD3 (0.01 pg/mL), anti-CD28 (1 pg/mL), IL-23 (50ng/mL), and the fixed bacterial strain (~2xl0 ⁷ CFUs) simultaneously. Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and l·. prausnitzii were tested individually. Cells were incubated for 72 hours and supernatants were collected and tested by ELISA for IL-17 secretion (see FIG. 6). Treatments were done in triplicate. As shown in FIG. 6, Streptococcus marimammalium M54/01/1 and Alistipes shahii WAL 8301 reduce IL-17 secretion. Example 3. Identification of bacterial strains associated with low IL-23/IL-17 pathway activation

[00198] Paired microbiome (16S) and RNAseq data were screened from biopsy samples collected from IBD and non-IBD patients (Table 3). The samples in Table 3 include the same samples as shown in Table 1 as well as additional samples.

Table 3. Samples

*May include inflamed, non-inflamed, active, remission, and/or different time points from the same patient.

Samples from 4 cohorts were clustered separately by their gene expression patterns as in Example 1, however, the list of genes was updated based on IPA updates and a filtering step was added (at least 5% of the genes had to show expression levels of the gene). Compared to the list of genes in Example 1, the updated list of genes included: AHR, CCR6, CSF2, ICOS, IFNG, IL10, IL12A, IL12B, IL17A, IL17F, IL1B, IL2, IL21, IL22, IL23A, IL23R, IL6, RORC, S100A8, TNF, and TNFSF11. The cluster with the lowest IL-23/IL-17 signal was identified and all remaining cluster(s) were compared to the“low” cluster to identify differentially abundant strains. A list of strains that had a q-value<0.05 after MTMA is shown in Table 4.

Table 4. Identified Strains

[00199] Additionally, samples from all cohorts were clustered together by gene expression patterns and the lowest IL-23/IL-17 signal was identified. Subsequently, each cohort was analyzed separately to identify differentially abundant strains between the "low" IL-23/IL-17 signal cluster and "higher" cluster(s). A list of strains that had a q-value<0.05 after MTMA is shown in Table 5.

Table 5. Identified Strains

OTHER EMBODIMENTS

1. A method of treating a subject in need thereof, the method comprising administering to the subject a composition comprising an effective amount of a bacterial strain, wherein the bacterial strain suppresses IL-23 -induced IL-17 secretion.

2. The method of embodiment 1, wherein the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str. HL, Howardella ureilytica GPC 589, Cupriavidus respiraculi au5353, Dialister invisus E7.25, Clostridium lituseburense VKM B-2279, Alistipes shahii WAL 8301, Coprococcus sp. HPP0074, Dialister pneumosintes DSM 11619, Streptococcus marimammalium M54/01/1, Clostridium glycyrrhizinilyticum ZM35, Lactobacillus rogosae ATCC 27753, Clostridium disporicum DS1, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2- 194, arabacteroides distasonis C103T12C09, and a combination thereof. The method of embodiment 1 or 2, wherein the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA,

Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2- 194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, and a combination thereof. The method of any one of embodiments 1-3, wherein the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof. The method of any one of embodiments 1-3, wherein the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, and a combination thereof. The method of any one of embodiments 1-3, wherein the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, and a combination thereof. A method for suppressing IL-23-induced IL-17 secretion in a subject in need thereof, the method comprising administering to the subject a composition comprising an effective amount of a bacterial strain selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof. The method of any one of embodiments 1-7, wherein the bacterial strain suppresses IL-23- induced IL-17 secretion in the intestine of the subject. A method for treating a subject in need thereof, the method comprising administering to the subject a composition comprising an effective amount of a bacterial strain selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41 A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof. The method of any one of embodiments 1-9, wherein the subject has been diagnosed with an inflammatory disease. A method for treating an inflammatory disease in a subject, the method comprising administering to the subject a composition comprising an effective amount of a bacterial strain selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, and a combination thereof.

12. A method for treating an inflammatory disease in a subject, the method comprising:

(a) detecting a dysbiosis associated with an inflammatory disease in a sample from the subject; and

(b) administering to the subject a composition comprising an effective amount of bacterial strain selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09, and a combination thereof.

13. The method of embodiment 12, wherein the sample is a biopsy sample.

14. The method of embodiment 13, wherein the sample is an intestinal biopsy sample.

15. The method of embodiment 13, wherein the sample is a colorectal biopsy sample.

16. The method of embodiment 12, wherein the sample is a fecal sample.

17. The method of any one of embodiments 12-16, wherein detecting the dysbiosis associated with an inflammatory disease comprises determining bacterial gene expression in the sample from the subject. The method of any one of embodiments 12-17, wherein detecting the dysbiosis associated with an inflammatory disease comprises detecting bacterial gene expression associated with high IL-23 activation in the sample from the subject. The method of any one of embodiments 12-18, wherein detecting the dysbiosis associated with an inflammatory disease comprises determining bacterial composition in the sample from the subject. The method of any one of embodiments 12-19, wherein detecting the dysbiosis associated with an inflammatory disease comprises detecting a bacterial strain associated with high IL- 23 activation in the sample from the subject. The method of embodiment any one of embodiments 12-20, wherein detecting the dysbiosis comprises determining that Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, Parabacteroides distasonis C103T12C09,or a combination thereof, are reduced in the sample from subject. The method of embodiment 21, wherein Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii

BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae ATCC 27753, and Parabacteroides distasonis C103T12C09, are reduced in the gastrointestinal tract of the subject. The method of any one of embodiments 12-22, wherein the inflammatory disease is selected from the group consisting of: an inflammatory bowel disease, multiple sclerosis, myocarditis, psoriasis, atrophic gastritis, inflammatory hemolytic anemia, arthritis, atopic dermatitis, pouchitis, graft rejection, inflammatory neutropenia, bullous pemphigoid, celiac disease, a demyelinating neuropathy, dermatomyositis, myositis, nasal polyps, chronic sinusitis, pemphigus vulgaris, primary glomerulonephritis, a surgical adhesion, stenosis or restenosis, scleritis, scleroderma, eczema, type I diabetes, vasculitis, pancreatitis, primary sclerosing cholangitis, benign stricture, a respiratory tract disease, nasolacrimal duct diseases, and a eustachean tube disease. The method of embodiment 23, wherein the inflammatory bowel disease is ulcerative colitis or Crohn’s disease. The method of any one of embodiments 7-24, wherein the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof. The method of any one of embodiments 7-24, wherein the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii BSD2780061688ST1 A9, Intestinibacter bartlettii DSM 16795, and a combination thereof. The method of any one of embodiments 7-24, wherein the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp. AM32 19, Roseburia inulinivorans A2-194, Lactobacillus rogosae atcc 27753, Parabacteroides distasonis C103T12C09, and a combination thereof. The method of any one embodiments 2-25, wherein the bacterial strain comprises Clostridium discporicum DS1. The method of any one embodiments 2-25, wherein the bacterial strain comprises wherein Streptococcus marimammalium M54/01/1. The method of any one embodiments 2-25, wherein the bacterial strain comprises Alistipes shahii WAL 8301. The method of any one embodiments 2-24 and 26-30, wherein the bacterial strain comprises Intestinibacter bartlettii 2789STDY5834879. The method of any one embodiments 2-24 and 26-31, wherein the bacterial strain comprises Clostridium sp. 1 1 41A1FAA. The method of any one embodiments 2-24 and 26-32, wherein the bacterial strain comprises Intestinibacter bartlettii BSD2780061688ST1 A9 The method of any one embodiments 2-24 and 26-33, wherein the bacterial strain comprises Intestinibacter bartlettii DSM 16795. The method of any one embodiments 2-24 and 27-34, wherein the bacterial strain comprises Lachnospira pectinoschiza 2789STDY5834886. The method of any one embodiments 2-24 and 27-35, wherein the bacterial strain comprises Butyricicoccus sp. AF15 40. The method of any one embodiments 2-24 and 27-36, wherein the bacterial strain comprises Butyricicoccus sp. AM28 25. The method of any one embodiments 2-24 and 27-37, wherein the bacterial strain comprises Butyricicoccus sp. AM32 19. The method of any one embodiments 2-24 and 27-38, wherein the bacterial strain comprises Roseburia inulinivorans A2-194. The method of any one embodiments 2-24 and 27-39, wherein the bacterial strain comprises Lactobacillus rogosae ATCC 27753. The method any one embodiments 2-24 and 27-40, wherein the bacterial strain comprises Parabacteroides distasonis C103T12C09. The method of any one of embodiments 2-25 and 28-41, wherein Clostridium discporicum DS1 has a 16S RNA gene that is at least 90% identical to SEQ ID NO:2. The method of any one of embodiments 2-25 and 28-42, wherein Clostridium discporicum DS1 has a 16S RNA gene that is at least 94% identical to SEQ ID NO:2.

The method of any one of embodiments 2-25 and 28-43, wherein Clostridium discporicum DS1 has a 16S RNA gene that is at least 99% identical to SEQ ID NO:2. The method of any one of embodiments 2-25 and 28-44, wherein Streptococcus marimammalium M54/01/1 has a 16S RNA gene that is at least 90% identical to SEQ ID NO:3. The method of any one of embodiments 2-25 and 28-45, wherein Streptococcus marimammalium M54/01/1 has a 16S RNA gene that is at least 94% identical to SEQ ID NO:3. The method of any one of embodiments 2-25 and 28-46, wherein Streptococcus marimammalium M54/01/1 has a 16S RNA gene that is at least 99% identical to SEQ ID NO:3. The method of any one of embodiments 2-25 and 28-47, wherein A listipes shahii WAL 8301 has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 1. The method of any one of embodiments 2-25 and 28-48, wherein A listipes shahii WAL 8301 has a 16S RNA gene that is at least 94% identical to SEQ ID NO: 1. The method of any one of embodiments 2-25 and 28-49, wherein A listipes shahii WAL 8301 has a 16S RNA gene that is at least 99% identical to SEQ ID NO: 1. The method of any one of embodiments 2-24, 26, and 28-50, wherein Intestinihacter bartlettii 2789STDY5834879 has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 14. The method of any one of embodiments 2-24, 26, and 28-51, wherein Intestinihacter bartlettii 2789STDY5834879 has a 16S RNA gene that is at least 94% identical to SEQ ID NO: 14. The method of any one of embodiments 2-24, 26, and 28-52, wherein Intestinihacter bartlettii 2789STDY5834879 has a 16S RNA gene that is at least 99% identical to SEQ ID NO: 14. The method of any one of embodiments 2-24, 26, and 28-53, wherein Clostridium sp. 1 1 41 A1FAA has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 15. The method of any one of embodiments 2-24, 26, and 28-54, wherein Clostridium sp. 1 1 41 A1FAA has a 16S RNA gene that is at least 94% identical to SEQ ID NO: 15. The method of any one of embodiments 2-24, 26, and 28-55, wherein Clostridium sp. 1 1 41 A1FAA has a 16S RNA gene that is at least 99% identical to SEQ ID NO: 15. The method of any one of embodiments 2-24, 26, and 28-56, wherein Intestinibacter bartlettii BSD2780061688ST1 A9 has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 16. The method of any one of embodiments 2-24, 26, and 28-57, wherein Intestinibacter bartlettii BSD2780061688ST1 A9 has a 16S RNA gene that is at least 94% identical to SEQ ID NO: 16. The method of any one of embodiments 2-24, 26, and 28-58, wherein Intestinibacter bartlettii BSD2780061688ST1 A9 has a 16S RNA gene that is at least 99% identical to SEQ ID NO: 16. The method of any one of embodiments 2-24, 26, and 28-59, wherein Intestinibacter bartlettii DSM 16795 has a 16S RNA gene that is at least 90% identical to SEQ ID NO:17. The method of any one of embodiments 2-24, 26, and 28-60, wherein Intestinibacter bartlettii DSM 16795 has a 16S RNA gene that is at least 94% identical to SEQ ID NO:17. The method of any one of embodiments 2-24, 26, and 28-61, wherein Intestinibacter bartlettii DSM 16795 has a 16S RNA gene that is at least 99% identical to SEQ ID NO:17. The method of any one of embodiments 2-24 and 27-62, wherein Lachnospira pectinoschiza 2789STDY5834886 has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 18. The method of any one of embodiments 2-24 and 27-63, wherein Lachnospira pectinoschiza 27 ^' 89STDY5834886 has a 16S RNA gene that is at least 94% identical to SEQ ID NO: 18. method of any one of embodiments 2-24 and 27-64, wherein Lachnospira pectinoschiza9STDY5834886 has a 16S RNA gene that is at least 99% identical to SEQ ID NO: 18. method of any one of embodiments 2-24 and 27-65, wherein Butyricicoccus sp. APT 5 has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 19. method of any one of embodiments 2-24 and 27-66, wherein Butyricicoccus sp. AF15 has a 16S RNA gene that is at least 94% identical to SEQ ID NO: 19. method of any one of embodiments 2-24 and 27-67, wherein Butyricicoccus sp. AF15 has a 16S RNA gene that is at least 99% identical to SEQ ID NO: 19. method of any one of embodiments 2-24 and 27-68, wherein Butyricicoccus sp. AM28 has a 16S RNA gene that is at least 90% identical to SEQ ID NO:20. method of any one of embodiments 2-24 and 27-69, wherein Butyricicoccus sp. AM28 has a 16S RNA gene that is at least 94% identical to SEQ ID NO:20. method of any one of embodiments 2-24 and 27-70, wherein Butyricicoccus sp. AM28 has a 16S RNA gene that is at least 99% identical to SEQ ID NO:20. method of any one of embodiments 2-24 and 27-71, wherein Butyricicoccus sp. AM32 has a 16S RNA gene that is at least 90% identical to SEQ ID NO:21. method of any one of embodiments 2-24 and 27-72, wherein Butyricicoccus sp. AM32 has a 16S RNA gene that is at least 94% identical to SEQ ID NO:21. method of any one of embodiments 2-24 and 27-73, wherein Butyricicoccus sp. AM32 has a 16S RNA gene that is at least 99% identical to SEQ ID NO:21. The method of any one of embodiments 2-24 and 27-74, wherein Roseburia inulinivorans A2-194 has a 16S RNA gene that is at least 90% identical to SEQ ID NO:22. The method of any one of embodiments 2-24 and 27-75, wherein Roseburia inulinivorans A2-194 has a 16S RNA gene that is at least 94% identical to SEQ ID NO:22. The method of any one of embodiments 2-24 and 27-76, wherein Roseburia inulinivorans A2-194 has a 16S RNA gene that is at least 99% identical to SEQ ID NO:22. The method of any one of embodiments 2-24 and 27-77, wherein Lactobacillus rogosae ATCC 27753 has a 16S RNA gene that is at least 90% identical to SEQ ID NO: 13. The method of any one of embodiments 2-24 and 27-78, wherein Lactobacillus rogosae ATCC 27753 has a 16S RNA gene that is at least 94% identical to SEQ ID NO: 13. The method of any one of embodiments 2-24 and 27-79, wherein Lactobacillus rogosae ATCC 27753 has a 16S RNA gene that is at least 99% identical to SEQ ID NO: 13. The method of any one of embodiments 2-24 and 27-80, Parabacteroides distasonis C103T12C09 has a 16S RNA gene that is at least 90% identical to SEQ ID NO:23. The method of any one of embodiments 2-24 and 27-81, wherein Parabacteroides distasonis C103T12C09 has a 16S RNA gene that is at least 94% identical to SEQ ID NO:23. The method of any one of embodiments 2-24 and 27-82, wherein Parabacteroides distasonis C103T12C09 has a 16S RNA gene that is at least 99% identical to SEQ ID NO:23. The method of any one of embodiments 1-83, wherein the bacterial strain in the composition is viable. The method of any one of embodiments 1-84, wherein the bacterial strain is lyophilized. The method of any one of embodiments 1-85, wherein the composition further comprises one or more cryopreservants. The method of any one of embodiments 1-86, wherein the effective amount of the bacterial strain comprises at least about 1 xlO ³ colony forming units (CFU) of the bacterial strain. The method of any one of embodiments 1-87, wherein the effective amount of the bacterial strain comprises about 1 xlO ⁴ to about 1 xlO ¹⁵ CFU of the bacterial strain. The method of any one of embodiments 1-88, wherein the effective amount of the bacterial strain comprises about 1 xlO ⁶ to about 1 xlO ¹⁰ CFU of the bacterial strain. The method of any one of embodiments 1-89, wherein the bacterial strain in the composition is non-viable. The method of embodiment 90, wherein the non-viable bacterial strain is heat-killed, irradiated, or lysed. The method of any one of embodiments 1-91, wherein the method comprises administering the composition to the subject once, twice, or three times per day. The method of any one of embodiments 1 -92, wherein the composition is formulated for oral administration. The method of any one of embodiments 1-92, wherein the composition is formulated for rectal administration. The method of any one of embodiments 1-94, wherein the composition is formulated as a tablet, a capsule, a powder, or a liquid. The method of any one of embodiments 1-95, wherein the composition is formulated as a tablet. The method of embodiment 96, wherein the tablet is coated. The method of embodiment 97, wherein the coating comprises an enteric coating. The method of any one of embodiments 1-99, wherein the composition is formulated for topical administration. The method of embodiment 99, wherein the composition is in the form of an ointment, spray, foam, or suspension. The method of any one of embodiments 1-100, wherein the method further comprises administering another treatment of an inflammatory disease and/or adjunct therapy to the subject. The method of embodiment 101, wherein the composition comprising the bacterial strain treatment and the treatment for inflammatory disease and/or adjunct therapy are administered simultaneously. The method of embodiment 101, wherein the composition comprising the bacterial strain treatment and the treatment for inflammatory disease and/or adjunct therapy are administered sequentially. The method of embodiment 102, wherein the composition comprising the bacterial strain further comprises the treatment for inflammatory disease and/or adjunct therapy. 105. The method of any one of embodiments 101-104, wherein the treatment for inflammatory disease and/or adjunct therapy comprises a probiotic.

106. The method of any one of embodiments 101-105, wherein the treatment for inflammatory disease and/or adjunct therapy comprises an anti-inflammatory agent, an immunosuppressant, an antibiotic, an anti-diarrheal agent, a pain reliever, an iron supplement, or a combination thereof.

107. The method of embodiment 106, wherein the anti-inflammatory agent comprises sulfasalazine, mesalamine, balsalazide, olsalazine, prednisone, hydrocortisone, or a combination thereof.

108. The method of embodiment 106 or 107, wherein the immunosuppressant comprises azathioprine, mercaptopurine, cyclosporine, infliximab, adalimumab, golimumab, vedolizumab, or a combination thereof.

[00200] It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention which is defined by the scope of the appended claims. Other aspects, advantages, and modification are within the scope of the following claims.