WO2020214739A1 - Procédés et compositions pour le traitement de maladies inflammatoires - Google Patents

Procédés et compositions pour le traitement de maladies inflammatoires Download PDF

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WO2020214739A1
WO2020214739A1 PCT/US2020/028370 US2020028370W WO2020214739A1 WO 2020214739 A1 WO2020214739 A1 WO 2020214739A1 US 2020028370 W US2020028370 W US 2020028370W WO 2020214739 A1 WO2020214739 A1 WO 2020214739A1
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Prior art keywords
butyricicoccus
bacterial strain
clostridium
seq
composition
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PCT/US2020/028370
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English (en)
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Mitsuko Lynn YAMAMOTO
Cheryl-Emiliane T. Chow
Nicole Rebecca NARAYAN
Laurens Kruidenier
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Second Genome, Inc.
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Publication of WO2020214739A1 publication Critical patent/WO2020214739A1/fr

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • A61K35/741—Probiotics
    • A61K35/742—Spore-forming bacteria, e.g. Bacillus coagulans, Bacillus subtilis, clostridium or Lactobacillus sporogenes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria

Definitions

  • 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.
  • IBD inflammatory bowel disease
  • restenosis rheumatoid arthritis
  • psoriasis multiple sclerosis
  • surgical adhesions tuberculosis
  • 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.
  • CD Crohn's disease
  • UC ulcerative colitis
  • 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.
  • probiotics 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.
  • live biotherapeutic products LBPs
  • LBPs live biotherapeutic products
  • methods and compositions for treating a subject in need thereof can include administering to the subject a composition that includes an effective amount of a bacterial strain.
  • the bacterial strain can suppress IL-23 -induced IL-17 secretion.
  • 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).
  • 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
  • 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).
  • 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).
  • the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1 , Alistipes shahii WAL 8301, and a combination thereof.
  • 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).
  • 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).
  • 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, Coprococc
  • 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.
  • 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.
  • 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).
  • the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1 , Alistipes shahii WAL 8301, and a combination thereof.
  • 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).
  • the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp.
  • the bacterial strain suppresses IL-23 -induced IL-17 secretion in the intestine of the subject.
  • 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.
  • 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.
  • 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).
  • the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof.
  • 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).
  • the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp.
  • the subject has been diagnosed with an inflammatory disease.
  • 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
  • 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.
  • 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.
  • 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.
  • 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).
  • the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof.
  • 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).
  • the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp.
  • 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.
  • a bacterial strain e.g., a bacterial strain that suppresses IL- 23 -induced IL-17 secretion.
  • the bacterial strain can be selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str.
  • the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str.
  • 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).
  • the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof.
  • the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii
  • the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp.
  • 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.
  • 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.
  • 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.
  • detecting the dysbiosis comprises determining that Intestinibacter bartlettii 2789STDY5834879, Clostridium sp.
  • detecting the dysbiosis comprises determining that Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp.
  • the bacterial strain is reduced in the gastrointestinal tract of the subject.
  • 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.
  • an inflammatory bowel disease multiple
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • CFU colony forming units
  • the bacterial strain in the composition is non-viable.
  • the non-viable bacterial strain is heat-killed, irradiated, fixed, or lysed.
  • the method comprises administering the composition to the subject once, twice, or three times per day.
  • the composition further includes one or more excipients.
  • the composition is formulated for oral administration.
  • the composition is formulated as a tablet, a capsule, a powder, or a liquid.
  • the composition is formulated as a tablet.
  • the tablet is coated.
  • the coating comprises an enteric coating.
  • the composition is formulated for topical delivery.
  • the composition is in the form of a paste, gel, cream, spray, suppository, mousse, emollient, ointment, foam, or suspension.
  • the composition is formulated for rectal administration. In some embodiments, the composition is formulated as a suppository.
  • the method further comprises administering one or more other treatments of an inflammatory disease to the subject.
  • 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.
  • the other treatment of an inflammatory disease is surgery.
  • the other treatment of an inflammatory disease is a therapeutic agent.
  • the method further comprises administering an adjunct therapy such as a therapeutic agent to control pain and/or inflammation to the subject.
  • an adjunct therapy such as a therapeutic agent to control pain and/or inflammation to the subject.
  • 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.
  • 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.
  • the anti-inflammatory agent comprises sulfasalazine, mesalamine, balsalazide, olsalazine, prednisone, hydrocortisone, or a combination thereof.
  • the immunosuppressant comprises azathioprine, mercaptopurine, cyclosporine, infliximab, adalimumab, golimumab, vedolizumab, or a combination thereof.
  • 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.
  • Bifidobacteria e.g., B. animal is, B. breve , B. lactis , B. longum , B. longum , or . infantis
  • Lactobacillus e.g., L.
  • 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.
  • 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.
  • 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.
  • the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof.
  • the bacterial strain is selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp.
  • the bacterial strain is selected from the group consisting of: Lachnospira pectinoschiza 2789STDY5834886, Butyricicoccus sp. AF15 40, Butyricicoccus sp. AM28 25, Butyricicoccus sp.
  • a bacterial strain described herein in the manucfacture of a medicament for treating an inflammatory disease.
  • 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.
  • the medicament includes one or more excipients.
  • the bacterial strain is selected from the group consisting of: Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str.
  • the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof.
  • 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).
  • 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).
  • the medicament includes one or more excipients.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • the composition is formulated for oral administration.
  • the composition is formulated as a tablet, a capsule, a powder, or a liquid.
  • the composition is formulated as a tablet.
  • the tablet is coated.
  • the coating comprises an enteric coating.
  • the composition is formulated for topical delivery.
  • the composition is in the form of a paste, gel, cream, spray, suppository, mousse, emollient, ointment, foam, or suspension.
  • 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.
  • 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.
  • 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.
  • the one or more bacterial strains are selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii.
  • the bacterial strain is selected from the group consisting of: Streptococcus marimammalium M54/01/1, Alistipes shahii WAL 8301, and a combination thereof.
  • 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).
  • 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).
  • the one or more bacterial strains suppress IL-23-induced IL- 17 secretion in the intestine of the subject.
  • 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.
  • the one or more bacterial strains are selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii.
  • the one or more bacterial strains are selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp.
  • 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.
  • 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.
  • the one or more bacterial strains are selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii.
  • the one or more bacterial strains are selected from the group consisting of: Intestinibacter bartlettii 2789STDY5834879, Clostridium sp. 1 1 41A1FAA, Intestinibacter bartlettii
  • 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.
  • the one or more bacterial strains are selected from the group consisting of: Clostridium discporicum DS1, Streptococcus marimammalium , and Alistipes shahii.
  • 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.
  • 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.
  • 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.
  • 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
  • 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.
  • the method further comprises obtaining a sample from the subject.
  • the sample is a biopsy sample.
  • detecting a bacterial strain associated with high IL-23 activation comprises analyzing the biopsy sample for intestinal gene expression and bacterial composition.
  • the Streptococcus marimammalium bacteria is the Streptococcus marimammalium M54/01/1 strain.
  • the Alistipes shahii bacteria is the Alistipes shahii WAL 8301 strain.
  • the inflammatory bowel disease is Crohn’s disease. In some embodiments, the inflammatory bowel disease is ulcerative colitis.
  • 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,
  • 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.
  • 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.
  • the Streptococcus marimammalium bacteria is the Streptococcus marimammalium M54/01/1 strain.
  • the Alistipes shahii bacteria is the Alistipes shahii WAL 8301 strain.
  • 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.
  • 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.
  • subject or “patient” refers to any subject, particularly a mammalian subject such as a human, for whom diagnosis, prognosis, or therapy is desired.
  • 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.
  • preventing 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.
  • administration 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.
  • Microbiome refers to the collection of microorganisms and viruses and/or their genes from a given environment.
  • 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.
  • “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).
  • the individuals in the control population meet one of the above control population qualifications.
  • the individuals in the control population meet two of the above control population qualifications.
  • 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.
  • 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
  • pathobionts e.g., a population of pathogenic bacteria
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • an“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.
  • an isolated microbe e.g., a bacterial strain
  • more than one microbe can be isolated.
  • “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.
  • the isolated microbes exist as isolated and biologically pure cultures.
  • 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).
  • 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.
  • 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.
  • a biologically pure composition contains no other bacterial strain in quantities that can be detected by typical bacteriological techniques.
  • mutation includes a natural or induced mutation comprising at least a single base or amino acid alteration in a DNA or protein sequence.
  • 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.
  • 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.
  • 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.
  • a composition as described herein includes a probiotic.
  • prebiotic refers to an agent that increases the number and/or activity of one or more microbes.
  • microbes can include microbes for restoring or altering the microbiota or microbiome of a subject.
  • 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).
  • 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.
  • A“combination” of two or more bacteria can refer to the physical co-existence of the bacteria, either in the same material or product.
  • a combination of two or more bacteria can include the temporal co-administration or co localization of the two or more bacteria.
  • 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.
  • the percent identity for two or more sequences 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.
  • 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.
  • 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
  • BLASTP can be used to align and compare the identity between amino acid sequences.
  • 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.
  • combination therapy 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • cocktail therapies e.g., the administration of three or more therapeutic agents.
  • FIGS. 1A and IB are principal coordinate analysis (PCoA) plots based on selected genes.
  • FIG. 2A is a PCoA plot showing that the clusters are differentiated on the IL-23 gene plot
  • FIG. 2B is a plot showing the cluster differentiation.
  • FIG. 3 is a plot showing the differentially abundant sequences between clusters 1 and 2
  • FIG. 4 is a plot showing the differentially abundant sequences between clusters 1 and 4.
  • 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
  • Strain 3 is Alistipes shahii WAL 8301.
  • 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
  • Strain 3 is Alistipes shahii WAL 8301. **indicates p ⁇ 0.01.
  • 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.
  • FIG. 8 is a table that contains the sequences for SEQ ID NOs: 1-39.
  • compositions and methods for treating subjects in need thereof e.g., subjects having an inflammatory disease
  • for suppressing IL-23-induced IL-17 secretion using one or more bacterial strains are also provided herein.
  • 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.
  • 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.
  • strains of bacteria 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.
  • methods for treating a subject in need thereof are provided herein.
  • IL-23 -induced IL-17 secretion is suppressed in a subject.
  • 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.
  • 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.
  • 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).
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • the bacterial strain in the composition comprises Clostridium discporicum DS1.
  • 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.
  • 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 .
  • 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.
  • 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.
  • the bacterial strain in the composition comprises Intestinibacter bartlettii 2789STDY5834879.
  • 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.
  • the bacterial strain in the composition comprises Clostridium sp. 1 1 41 A1FAA.
  • 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.
  • the bacterial strain in the composition comprises
  • 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.
  • the bacterial strain in the composition comprises
  • 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.
  • 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.
  • the bacterial strain in the composition comprises Lachnospira pectinoschiza 2789STDY5834886.
  • 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.
  • the bacterial strain in the composition comprises Butyricicoccus sp. AF15 40.
  • 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.
  • the bacterial strain in the composition comprises
  • 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.
  • the bacterial strain in the composition comprises
  • 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.
  • 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.
  • 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.
  • the bacterial strain in the composition comprises Parabacteroides distasonis C103T12C09.
  • 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.
  • the bacterial strain in the composition comprises Firmicutes bacterium ASF500.
  • 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.
  • the bacterial strain in the composition comprises Eubacterium coprostanoligenes str. HL.
  • 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.
  • the bacterial strain in the composition comprises Howardella ureilytica GPC 589.
  • 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.
  • the bacterial strain in the composition comprises Cupriavidus respiraculi au5353.
  • 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.
  • the bacterial strain in the composition comprises Dialister invisus E7.25.
  • 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.
  • the bacterial strain in the composition comprises Clostridium lituseburense VKM B-2279.
  • 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.
  • the bacterial strain in the composition comprises Coprococcus sp. HPP0074.
  • 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.
  • the bacterial strain in the composition comprises Firmicutes bacterium ASF500.
  • 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.
  • the bacterial strain in the composition comprises Clostridium glycyrrhizinilyticum ZM35.
  • 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.
  • the bacterial strain in the composition comprises Lactobacillus rogosae ATCC 27753.
  • Lactobacillus rogosae ATCC 27753 is also known as Lactobacillus rogosae VPI C37-38.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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).
  • 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).
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • the sample is a fecal sample.
  • detecting the dysbiosis associated with an inflammatory disease can include determining bacterial gene expression in the sample from the subject.
  • 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 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.
  • 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).
  • 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.
  • bacteria can be identified by their 16S rRNA gene sequence.
  • detecting bacterial gene expression can include performing, for example, RNAseq and/or RT-qPCR.
  • 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.
  • 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.
  • Clostridium discporicum DS1, Streptococcus marimammalium M54/01/1, and Alistipes shahii WAL 8301 are reduced in the gastrointestinal tract of the subject.
  • 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.
  • 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.
  • 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
  • an inflammatory disease include an inflammatory bowel disease (e.g., ulcerative colitis and Crohn'
  • 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.
  • EGPA Churg-Strauss Syndrome
  • the inflammatory disease is inflammatory bowel disease.
  • the inflammatory bowel disease is ulcerative colitis or Crohn’s disease.
  • IBD Inflammatory bowel disease
  • UC ulcerative colitis
  • CD Crohn's disease
  • UC ulcerative colitis
  • CD Crohn's disease
  • 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.
  • 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).
  • 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.
  • 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.
  • 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.
  • the composition can be administered two, three, four, or more times per day.
  • an effective amount of the bacterial strain is administered in one dose, e.g., once per day.
  • an effective amount of the bacterial strain is administered in more than one dose, e.g., more than once per day.
  • the method comprises administering the composition to the subject daily, every other day, every three days, or once a week.
  • a composition comprising a bacterial strain as described herein can be used in combination with one or more additional therapies or therapeutic agents.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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).
  • 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.
  • the treatment of an inflammatory disease can be surgery (e.g., a proctocolectomy).
  • 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.
  • 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.
  • the anti-inflammatory agent is a JAK inhibitor (e.g., tofacitinib, ruxolitinib, and baricitinib) sulfasalazine, mesalamine, balsalazide, olsalazine, prednisone, hydrocortisone, or a combination thereof).
  • JAK inhibitor e.g., tofacitinib, ruxolitinib, and baricitinib
  • the immunosuppressant is selected from the group consisting of: azathioprine, mercaptopurine, cyclosporine, infliximab, adalimumab, golimumab, vedolizumab, or a combination thereof.
  • 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.
  • 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.
  • 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.
  • the immunosuppressant comprises azathioprine, mercaptopurine, cyclosporine, infliximab, adalimumab, golimumab, vedolizumab, or a combination thereof.
  • 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).
  • a prebiotic and/or probiotic can be administered in combination with a composition comprising a bacterial strain as described herein.
  • 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 .
  • 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. lac
  • 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).
  • a fructooligosaccharide e.g., oligofructose, inulin, or an inulin- type fructan
  • galactooligosaccharide e.g., 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).
  • 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.
  • 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).
  • 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.
  • 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.
  • 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.
  • 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
  • CDAI Crohn's Disease Activity Index
  • 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).
  • 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).
  • 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.
  • 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, calprotect
  • 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.
  • 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.
  • 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.
  • 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).
  • 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.
  • 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 e.g., a
  • 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.
  • CT computerized tomography
  • MR magnetic resonance
  • 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)
  • excipients 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.
  • tablets or capsules can be prepared by conventional means with excipients such as binding agents, fillers, lubricants, disintegrants, or wetting agents.
  • 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.
  • 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.
  • a composition as described herein can be formulated for oral delivery.
  • the composition can be formulated as a tablet, a chewable tablet, a capsule, a stick pack, a powder, effervescent powder, or a liquid.
  • a composition can include coated beads that contain the bacterial strain.
  • a powder comprising the bacterial strain can be suspended or dissolved in a drinkable liquid such as water for administration.
  • the composition is a solid composition.
  • a composition described herein can be formulated for various immediate and controlled release profiles of the bacterial strain.
  • a controlled release formulation can include a controlled release coating disposed over the bacterial strain.
  • the controlled release coating is an enteric coating, a semi-enteric coating, a delayed release coating, or a pulsed release coating.
  • a coating can be suitable if it provides an appropriate lag in active release (i.e., release of the bacterial strain).
  • the composition can be formulated as a tablet that includes a coating (e.g., an enteric coating).
  • the composition can be formulated for topical delivery.
  • the composition can be in the form of a paste, gel, cream, spray, suppository, mousse, emollient, ointment, foam, or suspension.
  • the bacterial strain in the composition is a culture of a single strain of organism.
  • the composition comprises a bacterial strain that is isolated.
  • 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.
  • an effective amount of the bacterial strain in a composition described herein comprises at least about 1 xlO 3 CFU of the bacterial strain.
  • 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.
  • 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).
  • the composition can include biologically pure Firmicutes bacterium ASF500, biologically pure Eubacterium coprostanoligenes str.
  • 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.
  • 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.
  • each member of the same bacterial strain has a substantially identical 16S rRNA gene sequence.
  • 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.
  • a composition can include a lyophilized or cryopreserved bacterial strain such as Firmicutes bacterium ASF500, Eubacterium coprostanoligenes str.
  • the composition is a live bacterial product (LBP).
  • the bacterial strain in the composition is viable.
  • the viable bacterial strain can be, for example, cryopreserved and/or lyophilized.
  • 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.
  • 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.
  • the composition comprises elements that protect the bacterial strain from the acidic environment of the stomach (e.g., an enteric coating).
  • the bacterial strain in the composition can be non-viable.
  • the non-viable bacterial strain is heat-killed, irradiated, or lysed.
  • 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.
  • 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.
  • 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.
  • a bacterial strain administered can depend on a number of subject specific factors such as the subject's state of health and/or weight.
  • Example 1 Identification of bacterial strains associated with high or low IL-23 pathway activation
  • ** ASV refers to amplicon sequence variant
  • PBMCs Human peripheral blood mononuclear cells
  • PBMCs Human peripheral blood mononuclear cells
  • anti-CD3 (0.01 pg/mL
  • anti-CD28 (1 pg/mL
  • IL-23 50ng/mL
  • the fixed bacterial strain ⁇ 2xl0 7 CFUs
  • 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.
  • 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
  • Example 2 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.
  • a method of treating a subject in need thereof 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.
  • 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,
  • 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.
  • 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.
  • 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
  • a method for suppressing IL-23-induced IL-17 secretion in a subject in need thereof 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
  • a method for treating a subject in need thereof 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.
  • a method for treating an inflammatory disease in a subject 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.
  • a method for treating an inflammatory disease in a subject comprising:
  • 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.
  • bacterial strain selected from the group consisting of: Streptococcus marimam
  • 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.
  • 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.
  • 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.
  • 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 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 eustache
  • 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.
  • 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 bacterial strain comprises Clostridium discporicum DS1.
  • 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.
  • Clostridium discporicum DS1 has a 16S RNA gene that is at least 90% identical to SEQ ID NO:2.
  • Clostridium discporicum DS1 has a 16S RNA gene that is at least 94% identical to SEQ ID NO:2.
  • Clostridium discporicum DS1 has a 16S RNA gene that is at least 99% identical to SEQ ID NO:2.
  • a listipes shahii WAL 8301 has a 16S RNA gene that is at least 99% identical to SEQ ID NO: 1.
  • 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.
  • Intestinibacter bartlettii BSD2780061688ST1 A9 has a 16S RNA gene that is at least 99% identical to SEQ ID NO: 16.
  • Lachnospira pectinoschiza9STDY5834886 has a 16S RNA gene that is at least 99% identical to SEQ ID NO: 18.
  • 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.
  • Butyricicoccus sp. AM32 has a 16S RNA gene that is at least 90% identical to SEQ ID NO:21.
  • 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 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.
  • composition comprising the bacterial strain treatment and the treatment for inflammatory disease and/or adjunct therapy are administered sequentially.
  • composition comprising the bacterial strain further comprises the treatment for inflammatory disease and/or adjunct therapy.
  • treatment for inflammatory disease and/or adjunct therapy comprises a probiotic.
  • 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.
  • anti-inflammatory agent comprises sulfasalazine, mesalamine, balsalazide, olsalazine, prednisone, hydrocortisone, or a combination thereof.
  • the immunosuppressant comprises azathioprine, mercaptopurine, cyclosporine, infliximab, adalimumab, golimumab, vedolizumab, or a combination thereof.

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Abstract

La présente invention concerne une souche bactérienne, et des compositions associées, pouvant supprimer la sécrétion d'IL-17 induite par IL-23. Dans certains modes de réalisation, la souche bactérienne est sélectionnée dans le groupe constitué par : 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 Cl03T12C09, et une combinaison associée. De telles souches bactériennes, et des compositions associées, sont utiles pour le traitement de maladies inflammatoires.
PCT/US2020/028370 2019-04-15 2020-04-15 Procédés et compositions pour le traitement de maladies inflammatoires WO2020214739A1 (fr)

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WO2019041140A1 (fr) * 2017-08-29 2019-03-07 深圳华大基因研究院 Application de alistipes shahii dans la préparation d'une composition pour la prévention et/ou le traitement de maladies associées au métabolisme lipidique

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2019041140A1 (fr) * 2017-08-29 2019-03-07 深圳华大基因研究院 Application de alistipes shahii dans la préparation d'une composition pour la prévention et/ou le traitement de maladies associées au métabolisme lipidique

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Title
VAN DEN MUNCKHOF ET AL.: "Role of gut microbiota in chronic low-grade inflammation as potential driver for atherosclerotic cardiovascular disease: a systematic review of human studies", OBESITY REVIEWS., vol. 19, no. 12, December 2018 (2018-12-01), pages 1719 - 1734, XP055750406 *

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