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WO 2017/152137 A2 8 September 2017 (08.09.2017) P O P C T

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WO 2017/152137 A2 8 September 2017 (08.09.2017) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2017/152137 A2 8 September 2017 (08.09.2017) P O P C T (51) International Patent Classification: (74) Agents: BOLCOME, Robert, E., Ill et al; Mintz Levin A61K 39/295 (2006.01) A61K 39/02 (2006.01) Cohn Ferris Glovsky and Popeo, P.C., One Financial Cen ter, Boston, MA 021 11 (US). (21) International Application Number: PCT/US20 17/020809 (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, (22) International Filing Date: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, 3 March 2017 (03.03.2017) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, (25) Filing Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, (26) Publication Language: English KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, (30) Priority Data: MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, 62/304,087 4 March 2016 (04.03.2016) US NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, (71) Applicant: THE REGENTS OF THE UNIVERSITY TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, OF CALIFORNIA [US/US]; 1111 Franklin Street, ZA, ZM, ZW. Twelfth Floor, Okland, CA 94607 (US). (84) Designated States (unless otherwise indicated, for every (72) Inventors: LYNCH, Susan, V.; 1327 Grand Avenue, kind of regional protection available): ARIPO (BW, GH, Piedmont, CA 946 10 (US). KIMES, Nikole; 1615 25th GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, Avenue, San Francisco, CA 94122 (US). VALLADARES, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, Ricardo; 15 17 Cortez Lane NE, Brookhaven, GA 303 19 TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (US). LIN, Din, L.; I l l Highcrest Lane, South San Fran DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, cisco, CA 94080 (US). FUJIMURA, Kei; 513 Parnassus LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, Avenue, San Francisco, CA 941 17 (US). SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). [Continued on nextpage] (54) Title: MICROBIAL CONSORTIUM AND USES THEREOF (57) Abstract: Provided herein are, inter alia, microbial compositions and methods of using the same. The microbial compositions provided L iiTrial include, inter alia, therapeutically effective amounts of Lactobacillus johnsonii, Faecalibac- terium prausnitzii, Akkermansia muciniphila, p G 2 Myxococcus xanthus and Pediococcus pentosaceus and are particularly useful for meth ods of treating and preventing inflammatory dis- & - · 1 T * V w o 2017/152137 A2 1I 11 II I 1 I 1 II I III I II III lllll i ll s e — with sequence listing part of description (Rule 5.2(a)) — without international search report and to be republished upon receipt of that report (Rule 48.2(g)) MICROBIAL CONSORTIUM AND USES THEREOF CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit of priority to U.S. Provisional Application No. 62/304,087, filed March 4, 2016, which is hereby incorporated in its entirety and for all purposes. STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT [0002] This invention was made with government support under grant numbers R21 AT004732, P01 AI089473, and HL080074 awarded by the National Institutes of Health. The Government has certain rights in the invention. INCORPORATION-BY-REFERENCE OF SEQUENCE LISTING [0003] The content of the text file named "48536-575001WO_SequenceListing.TXT", which was created on March 3, 2017, and is 107,536 bytes in size, is hereby incorporated by reference in its entirety. BACKGROUND OF THE INVENTION [0004] Recent studies provide evidence that microbial communities residing in the human gut play a key role in the development and modulation of the host immune response. For instance, the presence of particular Clostridium species has been shown to induce specific T-cell repertoires [Atarashi, et al. (201 1) Induction of colonic regulatory T cells by indigenous Clostridium species. Science 33 1(601 5):337-341]. Despite the complexity of the gut microbiome, the presence or absence of specific bacterial species can dramatically alter the adaptive immune environment. BRIEF SUMMARY OF THE INVENTION [0005] Provided herein are novel methods and microbial compositions including Lactobacillus johnsonii, Faecalibacteriumprausnitzii, Akkermansia muciniphila, Myxococcus xanthus, and Pediococcuspentosaceus, which are surprisingly useful for the treatment of dysbiosis, infections, and inflammatory diseases. [0006] An aspect provides methods and compositions comprising a bacterial population that comprises, consists essentially of, or consists of, 1, 2, 3, 4, 5, 6, 7, or 8 (or at least 1, 2, 3, 4, 5, 6, 7, or 8) bacterial species. In embodiments, the bacterial population comprises, consists essentially of, or consists of any 1, 2, 3, 4, 5, 6, 7, or 8 of Lactobacillus sp., Faecalibacterium sp., Akkermansia sp., Myxococcus sp., Cystobacter sp., Pediococcus sp., Bifidobacterium sp., and Clostridium sp. In embodiments, the bacterial population comprises Lactobacillus sp. and Faecalibacterium prausnitzii. In embodiments, the bacterial population comprises Lactobacillus sp. a Akkermansia muciniphila. In embodiments, the bacterial population comprises Lactobacillus sp., and Myxococcus xanthus. In embodiments, the bacterial population comprises Lactobacillus sp. and Cystobacterfiuscus. In embodiments, the bacterial population comprises Lactobacillus sp. and Pediococcus pentosaceus, Pediococcus acidilactici, Pediococcus damnosus, Pediococcus ethanolidurans, or Pediococcus parvulus. In embodiments, the bacterial population comprises Lactobacillus sp. and Bifidobacterium bifidum, Bifidobacterium pseudolongum, Bifidobacterium saeculare, or Bifidobacterium subtile. In embodiments, the bacterial population comprises Lactobacillus sp. and Clostridium hiranonis. In embodiments, the Lactobacillus sp. is Lactobacillus johnsonii, Lactobacillus rhamnosus, Lactobacillus zeae, Lactobacillus acidipiscis, Lactobacillus acidophilus, Lactobacillus agilis, Lactobacillus aviarius, Lactobacillus brevis, Lactobacillus coleohominis, Lactobacillus crispatus, Lactobacillus crustorum, Lactobacillus curvatus, Lactobacillus diolivorans, Lactobacillus fiarraginis, Lactobacillus fiermentum, Lactobacillus fiuchuensis, Lactobacillus harbinensis, Lactobacillus helveticus, Lactobacillus hilgardii, Lactobacillus intestinalis, Lactobacillus jensenii, Lactobacillus kefiranofaciens, Lactobacillus kefiri, Lactobacillus lindneri, Lactobacillus mali, Lactobacillus manihotivorans, Lactobacillus mucosae, Lactobacillus oeni, Lactobacillus oligqfermentans, Lactobacillus panis, Lactobacillus pantheris, Lactobacillus parabrevis, Lactobacillus paracollinoides, Lactobacillus parakefiri, Lactobacillus paraplantarum, Lactobacillus pentosus, Lactobacillus pontis, Lactobacillus reuteri, Lactobacillus rossiae, Lactobacillus salivarius, Lactobacillus siliginis, Lactobacillus sucicola, Lactobacillus vaccinostercus, Lactobacillus vaginalis, Lactobacillus vini, Lactococcus garvieae, or Lactococcus lactis. In embodiments, the Lactobacillus sp. is Lactobacillus johnsonii. In embodiments, the bacterial population comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or from 1-5, 1-10, 1-5, or 1-20 of any combination of the following: Lactobacillus johnsonii, Lactobacillus rhamnosus, Lactobacillus zeae, Lactobacillus acidipiscis, Lactobacillus acidophilus, Lactobacillus agilis, Lactobacillus aviarius, Lactobacillus brevis, Lactobacillus coleohominis, Lactobacillus crispatus, Lactobacillus crustorum, Lactobacillus curvatus, Lactobacillus diolivorans, Lactobacillus farraginis, Lactobacillusfermentum, Lactobacillusfuchuensis, Lactobacillus harbinensis, Lactobacillus helveticus, Lactobacillus hilgardii, Lactobacillus intestinalis, Lactobacillusjensenii, Lactobacillus kefiranofaciens, Lactobacillus kefiri, Lactobacillus lindneri, Lactobacillus mali, Lactobacillus manihotivorans, Lactobacillus mucosae, Lactobacillus oeni, Lactobacillus oligqfermentans, Lactobacillus panis, Lactobacillus pantheris, Lactobacillus parabrevis, Lactobacillus pamcollinoides, Lactobacillus parakefiri, Lactobacillus paraplantarum, Lactobacillus pentosus, Lactobacillus pontis, Lactobacillus reuteri, Lactobacillus rossiae, Lactobacillus salivarius, Lactobacillus siliginis, Lactobacillus sucicola, Lactobacillus vaccinostercus, Lactobacillus vaginalis, Lactobacillus vini, Lactococcus garvieae, Lactococcus lactis, Faecalibacterium prausnitzii, Akkermansia muciniphila, Myxococcus xanthus, Cystobacterfuscus, Pediococcus pentosaceus, Pediococcus acidilactici, Pediococcus damnosus, Pediococcus ethanolidurans, and Pediococcus parvulus. In embodiments, the bacterial population includes Lactobacillus johnsonii, Faecalibacterium prausnitzii, Akkermansia muciniphila, Myxococcus xanthus, and/or Pediococcus pentosaceus. [0007] In an aspect, a method for administering isolated bacteria is provided. In embodiments, the method comprises administering to the subject an effective amount of a bacterial population comprising Lactobacillus sp., Faecalibacterium sp., Akkermansia sp., Myxococcus sp., and/or Pediococcus sp. In embodiments, the method comprises administering to the subject an effective amount of a bacterial population comprising Lactobacillus sp.,
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