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WO 2014/121304 Al 7 August 2014 (07.08.2014) P O P C T

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WO 2014/121304 Al 7 August 2014 (07.08.2014) 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 2014/121304 Al 7 August 2014 (07.08.2014) P O P C T (51) International Patent Classification: 1A, Cambridge, MA 02142 (US). GOODMAN, Brian; c/o C12N 1/00 (2006.01) Seres Health, Inc., 161 First Street, Suite 1A, Cambridge, MA 02 142 (US). (21) International Application Number: PCT/US2014/014747 (74) Agents: HUBL, Susan T. et al; Fenwick & West LLP, Silicon Valley Center, 801 California Street, Mountain (22) International Filing Date: View, CA 94041 (US). 4 February 2014 (04.02.2014) (81) Designated States (unless otherwise indicated, for every English (25) Filing Language: kind of national protection available): AE, AG, AL, AM, (26) Publication Language: English AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (30) Priority Data: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 61/760,574 4 February 2013 (04.02.2013) US HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 61/760,585 4 February 2013 (04.02.2013) US KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/760,606 4 February 2013 (04.02.2013) us MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/760,584 4 February 2013 (04.02.2013) us OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 61/798,606 15 March 2013 (15.03.2013) us SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, 61/926,918 13 January 2014 (13.01.2014) us TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, (71) Applicant: SERES HEALTH, INC. [US/US]; 161 First ZW. Street, Suite 1A, Cambridge, MA 02 142 (US). (84) Designated States (unless otherwise indicated, for every (72) Inventors: AFEYAN, Noubar, B.; c/o Seres Health, Inc., kind of regional protection available): ARIPO (BW, GH, 161 First Street, Suite 1A, Cambridge, MA 02142 (US). GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, MCKENZIE, Mary-Jane, Lombardo; c/o Seres Health, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, Inc., 161 First Street, Suite 1A, Cambridge, MA 02142 TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, (US). LITCOFSKY, Kevin, Daniel; c/o Seres Health, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, Inc., 161 First Street, Suite 1A, Cambridge, MA 02142 MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, (US). COOK, David, N.; c/o Seres Health, Inc., 161 First TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, SN, Street, Suite 1A, Cambridge, MA 02142 (US). AFEYAN, KM, ML, MR, NE, TD, TG). Noubar, B.; c/o Seres Health, Inc., 161 First Street, Suite [Continued on nextpage] (54) Title: COMPOSITIONS AND METHODS C, i rt r S 6 7 o Figure 6 (57) Abstract: Provided are defined bacterial compositions for the maintenance or restoration of a healthy microbiota in the gastrointestinal tract of a mammalian subject, and methods for populating the gastrointestinal tract of a subject. Provided also are bacterial formulations for oral or gastric administration to a mammalian subject in an effective amount for prevention or treatment of a gastrointestinal disease, disorder or condition. w o 2014/121304 Al II II II I III IIII II I ll ll III II ill II I II Published: — with sequence listing part of description (Rule 5.2(a)) — with international search report (Art. 21(3)) — before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) TITLE [001] Compositions and Methods RELATED APPLICATIONS [002] This application is related to U.S. Provisional Application No. 61/760,584, filed on Feb. 4 , 2013, and to U.S. Provisional Application No. 61/760,585, filed on Feb. 4 , 2013, and to U.S. Provisional Application No. 61/760,574, filed on Feb. 4 , 2013, and to U.S. Provisional Application No. 61/760,606, filed on Feb. 4 , 2013, and to U.S. Provisional Application No. 61/926,928, filed on Jan. 13, 2014, which are each incorporated by reference in its entirety for all purposes. REFERENCE TO A SEQUENCE LISTING [003] This application includes a Sequence Listing submitted electronically as a text file named 25968PCT_CRF_sequencelisting.txt, created on Feb. 4 , 2014, with a size of 9 11,051 bytes. The sequence listing is incorporated by reference. BACKGROUND [004] Mammals are colonized by microbes in the gastrointestinal (Gl) tract, on the skin, and in other epithelial and tissue niches such as the oral cavity, eye surface and vagina. The gastrointestinal tract harbors an abundant and diverse microbial community. It is a complex system, providing an environment or niche for a community of many different species or organisms, including diverse strains of bacteria. Hundreds of different species may form a commensal community in the Gl tract in a healthy person, and this complement of organisms evolves from the time of birth to ultimately form a functionally mature microbial population by about 3 years of age. Interactions between microbial strains in these populations and between microbes and the host, e.g. the host immune system, shape the community structure, with availability of and competition for resources affecting the distribution of microbes. Such resources may be food, location and the availability of space to grow or a physical structure to which the microbe may attach. For example, host diet is involved in shaping the Gl tract flora. [005] A healthy microbiota provides the host with multiple benefits, including colonization resistance to a broad spectrum of pathogens, essential nutrient biosynthesis and absorption, and immune stimulation that maintains a healthy gut epithelium and an appropriately controlled systemic immunity. In settings of 'dysbiosis' or disrupted symbiosis, microbiota functions can be lost or deranged, resulting in increased susceptibility to pathogens, altered metabolic profiles, or induction of proinflammatory signals that can result in local or systemic inflammation or autoimmunity. Thus, the intestinal microbiota plays a significant role in the pathogenesis of many diseases and disorders, including a variety of pathogenic infections of the gut. For instance, subjects become more susceptible to pathogenic infections when the normal intestinal microbiota has been disturbed due to use of broad-spectrum antibiotics. Many of these diseases and disorders are chronic conditions that significantly decrease a subject's quality of life and can be ultimately fatal. [006] Manufacturers of probiotics have asserted that their preparations of bacteria promote mammalian health by preserving the natural microflora in the Gl tract and reinforcing the normal controls on aberrant immune responses. See, e.g., U.S. Patent No. 8,034,601 . Probiotics, however, have been limited to a very narrow group of genera and a correspondingly limited number of species; as such, they do not adequately replace the missing natural microflora of the Gl tract in many situations. [007] Thus, there is a need for a method of populating a subject's gastrointestinal tract with a diverse and useful selection of microbiota in order to alter a dysbiosis. In response to the need for durable, efficient, and effective compositions and methods for treatment of Gl diseases by way of restoring or enhancing microbiota functions, Applicants address these and other shortcomings of the art by providing compositions and methods for treating subjects. SUMMARY OF THE INVENTION [008] Disclosed herein are therapeutic compositions comprising a bacterial population comprising at least three but fewer than nine bacterial strains selected from the group consisting of Escherichia coli, Enterococcus faecalis, Clostridium innocuum, Clostridium ramosum, Clostridium bifermentans, Bacteroides ovatus, Bacteroides vulgatus, Bacteroides thetaiotaomicron, and Blautia producta, wherein the composition is formulated for oral or gastric administration to a mammalian subject in an effective amount for prevention or treatment of a gastrointestinal disease, disorder or condition. In some embodiments, the bacterial strains are not a colonic bacterium and/or are not obtained from a fecal culture. In some embodiments, at least one Bacteroides species is detectably present in the mammalian subject prior to administration of the composition or, in other embodiments at least one Bacteroides species is not detectably present in the mammalian subject prior to administration of the composition, but is detectably present in the mammalian subject at least one hour after administration of the composition. In some embodiments, the mammalian subject has not received at least two doses of vancomycin, metronidazole and/or or similar antibiotic compound within one week prior to administration of the therapeutic composition. In some embodiments, a single administration is substantially effective to reduce C. difficile and/or C. difficile toxin content in a mammalian subject to whom the composition is administered. In some embodiments, one strain of E. coli is present in amounts at least 2 , 5 , 10 , 50, 100 or more than 100 times greater than any other strain of E. coli present in the composition. In some embodiments, at least three bacterial strains are not present in the composition in equal ratios or are present in a ratio equivalent to the ratio of the bacterial strains in a reference mammalian subject. In some embodiments, at least one of the bacterial strains is provided in a concentration of greater than 1x1 09 viable bacteria per gram of composition or is provided in a concentration of less than 1x108 viable bacteria per gram of composition.
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