(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 2014/121298 A2 7 August 2014 (07.08.2014) P O P C T (51) International Patent Classification: VULIC, Marin; c/o Seres Health, Inc., 161 First Street, A61K 39/02 (2006.01) Suite 1A, Cambridge, MA 02142 (US). (21) International Application Number: (74) Agents: HUBL, Susan, T. et al; Fenwick & West LLP, PCT/US2014/014738 Silicon Valley Center, 801 California Street, Mountain View, CA 94041 (US). (22) International Filing Date: 4 February 2014 (04.02.2014) (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, English (25) Filing Language: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (26) Publication Language: English BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (30) Priority Data: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 61/760,584 4 February 2013 (04.02.2013) US KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/760,585 4 February 2013 (04.02.2013) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/760,574 4 February 2013 (04.02.2013) us OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 61/760,606 4 February 2013 (04.02.2013) 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: VON MALTZAHN, Geoffrey; c/o Seres kind of regional protection available): ARIPO (BW, GH, Health, Inc., 161 First Street, Suite 1A, Cambridge, MA GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, 02142 (US). HENN, Matthew, R.; c/o Seres Health, Inc., UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 161 First Street, Suite 1A, Cambridge, MA 02142 (US). TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, COOK, David, N.; c/o Seres Health, Inc., 161 First Street, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, Suite 1A, Cambridge, MA 02142 (US). BARRY, David, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, A.; c/o Seres Health, Inc., 161 First Street, Suite 1A, Cam TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, bridge, MA 02142 (US). AFEYAN, Noubar, B.; c/o Seres KM, ML, MR, NE, SN, TD, TG). Health, Inc., 161 First Street, Suite 1A, Cambridge, MA Published: 02142 (US). GOODMAN, Brian; c/o Seres Health, Inc., — without international search report and to be republished 161 First Street, Suite 1A, Cambridge, MA 02142 (US). upon receipt of that report (Rule 48.2(g)) LOMBARDO, Mary-Jane; c/o Seres Health, Inc., 161 First Street, Suite 1A, Cambridge, MA 02142 (US). — with sequence listing part of description (Rule 5.2(a)) (54) Title: METHODS OF POPULATING A GASTROINTESTINAL TRACT < FIG. 3 (57) Abstract: Methods and compositions for populating the gastrointestinal tract of a subject are described. Methods include ad o ministering to a subject a therapeutic composition comprising a purified population of spore-forming bacteria produced by providing a fecal material and subjecting the material to a treatment step resulting in purification of spore- forming bacteria. Methods include administering an amount effective to engraft and/or augment in the gastrointestinal tract in order to treat or prevent a dysbiosis in the mammalian subject. TITLE [001] Methods of Populating a Gastrointestinal Tract RELATED APPLICATIONS [002] This application is related to U.S. Provisional Application No. 61/760,584, filed on Feb. 4, 201 3, and to U.S. Provisional Application No. 61/760,585, filed on Feb. 4, 201 3, 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, 201 3, and to U.S. Provisional Application No. 61/926,928, filed on Jan. 13, 2014, which are each incorporated by reference in its entirety. REFERENCE TO A SEQUENCE LISTING [003] This application includes a Sequence Listing submitted electronically as a text file named 25967PCT_CRF_sequencelisting.txt, created on February 4, 2013, with a size of 9 1 1,074 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 methods of populating a subject's gastrointestinal tract with a wider selection of microbiota in order to alter a dysbiosis. There is also a need to design microbial compositions of isolated bacterial strains with a plurality of beneficial properties based on current understanding of bacterial strains and analysis of the properties that would enhance the utility and commercialization of a microbial composition. [008] Therefore, there exists a need for durable, efficient, and effective compositions and methods for treatment of Gl diseases by way of restoring or enhancing microbiota functions and for addressing these and other shortcomings in the art. SUMMARY OF THE INVENTION [009] Disclosed herein are methods of populating the gastrointestinal tract of a mammalian subject, including the step of orally administering to the mammalian subject an effective amount of a therapeutic composition comprising a purified population of spore-forming bacteria produced by the steps of a) providing a fecal material and b) subjecting the material to a treatment step resulting in purification of spore-forming bacteria, wherein the purified population is present in an amount effective to engraft and/or augment in the gastrointestinal tract in order to treat or prevent a dysbiosis in the mammalian subject. [010] Disclosed herein are methods for populating the gastrointestinal tract of a mammalian subject, comprising the step of orally administering to the subject an effective amount of a therapeutic composition comprising a purified population of spore-forming bacteria in an amount effective to engraft and/or augment in the gastrointestinal tract in order to treat or prevent a dysbiosis in a mammalian subject. [01 1] Also described are therapeutic compositions comprising a purified population of spore-forming bacteria or bacteria having a substantial activity of spore-forming bacteria in an amount effective to populate the gastrointestinal tract of a mammalian subject to whom the therapeutic composition is administered. In some embodiments, the population is effective to i) treat a gastrointestinal dysbiosis, and/or ii) engraft at least one type of bacteria present in the therapeutic composition but not present in a mammalian subject prior to treatment; and/or iii) augment at least one type of bacteria not present in the therapeutic composition in a mammalian subject to whom the therapeutic composition is administered. [012] Also provided are therapeutic compositions comprising a purified population of spore-forming bacteria in an amount effective to populate the gastrointestinal tract of a mammalian subject to whom the therapeutic composition is administered, wherein the purified population is obtained by the steps of a) providing a fecal material comprising spore-forming bacteria and b) subjecting the spore- forming bacteria to a treatment step resulting in purification of the spore-forming bacteria.