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WO 2016/086209 Al June 2016 (02.06.2016) W 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 2016/086209 Al June 2016 (02.06.2016) W P O P C T (51) International Patent Classification: (74) Agents: MELLO, Jill, Ann et al; Mccarter & English, A61K 35/74 (2015.01) A61P 1/00 (2006.01) LLP, 265 Franklin Street, Boston, MA 021 10 (US). A61K 35/741 (2015.01) (81) Designated States (unless otherwise indicated, for every (21) International Application Number: kind of national protection available): AE, AG, AL, AM, PCT/US20 15/062809 AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (22) International Filing Date: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 25 November 2015 (25.1 1.2015) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (25) Filing Language: English KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (26) Publication Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (30) Priority Data: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 62/084,536 25 November 2014 (25. 11.2014) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. 62/084,537 25 November 2014 (25. 11.2014) US (84) Designated States (unless otherwise indicated, for every 62/084,540 25 November 2014 (25. 11.2014) us kind of regional protection available): ARIPO (BW, GH, 62/1 17,639 18 February 2015 (18.02.2015) us GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 62/1 17,637 18 February 2015 (18.02.2015) us TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, 62/1 17,632 18 February 2015 (18.02.2015) us TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, 62/162,562 15 May 2015 (15.05.2015) us DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, 62/257,714 19 November 2015 (19. 11.2015) us LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, (71) Applicant: EPIVA BIOSCIENCES, INC. [US/US]; 790 SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, Memorial Drive, 3rd Floor, Cambridge, MA 02139 (US). GW, KM, ML, MR, NE, SN, TD, TG). (72) Inventor; and Published: (71) Applicant : RAHMAN, Shila [US/US]; 790 Memorial — with international search report (Art. 21(3)) Drive, 3rd Floor, Cambridge, MA 02139 (US). — with sequence listing part of description (Rule 5.2(a)) (72) Inventors: BERRY, David; 155 Beethoven Avenue, Waban, MA 02468 (US). AFEYAN, Noubar, B.; 1 Sunset Ridge, Lexington, MA 0242 1 (US). KAPLAN, Johanne; 123 Mill Street, Sherborn, MA 01770 (US). © 00 © - (54) Title: PROBIOTIC AND PREBIOTIC COMPOSITIONS, AND METHODS OF USE THEREOF FOR TREATMENT OF © GASTROINTESTINAL DISORDERS (57) Abstract: Probiotic compositions containing non-pathogenic microbial entities, e.g., bacterial entities, are described herein. The probiotic compositions may optionally contain or be used in conjunction with one or more prebiotics. Uses of the probiotic composi tions to treat or prevent disorders of the local or systemic microbiome, e.g., gastrointestinal disorders, in a subject are also provided. PROBIOTIC AND PREBIOTIC COMPOSITIONS, AND METHODS OF USE THEREOF FOR TREATMENT OF GASTROINTESTINAL DISORDERS RELATED APPLICATIONS [001] This application claims priority to U.S. Provisional Patent Application No. 62/084,536, filed November 25, 2014; U.S. Provisional Patent Application No. 62/084,537, filed November 25, 2014; U.S. Provisional Patent Application No. 62/084,540, filed November 25, 2014; U.S. Provisional Patent Application No. 62/117,632, filed February 18, 2015; U.S. Provisional Patent Application No. 62/117,637, filed February 8, 2015; U.S. Provisional Patent Application No. 62/1 17.639. filed February 18, 2015; U.S. Provisional Patent Application No. 62/162,562, filed May 15, 2015; and U.S. Provisional Patent Application No. 62/257,714, filed November 19, 2015. The entire contents of each of the foregoing applications are incorporated herein by reference. SEQUENCE LISTING [002] The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on November 25, 2015, is named 126383-02020_SL.txt and is 4,147,486 bytes in size. BACKGROUND [003] Humans and other mammals have numerous microbial niches, and interventions to modulate th microbiota thereof have been focused o antibiotics (which effect largely non-specific eradication of the microbiota in an effort to target a pathogen), probiotics (largely in the form of lactic acid-producing bacteria in food products), prebiotics (stimulatory materials, primarily carbohydrates, that increase bacterial growth and/or activity), and synbiotics (combinations of prebiotics and probiotics). See, e.g., WO20 11/022542. Autoimmune and inflammatory diseases are characterized by an inappropriate immunological intolerance or an abnormal immune response, and affect up to 50 million Americans. Current treatments for such conditions, such as immunosuppressant drugs, carry a risk of dangerous systemic side effects such as infection, organ damage, and the development of new autoimmunities. There is therefore a need for improved diagnostic and prognostic measures, preventative measures, and treatments for autoimmune and inflammatory diseases. [004] It is recognized that mammals are colonized by microbes in the gastrointestinal (GI) tract, on the skin, and in other epithelial and tissue niches such as the oral cavity, eye surface and vagina. The gastrointestinal tract, vagina and other niches harbor 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 GI tract or vagina of 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. A substantial diversity of species may form a commensal community in the gut and the vagina in a healthy person. Interactions between microbial strains in these populations, and between microbes and the host, e.g. the host immune system, shape the community structure as well as microbiotal niches distal to the intestinal lumen, 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 GI tract flora and vaginal 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 distal to the gastrointestinal tract. 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. Thus practitioners have 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. Also, practitioners have a need for a method of populating a subject's vagina, either directly or indirectly, e.g., through the gastrointestinal tract, with a diverse and useful selection of microbiota in order to alter a dysbiosis. Therefore, in response to the need for durable, efficient, and effective compositions and methods for treatment of immune and inflammatory diseases by way of restoring or enhancing microbiota functions, the present invention provides compositions and methods for treatment and prevention of immune and inflammatory conditions associated with dysbiosis, including dysbiosis distal to the gastrointestinal tract, gastrointestinal dysbiosis, and gastrointestinal diseases, disorders and conditions. [006] Antibiotic resistance is an emerging public health issue (Ca et J, Collignon P, Goldmann D, Goossens H, Gyssens C, Harbarth S, Jarlier V, Levy SB, N'Doye B, Pittet D, et a . 2011. Society's failure to protect a precious resource: antibiotics. Lancet 378: 369- 371.). Numerous genera of bacteria harbor species that are developing resistance to antibiotics. These include but are not limited to Vancomycin Resistant Enterococcus (VRE) and Carbapenem resistant Klebsiella (CRKp) Klebsiella pneumoniae and Escherichia coli strains are becoming resistant to carbapenems and require the use of old antibiotics characterized by high toxicity, such as colist i (Canton R, Akova M, Carmeli Y, Giske CG, Glupczynski Y, Gniadkowski M, Livermore DM, Miriagou V, Naas T, Rossolini GM, et al. 2012. Rapid evolution and spread of carbapenemases among Enterobacteriaceae
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