(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 2016/086208 Al 2 June 2016 (02.06.2016) P O P C T (51) International Patent Classification: (74) Agents: MELLO, Jill Ann et al; McCarter & English, A61K 35/74 (2015.01) A61P 29/00 (2006.01) LLP, 265 Franklin Street, Boston, MA 021 10 (US). A61K 35/741 (2015.01) A61P 37/00 (2006.01) (81) Designated States (unless otherwise indicated, for every A61P 1/00 (2006.01) A61P 43/00 (2006.01) kind of national protection available): AE, AG, AL, AM, (21) International Application Number: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, PCT/US20 15/062808 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, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 25 November 2015 (25.1 1.2015) KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, (25) Filing Language: English MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (26) Publication Language: English SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, (30) Priority Data: 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 62/084,536 25 November 2014 (25. 11.2014) us kind of regional protection available): ARIPO (BW, GH, 62/084,540 25 November 2014 (25. 11.2014) 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 17,639 18 February 2015 (18.02.2015) us TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, 62/1 17,632 18 February 2015 (18.02.2015) us DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, 62/162,562 15 May 2015 (15.05.2015) us LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, 62/257,714 19 November 2015 (19. 11.2015) us SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, (71) Applicant: EPIVA BIOSCIENCES, INC. [US/US]; 790 GW, KM, ML, MR, NE, SN, TD, TG). Memorial Drive, 3rd Floor, Cambridge, MA 02139 (US). Published: (72) Inventor; and — with international search report (Art. 21(3)) (71) Applicant : RAHMAN, Shaila [US/US]; 790 Memorial — before the expiration of the time limit for amending the Drive, 3rd Floor, Cambridge, MA 02139 (US). claims and to be republished in the event of receipt of (72) Inventors: BERRY, David; 155 Beethoven Avenue, amendments (Rule 48.2(h)) Waban, MA 02468 (US). AFEYAN, Noubar, B.; 1 Sunset — with sequence listing part of description (Rule 5.2(a)) Ridge, Lexington, MA 0242 1 (US). KAPLAN, Johanne; 123 Mill Street, Sherborn, MA 01770 (US). GORDON, Neal; 4 1 Dwight Street, #2, Brookline, MA 02446 (US). 0 o0 00 © v (54) Title: PROBIOTIC AND PREBIOTIC COMPOSITIONS, AND METHODS OF USE THEREOF FOR TREATMENT AND o PREVENTION OF GRAFT VERSUS HOST DISEASE (57) Abstract: Probiotic compositions containing non-pathogenic microbial entities, e.g., bacterial or fungal entities, are described herein. The probiotic compositions may optionally contain or be used in conjunction with one or more prebiotics. Uses of the probi otic compositions to treat or prevent transplant disorders, e.g., graft- versus-host disease (GVHD), in a subject are also provided. PROBIOTIC AND PREBIOTIC COMPOSITIONS, AND METHODS OF USE THEREOF FOR TREATMENT AND PREVENTION OF GRAFT VERSUS HOST DISEASE 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 18, 2015; U.S. Provisional Patent Application No. 62/117,639, 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_01920_SL.txt and is 4,147,507 bytes in size. BACKGROUND [003] Graft versus host disease (GVHD) is a common and devastating complication following a hematopoietic or tissue transplant and occurs in approximately 50% of transplant recipients. Acute GVHD is a major source of morbidity and mortality following allogeneic hematopoietic cell transplantation. Approximately 25,000 allogeneic hematopoietic cell transplants (e.g., bone marrow, peripheral blood stem cell [PBSC], or cord blood transplants) are performed annually worldwide. Over time, the number of transplants from unrelated donors, and in the number of allogeneic transplants for AML, ALL, MDS, and lymphomas, continues to rise. There is also an increase in the number of allogeneic transplantants for non- malignant diseases, and an increase in the number of transplant patients over 50 years of age. The global incidence of acute GVHD ranges from 26% - 34% in recipients of fully matched, sibling donor grafts to 42% - 52% in recipients of matched, unrelated donor grafts. Evidence from the US suggests that incidence ranges from 30% in recipients of fully histocompatible transplants to 60% - 70% in recipients of mismatched hematopoietic cells or hematopoietic cells from an unrelated donor. There is no FDA approved treatment for either acute or chronic GVHD. Treatment strategies for acute GVHD aim to reduce the immune reaction of the donor T cells against host tissues and therefore includes immunosuppressive treatment like cyclosporine, high dose steroids, and methotrexate. The standard therapy for de novo acute GVHD is high dose methylprednisolone, with expected response rates of 18% - 50%. For patients who develop steroid-refractory acute GVHD, there is no standard of care therapy, and expected survival is less than 30%. Therefore, novel therapies are urgently needed for the treatment and prevention of GVHD. SUMMARY OF THE INVENTION [004] Disclosed herein are therapeutic compositions containing probiotic, non- pathogenic bacterial populations and networks thereof, for the prevention, control, and treatment of transplant disorders and conditions, in particular diseases associated with graft versus host disease (GVHD). In some embodiments, the therapeutic compositions contain prebiotics, e.g., carbohydrates, in conjunction with microbial populations and/or networks thereof. These compositions are advantageous in being suitable for safe administration to humans and other mammalian subjects and are efficacious in numerous dysbiotic diseases, disorders and conditions and in general nutritional health. [005] In one aspect, the instant invention provides a method of increasing the duration of survival of a subject receiving a transplant, e.g., a bone marrow transplant, comprising administering to the subject a probiotic composition comprising an isolated bacterial population, such that the duration of survival of the subject is increased. [006] In one embodiment of the foregoing aspect, the bacterial population is a human- derived bacterial population. [007] In one embodiment of the foregoing aspect, administration of the probiotic composition reduces the likelihood that the subject will develop sepsis following the bone marrow transplant. In one embodiment of the foregoing aspect, administration of the probiotic composition reduces the likelihood that the subject will develop graft versus host disease (GVHD) following the bone marrow transplant. [008] In one embodiment of the foregoing aspect, the probiotic composition is administered to the subject prior to receiving the bone marrow transplant. In one embodiment of the foregoing aspect, the probiotic composition is administered to the subject after receiving the bone marrow transplant. In one embodiment of the foregoing aspect, the probiotic composition is administered to the subject concurrently with the bone marrow transplant. [009] In one embodiment of the foregoing aspect, the probiotic composition reduces intestinal permeability in the subject. [010] In one embodiment of the foregoing aspect, the probiotic composition comprises a bacterial population that produces short chain fatty acids. In one embodiment of the foregoing aspect, the bacterial population produces a short chain fatty acid selected from the group consisting of butyrate, acetate, propionate, valerate, and combinations thereof. [011] In one embodiment of the foregoing aspect, the probiotic composition reduces inflammation in the gastrointestinal tract of the subject. In one embodiment of the foregoing aspect, the probiotic composition comprises an anti-inflammatory bacterial population. In one embodiment of the foregoing aspect, the anti-inflammatory bacterial population decreases secretion of pro-inflammatory cytokines and/or increases secretion of anti- inflammatory cytokines by human peripheral blood mononuclear cells (PBMCs). In one embodiment of the foregoing aspect, the anti-inflammatory bacterial population decreases secretion of a pro-inflammatory cytokine selected from the group consisting of IFNγ, IL- 12p70, IL-1α, IL-6, IL-8, MCP1, MIP1α, MIP1β, TNFα, and combinations thereof. In one embodiment of the foregoing aspect, the anti-inflammatory bacterial population increases secretion of an anti-inflammatory cytokine selected from the group consisting of IL-10, IL- 13, IL-4, IL-5, TGFβ and combinations thereof.