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(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 2016/086210 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, A61P 1/00 (2006.01) A61P 37/00 (2006.01) LLP, 265 Franklin Street, Boston, MA 021 10 (US). A61P 29/00 (2006.01) A61K 35/74 (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 15/0628 10 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, 62/084,537 25 November 2014 (25. 11.2014) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. 62/084,536 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, Shaila [US/US]; 790 Memorial — with international search report (Art. 21(3)) Drive, 3rd Floor, Cambridge, MA 02139 (US). — before the expiration of the time limit for amending the (72) Inventors: BERRY, David; 155 Beethoven Avenue, claims and to be republished in the event of receipt of Waban, MA 02468 (US). AFEYAN, Noubar, B.; 1 Sunset amendments (Rule 48.2(h)) Ridge, Lexington, MA 0242 1 (US). KAPLAN, Johanne; — with sequence listing part of description (Rule 5.2(a)) 123 Mill Street, Sherborn, MA 01770 (US). GORDON, Neal; 4 1 Dwight Street, #2, Brookline, MA 02446 (US). < © 00 © v (54) Title: PROBIOTIC AND PREBIOTIC COMPOSTIONS, AND METHODS OF USE THEROF 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 126383-01921_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 IFNy, IL- 12p70, IL-la, IL-6, IL-8, MCP1, ΜΙΡΙα, ΜΙΡΙβ, TNF , 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, TGF and combinations thereof. In one embodiment of the foregoing aspect, the anti-inflammatory bacterial population produces short chain fatty acids.
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    life Article Effects of Heavy Ion Particle Irradiation on Spore Germination of Bacillus spp. from Extremely Hot and Cold Environments Vincenzo Zammuto 1 , Maria G. Rizzo 1,*, Laura M. De Plano 1, Domenico Franco 1 , Salvatore Guglielmino 1, Maria T. Caccamo 2 , Salvatore Magazù 2, Akira Fujimori 3, Angelina Lo Giudice 4 , Mauro Guglielmin 5, Kevin Roderick McAlpin 6,7, Ralf Moeller 6,7 and Concetta Gugliandolo 1 1 Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Research Centre for Extreme Environments and Extremophiles, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; [email protected] (V.Z.); [email protected] (L.M.D.P.); [email protected] (D.F.); [email protected] (S.G.); [email protected] (C.G.) 2 Department of Mathematics, Computer Sciences, Physics and Earth Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; [email protected] (M.T.C.); [email protected] (S.M.) 3 Department of Basic Medical Sciences for Radiation Damages, Molecular and Cellular Radiation Biology Group, NIRS/QST, Chiba 263-8555, Japan; [email protected] 4 Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata San Raineri 86, 98122 Messina, Italy; [email protected] 5 Department of Theoretical and Applied Sciences, University of Insubria, Via J.H. Dunant, 21100 Varese, Italy; [email protected] 6 Institute of Aerospace Medicine, Radiation Biology Department, German Aerospace Center, Aerospace Microbiology, DLR, Linder Höhe, D-51147 Cologne/Köln, Germany; [email protected] (R.M.); [email protected] (K.R.M.) 7 Natural Sciences Department, University of Applied Sciences Bonn-Rhein-Sieg (BRSU), D-53359 Rheinbach, Germany * Correspondence: [email protected] Received: 13 October 2020; Accepted: 28 October 2020; Published: 30 October 2020 Abstract: Extremophiles are optimal models in experimentally addressing questions about the effects of cosmic radiation on biological systems.
  • Construction of Probe of the Plant Growth-Promoting Bacteria Bacillus Subtilis Useful for fluorescence in Situ Hybridization

    Construction of Probe of the Plant Growth-Promoting Bacteria Bacillus Subtilis Useful for fluorescence in Situ Hybridization

    Journal of Microbiological Methods 128 (2016) 125–129 Contents lists available at ScienceDirect Journal of Microbiological Methods journal homepage: www.elsevier.com/locate/jmicmeth Construction of probe of the plant growth-promoting bacteria Bacillus subtilis useful for fluorescence in situ hybridization Luisa F. Posada a,JavierC.Alvarezb, Chia-Hui Hu e, Luz E. de-Bashan c,d,e, Yoav Bashan c,d,e,⁎ a Department of Process Engineering, Cra 49 #7 sur-50, Universidad EAFIT, Medellín, Colombia b Departament of Biological Sciences, Cra 49 #7 sur-50, Universidad EAFIT, Medellín, Colombia c The Bashan Institute of Science, 1730 Post Oak Ct., AL 36830, USA d Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Av. IPN 195, La Paz, B.C.S. 23096, Mexico e Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA article info abstract Article history: Strains of Bacillus subtilis are plant growth-promoting bacteria (PGPB) of many crops and are used as inoculants. Received 13 April 2016 PGPB colonization is an important trait for success of a PGPB on plants. A specific probe, based on the 16 s rRNA of Received in revised form 30 May 2016 Bacillus subtilis, was designed and evaluated to distinguishing, by fluorescence in situ hybridization (FISH), be- Accepted 31 May 2016 tween this species and the closely related Bacillus amyloliquefaciens. The selected target for the probe was be- Available online 2 June 2016 tween nucleotides 465 and 483 of the gene, where three different nucleotides can be identified. The designed Keywords: probe successfully hybridized with several strains of Bacillus subtilis, but failed to hybridize not only with Bacillus subtilis B.