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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 2014/121301 Al 7 August 2014 (07.08.2014) P O P C T (51) International Patent Classification: (US). OHSUMI, Toshiro; c/o Seres Health, Inc., 161 First C12N 1/20 (2006.01) A61K 35/66 (2006.01) Street, Suite 1A, Cambridge, MA 02142 (US). A61K 35/74 (2006.01) (74) Agents: HUBL, Susan T. et al; Fenwick & West LLP, (21) International Application Number: Silicon Valley Center, 801 California Street, Mountain PCT/US2014/014744 View, CA 94041 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 4 February 2014 (04.02.2014) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (25) Filing Language: English BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (26) Publication Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/760,574 4 February 2013 (04.02.2013) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/760,585 4 February 2013 (04.02.2013) US OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 61/760,584 4 February 2013 (04.02.2013) us SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, 61/760,606 4 February 2013 (04.02.2013) us TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, 61/926,918 13 January 2014 (13.01.2014) us ZW. (71) Applicant: SERES HEALTH, INC. [US/US]; 161 First (84) Designated States (unless otherwise indicated, for every Street, Suite 1A, Cambridge, MA 02 142 (US). kind of regional protection available): ARIPO (BW, GH, (72) Inventors: COOK, David, N.; c/o Seres Health, Inc., 161 GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, First Street, Suite 1A, Cambridge, MA 02142 (US). UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, ZHANG, Angela; c/o Seres Health, Inc., 161 First Street, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, Suite 1A, Cambridge, MA 02142 (US). D'ONOFRIO, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, Anthony, A.; c/o Seres Health, Inc., 161 First Street, Suite MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, 1A, Cambridge, MA 02142 (US). BERRY, David, A.; c/o KM, ML, MR, NE, SN, TD, TG). Seres Health, Inc., 161 First Street, Suite 1A, Cambridge, MA 02142 (US). MCKENZIE, Mary-Jane, Lombardo; Published: c/o Seres Health, Inc., 161 First Street, Suite 1A, Cam — with international search report (Art. 21(3)) bridge, MA 02142 (US). AUNINS, John, G.; c/o Seres Health, Inc., 161 First Street, Suite 1A, Cambridge, MA — with sequence listing part of description (Rule 5.2(a)) 02142 (US). MCKENZIE, Gregory; c/o Seres Health, Inc., 161 First Street, Suite 1A, Cambridge, MA 02142 © o (54) Title: COMPOSITIONS AND METHODS FOR INHIBITION OF PATHOGENIC BACTERIAL GROWTH (57) Abstract: Compositions for methods of preventing or reducing pathogenic bacterial growth, proliferation, and/or colonization are described containing one or more types of non-pathogenic bacteria to be introduced into the gastrointestinal tract and effectively compete with pathogemc bacteria for monomeric or polymeric carbohydrate nutrients, and/or amino acid nutrients, and/or vitamin nutrients. TITLE [001] Compositions and Methods for Inhibition of Pathogenic Bacterial Growth. RELATED APPLICATIONS [002] This application claims priority to U.S. Provisional Application No. 61/760,584, filed February 4 , 2013 and U.S. Provisional Application No. 61/760,585, filed February 4 , 2013 and U.S. Provisional Application No. 61/760,574, filed February 4 , 2013 and U.S. Provisional Application No. 61/760,606, filed February 4, 201 3 and U.S. Provisional Application No. 61/926,918, filed January 13, 2014. These applications are all incorporated by reference in their entirety for all purposes. REFERENCE TO A SEQUENCE LISTING [003] This application includes a Sequence Listing submitted electronically as a text file named 25969PCT_sequencelisting.txt, created on February 2 , 2014, with a size of 4,1 00,000 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 nor correct dysbioses of the Gl tract in many situations. Additionally, such probiotics are insufficient to prevent, reduce or treat a pathogenic bacterial infection of the gastrointestinal tract, such as by Clostridium difficile, by reducing the population of the gastrointestinal tract by the pathogenic bacteria. [007] Thus practitioners have a need for methods and compositions for preventing or treating pathogenic bacterial infections. We have designed bacterial compositions of isolated bacterial strains with a plurality of beneficial properties, including the ability to metabolize nutrients at rates above and at concentrations below those of pathogenic bacteria, based on our understanding of those bacterial strains and our analysis of the properties that enhance the utility and commercialization of a microbial composition. [008] Therefore, in response to the need for durable, efficient, and effective compositions and methods for prevention, diagnosis and/or treatment of gastrointestinal diseases by way of restoring or enhancing microbiota functions, we address these and other shortcomings of the prior art by providing compositions and methods for treating subjects. SUMMARY OF THE INVENTION [009] The present invention demonstrates effective compositions for and methods of preventing or reducing pathogenic bacterial growth, proliferation, and/or colonization, whereby bacterial compositions that contain one or more types of no n pathogenic bacteria are introduced into the gastrointestinal tract and effectively compete with pathogenic bacteria for monomeric or polymeric carbohydrate nutrients, and/or amino acid nutrients, and/or vitamin nutrients. Alternatively, organisms may prevent disease by metabolizing available germinants utilized by the pathogenic bacteria and prevent pathogenic spore germination. Alternatively, competition for overlapping nutrients among two or more types of non-pathogenic bacteria that are introduced into the gastrointestinal tract may leads to secretion of molecules inhibitory to a pathogen and/or pathobiont by one or multiple of the types of introduced non-pathogenic bacteria. In certain instances, the inhibitory compound may be a toxin, antibiotic, or a bacterocin (see Chiuchiolo et al. Growth-phase-dependent expression of the cyclopeptide antibiotic microcin J25 J Bacteriol. 2001 Mar;1 83(5): 1755-64). BRIEF DESCRIPTION OF THE DRAWINGS [0 0] Figure 1 illustrates variable regions mapped onto the 16s sequence (Figure 1A) and annotated 16s sequence (Figure 1B) with bolded variable regions. according to an embodiment of the invention. [01 1] Figure 2 is a photograph of a CsCI gradient demonstrating spore separation from other material. [012] Figure 3 illustrates population of fecal bacterial cell suspension (left) after CsCI separation (center) and after a CsCI and sucrose gradient (right) demonstrates enrichment of spores. [013] Figure 4 illustrates a prophylaxis model with the ethanol treated spore preparation and the ethanol treated, gradient-purified spore preparation. [014] Figure 5 illustrates a relapse prevention model with ethanol treated spores and ethanol treated, gradient purified spores.
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  • The Mouse Intestinal Bacterial Collection (Mibc) Provides Host-Specific Insight Into Cultured Diversity and Functional Potential of the Gut Microbiota

    The Mouse Intestinal Bacterial Collection (Mibc) Provides Host-Specific Insight Into Cultured Diversity and Functional Potential of the Gut Microbiota

    Downloaded from orbit.dtu.dk on: Oct 02, 2021 The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte; Foesel, Bärbel U.; Meier-Kolthoff, Jan P.; Kumar, Neeraj; Bresciani, Anne Gøther; Martínez, Inés; Just, Sarah; Ziegler, Caroline Total number of authors: 28 Published in: Nature Microbiology Link to article, DOI: 10.1038/nmicrobiol.2016.131 Publication date: 2016 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Lagkouvardos, I., Pukall, R., Abt, B., Foesel, B. U., Meier-Kolthoff, J. P., Kumar, N., Bresciani, A. G., Martínez, I., Just, S., Ziegler, C., Brugiroux, S., Garzetti, D., Wenning, M., Bui, T. P. N., Wang, J., Hugenholtz, F., Plugge, C. M., Peterson, D. A., Hornef, M. W., ... Clavel, T. (2016). The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nature Microbiology, 1(10), [16131]. https://doi.org/10.1038/nmicrobiol.2016.131 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.