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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 2017/160711 Al 21 September 2017 (21.09.2017) P O P C T (51) International Patent Classification: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, A61K 35/74 (2015.01) A61P 25/18 (2006.01) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, A61K 35/745 (2015.01) A61P 25/22 (2006.01) KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, A61K 35/742 (2015.01) A61P 25/24 (2006.01) MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, A61P 25/00 (2006.01) A61P 43/00 (2006.01) NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, (21) International Application Number: TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, PCT/US20 17/022091 ZA, ZM, ZW. (22) International Filing Date: (84) Designated States (unless otherwise indicated, for every 13 March 2017 (13.03.2017) kind of regional protection available): ARIPO (BW, GH, (25) Filing Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, (26) Publication Language: English TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (30) Priority Data: DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, 62/307,991 14 March 2016 (14.03.2016) US LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, (71) Applicant: HOLOBIOME, INC. [US/US]; 97F Street, GW, KM, ML, MR, NE, SN, TD, TG). South Boston, Massachusetts 02127 (US). Declarations under Rule 4.17 : (72) Inventors: STRANDWITZ, Philip; 12 Henley Street, — as to applicant's entitlement to apply for and be granted a Medford, Massachusetts 02155 (US). LEWIS, Kim; 49 patent (Rule 4.1 7(H)) Glendale Road, Newton, Massachusetts 02459 (US). Published: (74) Agents: FARMER, J. Dean et al; Cooley LLP, 1299 Pennsylvania Avenue, Suite 700, Washington, District of — with international search report (Art. 21(3)) Columbia 20004 (US). — before the expiration of the time limit for amending the (81) Designated States (unless otherwise indicated, for every claims and to be republished in the event of receipt of kind of national protection available): AE, AG, AL, AM, amendments (Rule 48.2(h)) AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, — with sequence listing part of description (Rule 5.2(a)) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, o (54) Title: MODULATION OF THE GUT MICROBIOME TO TREAT MENTAL DISORDERS OR DISEASES OF THE CENT o RAL NERVOUS SYSTEM (57) Abstract: The present disclosure relates to methods of treating at least one symptom of a mental disorder or disease of the cent ral nervous system in a subject by modulating the amount of GABA produced in the subject's gut. The present disclosure also relates to methods of culturing the bacterial strain new bacterial strains. Also disclosed are methods of identifying bacterial strains capable of producing GABA, and engineering strains to produce GABA. MODULATION OF THE GUT MICROBIOME TO TREAT MENTAL DISORDERS OR DISEASES OF THE CENTRAL NERVOUS SYSTEM Cross Reference to Related Applications [0001] This application claims priority to, and benefit of, US Provisional Application No. 62/307,991, filed March 14, 2016, the contents of which is incorporated by reference in its entirety. Incorporation of Seqnence Listing [0002] The contents of the text file named ΟΒΕ 001001 WOSeqList.ixt," which was created on March 13, 2017 and is 7.6 MB in size, are hereby incorporated by reference in their entirety. [0003] This invention was made with government support under 3R01HG005824-02S1 awarded by the National Institute of Health. The government has certain rights in the invention. Field of the Disclosure [0004] The present disclosure relates to compositions and methods for treating at least one symptom of a disease in a subject. In some cases, the disease s a mental disorder or a disease of the central nervous system. The present disclosure teaches treatment of the disease by modulating (e.g., increasing) the amount of endogenous GABA in a subject's body. n some embodiments, the present disclosure teaches modulating (e.g., increasing) the amount of GABA produced in the subject's gut by bacteria in the gut. For example, the present disclosure teaches administration to a subject in need thereof bacteria that are capable of producing GABA (e.g., inside a human gut). [0005] The present disclosure also relates to methods of culturing previously uncultured bacterial strains. For instance, the present disclosure teaches the previously uncultured bacterial strain Evtepia gahavorous KLE1738. As set forth herein, newly uncultured bacterial strains such as Evtepia gahavorous KLE1738 can be cultured by providing growth factors necessary for the bacteria's growth and reproduction. Also disclosed are methods of identifying bacterial strains capable of producing certain growth factors. For instance, described herein are methods of identifying bacterial strains capable of producing GABA, for instance under physiologically relevant conditions such as at a physiologically relevant pH. |0007] The gut microbiome affects certain gastrointestinal and metabolic disorders, such as irritable bowel syndrome (IBS), Crohn's disease, ulcerative colitis, celiac disease, obesity, heart disease, type 1 and II diabetes, and colon cancer. Microbiological studies have so far been limited, by necessity, to cultivable microorganisms. By some estimates, in external environments, 99% of bacteria are thought to be uncultured. The development of new techniques for culturing previously uncultured or uneuiturable bacteria can thus help to expand the scope of microbiology research. The present disclosure provides compositions and methods for treating diseases such as mental illness or diseases of the central nervous system. In some embodiments, the present disclosure teaches therapeutic compositions comprising one or more bacteria (e.g., purified bacteria) that are capable of producing GABA. The bacteria can be capable of producing GABA under physiologically relevant conditions, including within a human gut. The present disclosure also provides methods of treating a subject in need thereof comprising administering to a subject a therapeutic composition comprising GABA- producing bacteria. As set forth herein, the GABA-producmg bacteria can produce GABA in the subject's gut. The GABA can diffuse into other systems of the subject's body (e.g., the circulatory and nervous systems). There, the endogenous GABA can act as a neurotransmitter. In some embodiments, increased levels of GABA (e.g., in the nervous sy stem) can improve the symptoms of the mental illness or disease of the central nervous system. [0010] In some embodiments, the present disclosure also provides methods for identifying bacteria that produce GABA in humans at a physiologically relevant pH range and uses for these bacteria to modulate GABA levels in humans to treat mental illness. [0011] The present disclosure a so relates to a method of culturing previously uncultivated bacterial species. For instance the present disclosure teaches the isolation and characterization of a bacterial species KLE1738, provisionally named Evtepia gabavorous. Growth of E. gabavorous requires the presence of the growth factor GABA, which can be supplied by GABA-producing bacteria such as Bacteroides fragilis KLE1758. [0012] In one aspect, the present disclosure provides a therapeutic composition comprising at least one purified bacterial population consisting of bacteria capable of producing GABA in a subject in need thereof. [0013] In some embodiments, the at least one bacterial population consists of a bacteria comprising a 16S rDNA sequence at least about 95% identical to a 6S rDNA sequence selected from one of Seq. ID. Nos. 1-31 set forth in Table 1. In some embodiments, the at least one purified bacterial population consists of bacteria selected from the group consisting of: Bacteroides caccae KLE1911; Bacteroides darns KLE1930; Bacteroides dorei KLE1912; Bacteroides finegoldii KLE1931; Bacteroides fragilis KLE1958; Bacteroides massi!iensis KLE1932; Bacteroides ovatus KLE1770; Bacteroides stercoris KLE1933; Bacteroides thetaiotaomicron KLE1934; Bacteroides uniformis KLE1913; Bacteroides vulgatus KLE1910; Bacteroides xylanisolvens KLE1935; Bifidobacterium adoiescentis KLE 1879; Blautia obeum KLE1914; Blautia wexlerae LE1916; Butyricimonas virosa KLE1938; Clostridium perfringens KLE1937; Clostridium sordellii KLE1939; Clostridium sp. KLE 1862; Clostridium sp. KLE1918; Coprobacillus sp. KLE1779; Coprococcus sp KLE1880; Dorea longicatena KI .E 9 ; Eggerthella lenta KLE 1926; Eubacterium rectale KLE1922; Gordonihacter pamelaeae KLE1915; Oscillibacler sp KLE 1928; Parabacteroides distasonis KLE2020; Parabacteroides merdae KLE1863; Ruminococcus gnavus KLE1940; Turicibacter sanguinis KLE1941, and combinations thereof. [0014] In some embodiments, the at least one purified bacterial population consists of a bacteria comprising a 16S rDN sequence at least about 95% identical to a 6S rDNA sequence selected from one of Seq. ID. Nos. 32-274 set forth in Table 2. In some embodiments, the at least one purified bacterial population consists of bacteria comprising a 16S rDNA sequence having at least 95% similarity to the 16S rDNA sequence selected from one of Seq. ID. Nos. 305-221 set forth in Table 10. In some embodiments, the at least one purified bacterial population consists of bacteria comprising a DNA sequence which encodes an enzyme selected from: glutamate decarboxylase; putrescine aminotransferase; garnma-aminobutyraldehyde dehydrogenase; arginine decarboxylase; agmatinase; ornithine decarboxylase; or a combination thereof. In some embodiments, the glutamate decarboxylase; putrescine aminotransferase; gamma- aminobutyraldehyde dehydrogenase; arginine decarboxylase; agmatinase; ornithine decarboxylase; or a combination thereof, is encoded by a DNA sequence at least 70% similar in DNA sequence to any one of Seq. ID. Nos.
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  • Redalyc.Bacterial Diversity in Bovine Rumen by Metagenomic 16S Rdna

    Redalyc.Bacterial Diversity in Bovine Rumen by Metagenomic 16S Rdna

    Acta Scientiarum. Animal Sciences ISSN: 1806-2636 [email protected] Universidade Estadual de Maringá Brasil Barbetta de Jesus, Raphael; Pine Omori, Wellington; de Macedo Lemos, Eliana Gertrudes; Marcondes de Souza, Jackson Antônio Bacterial diversity in bovine rumen by metagenomic 16S rDNA sequencing and scanning electron microscopy Acta Scientiarum. Animal Sciences, vol. 37, núm. 3, julio-septiembre, 2015, pp. 251-257 Universidade Estadual de Maringá Maringá, Brasil Available in: http://www.redalyc.org/articulo.oa?id=303141017006 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative Acta Scientiarum http://www.uem.br/acta ISSN printed: 1806-2636 ISSN on-line: 1807-8672 Doi: 10.4025/actascianimsci.v37i3.26535 Bacterial diversity in bovine rumen by metagenomic 16S rDNA sequencing and scanning electron microscopy Raphael Barbetta de Jesus1,2, Wellington Pine Omori1,2, Eliana Gertrudes de Macedo Lemos1,3 and Jackson Antônio Marcondes de Souza1,2* 1Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de Acesso Professor Paulo Donato Castellane, s/n, 14884- 900, Jaboticabal, São Paulo, Brazil. 2Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil. 3Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil. *Author for correspondence. E-mail: [email protected] ABSTRACT. The bacterial diversity by 16S rDNA partial sequencing and scanning electron microscope (SEM) of the rumen microbiome was characterized. Three Nellore bovines, cannulated at the rumen, were utilized.