DOCSLIB.ORG

WO 2017/160711 Al 21 September 2017 (21.09.2017) P O P C T

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
WO 2017/160711 Al 21 September 2017 (21.09.2017) 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 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.
Load more

Recommended publications
  • Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
    www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
    [Show full text]
  • Product Sheet Info
    Product Information Sheet for HM-13 Oribacterium sinus, Strain F0268 2% yeast extract (ATCC medium 1834) or equivalent Wilkins-Chalgren anaerobe agar with 5% defibrinated sheep blood or equivalent Catalog No. HM-13 Incubation: Temperature: 37°C For research use only. Not for human use. Atmosphere: Anaerobic (80% N2:10% CO2:10% H2) Propagation: Contributor: 1. Keep vial frozen until ready for use, then thaw. Jacques Izard, Assistant Member of the Staff, Department of 2. Transfer the entire thawed aliquot into a single tube of Molecular Genetics, The Forsyth Institute, Boston, broth. Massachusetts 3. Use several drops of the suspension to inoculate an agar slant and/or plate. Manufacturer: 4. Incubate the tube, slant and/or plate at 37°C for 48 to BEI Resources 72 hours. Product Description: Citation: Bacteria Classification: Lachnospiraceae, Oribacterium Acknowledgment for publications should read “The following Species: Oribacterium sinus reagent was obtained through BEI Resources, NIAID, NIH as Strain: F0268 part of the Human Microbiome Project: Oribacterium sinus, Original Source: Oribacterium sinus (O. sinus), strain F0268 Strain F0268, HM-13.” was isolated in June 1980 from the subgingival plaque of a 27-year-old white female patient with severe periodontitis in Biosafety Level: 1 the United States.1,2 Appropriate safety procedures should always be used with Comments: O. sinus, strain F0268 (HMP ID 6123) is a this material. Laboratory safety is discussed in the following reference genome for The Human Microbiome Project publication: U.S. Department of Health and Human Services, (HMP). HMP is an initiative to identify and characterize Public Health Service, Centers for Disease Control and human microbial flora.
    [Show full text]
  • WO 2018/064165 A2 (.Pdf)
    (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 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, 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, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
    [Show full text]
  • 1587714682 277 2.Pdf
    Systematic and Applied Microbiology 42 (2019) 107–116 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm The diverse and extensive plant polysaccharide degradative apparatuses of the rumen and hindgut Prevotella species: A factor in their ubiquity? ∗ Tomazˇ Accetto , Gorazd Avgustinˇ University of Ljubljana, Biotechnical faculty, Animal Science Department, Groblje 3, 1230 Domzale,ˇ Slovenia a r t i c l e i n f o a b s t r a c t Article history: Although the Prevotella are commonly observed in high shares in the mammalian hindgut and rumen Received 2 August 2018 studies using NGS approach, the knowledge on their actual role, though postulated to lie in soluble fibre Received in revised form 2 October 2018 degradation, is scarce. Here we analyse in total 23, more than threefold of hitherto known rumen and Accepted 3 October 2018 hindgut Prevotella species and show that rumen/hindgut Prevotella generally possess extensive reper- toires of polysaccharide utilization loci (PULs) and carbohydrate active enzymes targeting various plant Keywords: polysaccharides. These PUL repertoires separate analysed Prevotella into generalists and specialists yet a Prevotella finer diversity among generalists is evident too, both in range of substrates targeted and in PUL combi- Rumen Hindgut nations targeting the same broad substrate classes. Upon evaluation of the shares of species analysed in this study in rumen metagenomes we found firstly, that they contributed significantly to total Prevotella Polysaccharide utilization locus CAZYme abundance though much of rumen Prevotella diversity may still be unknown. Secondly, the hindgut Pre- Metagenome votella species originally isolated in pigs and humans occasionally dominated among the Prevotella with surprisingly high metagenome read shares and were consistently found in rumen metagenome samples from sites as apart as New Zealand and Scotland.
    [Show full text]
  • Mycoplasma Orale “Types” 2 and 3, Respectively E
    INTERNATIONAL JOURNAL of SYSTEMATIC BACTERIOLOGY Vol. 24, No. 2 April 1974, p. 252-255 Printed in U.S.A. Copyright 0 1974 International Association of Microbiological Societies Proposal of Mycoplasma buccale nom. nov. and Mycoplasmafaucium nom. nov. for Mycoplasma orale “Types” 2 and 3, Respectively E. A. FREUNDT, D. TAYLOR-ROBINSON, R. H. PURCELL, R. M. CHANOCK, and F. T. BLACK Institute of Medical Microbiology, University of Aarhus, Aarhus, Denmark; MRC Clinical Research Centre, Harrow, Middlesex, England; and Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20014 Following recommendations made by the Subcommittee on the Taxonomy of Mycoplasrnatales of the International Committee on Systematic Bacteriology, it is proposed that Mycoplasma orale 2 and Mycoplasrna orale 3 be recognized as two separate species, Mycoplasrna buccale nom. nov. (type strain: CH20247; ATCC 23636) and Mycoplasrna fauciurn nom. nov. (type strain: DC-333; ATCC 25293), respectively. The general properties and distinctive characteristics of the newly named species are summarized. At present, three “types” of Mycoplasrna (22) be recognized as a species under the new orale are recognized: M. orale 1 Taylor- name Mycoplasrna buccale (L. adj. buccalis Robinson et al. 1964 (21), M. orale 2 Taylor- buccal), and (ii) Mycoplasrna orale 3 Fox et al. Robinson et al. 1965 (22), and M. orale 3 Fox 1969 (7) be recognized as a species under the et al. 1969 (7). However, the authors who new name Mycoplasma fauciurn (L. noun described the latter two “types” or “serotypes” fauces the throat; L. gen. pl. noun fauciurn of did, in fact, regard them as distinct new species throats).
    [Show full text]
  • A Broadly Distributed Toxin Family Mediates Contact-Dependent Antagonism Between Gram-Positive Bacteria
    1 A Broadly Distributed Toxin Family Mediates Contact-Dependent 2 Antagonism Between Gram-positive Bacteria 3 John C. Whitney1,†, S. Brook Peterson1, Jungyun Kim1, Manuel Pazos2, Adrian J. 4 Verster3, Matthew C. Radey1, Hemantha D. Kulasekara1, Mary Q. Ching1, Nathan P. 5 Bullen4,5, Diane Bryant6, Young Ah Goo7, Michael G. Surette4,5,8, Elhanan 6 Borenstein3,9,10, Waldemar Vollmer2 and Joseph D. Mougous1,11,* 7 1Department of Microbiology, School of Medicine, University of Washington, Seattle, 8 WA 98195, USA 9 2Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, 10 Newcastle University, Newcastle upon Tyne, NE2 4AX, UK 11 3Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA 12 4Michael DeGroote Institute for Infectious Disease Research, McMaster University, 13 Hamilton, ON, L8S 4K1, Canada 14 5Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, 15 ON, L8S 4K1, Canada 16 6Experimental Systems Group, Advanced Light Source, Berkeley, CA 94720, USA 17 7Northwestern Proteomics Core Facility, Northwestern University, Chicago, IL 60611, 18 USA 19 8Department of Medicine, Farncombe Family Digestive Health Research Institute, 20 McMaster University, Hamilton, ON, L8S 4K1, Canada 21 9Department of Computer Science and Engineering, University of Washington, Seattle, 22 WA 98195, USA 23 10Santa Fe Institute, Santa Fe, NM 87501, USA 24 11Howard Hughes Medical Institute, School of Medicine, University of Washington, 25 Seattle, WA 98195, USA 26 † Present address: Department of Biochemistry and Biomedical Sciences, McMaster 27 University, Hamilton, ON, L8S 4K1, Canada 28 * To whom correspondence should be addressed: J.D.M. 29 Email – [email protected] 30 Telephone – (+1) 206-685-7742 1 31 Abstract 32 The Firmicutes are a phylum of bacteria that dominate numerous polymicrobial 33 habitats of importance to human health and industry.
    [Show full text]
  • Targeting the Gut Microbiome in Allogeneic Hematopoietic Stem Cell Transplantation
    medRxiv preprint doi: https://doi.org/10.1101/2020.04.08.20058198; this version posted June 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Targeting the gut microbiome in allogeneic hematopoietic stem cell transplantation Marcel A. de Leeuw & Manuel X. Duval, GeneCreek List of Figures Contents 1 GM composition evolution across allo-HSCT . 2 I 2 Baseline GM composition and conditioning level . 3 NTRODUCTION 1 3 Top 10 variable importances estimated by the ran- dom survival forest models .............. 3 MATERIALS & METHODS 2 4 Biological safety level and aGvHD at onset . 3 DATA ANALYSIS .................. 2 5 Relative importance of regressors explaining the RESULTS 2 aGvHD status ...................... 3 OVERALL GM COMPOSITION EVOLUTION ACROSS 6 Co-exclusion by and co-occurrence with QPS species 4 ALLO-HSCT ................. 2 List of Tables CORRELATION BETWEEN CONDITIONING AND THE GM 2 BASELINE GM COMPOSITION AND SURVIVAL . 3 1 Prospective data sets used in the study . 1 AGVHD CASES, CONTROLS AND GM COMPOSITION 3 IMMUNO-MODULATING METABOLITES . 4 IN SILICO SCREENING OF THE ALLO-HSCT GM . 4 DISCUSSION 4 CONCLUSIONS 6 SUMMARY 6 DECLARATIONS 6 BIBLIOGRAPHY 7 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. Revised manuscript medRxiv preprint doi: https://doi.org/10.1101/2020.04.08.20058198; this version posted June 9, 2020.
    [Show full text]
  • Enterobacter Massiliensis Sp. Nov
    Standards in Genomic Sciences (2013) 7:399-412 DOI:10.4056/sigs.3396830 Non contiguous-finished genome sequence and descrip- tion of Enterobacter massiliensis sp. nov. Jean-Christophe Lagier1, Khalid El Karkouri1, Ajay Kumar Mishra1, Catherine Robert1, Didier Raoult1 and Pierre-Edouard Fournier1* 1Aix-Marseille Université, Faculté de médecine, Marseille, France *Corresponding author: Pierre-Edouard Fournier ([email protected]) Keywords: Enterobacter massiliensis, genome Enterobacter massiliensis strain JC163T sp. nov. is the type strain of E. massiliensis sp. nov., a new species within the genus Enterobacter. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. E. massiliensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,922,247 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 55.1% and contains 4,644 protein-coding and 80 RNA genes, including 5 rRNA genes. Introduction Enterobacter massiliensis strain JC163T (= CSUR Enterobacter spp. were isolated from the normal P161 = DSM 26120) is the type strain of E. fecal flora. massiliensis sp. nov. This bacterium is a Gram- negative, aerobic, flagellate, indole-positive bacil- Classification and features lus that was isolated from the feces of a healthy A stool sample was collected from a healthy 16- Senegalese patient in a study aiming at cultivating year-old male Senegalese volunteer patient living all bacterial species in human feces [1]. The cur- in Dielmo (rural village in the Guinean-Sudanian rent classification of prokaryotes, known as zone in Senegal), who was included in a research polyphasic taxonomy, relies on a combination of protocol.
    [Show full text]
  • Bismis-2016 Abstract Book
    BISMiS-2016 Abstract Book Third Meeting of Bergey's International Society for Microbial Systematics on Microbial Systematics and Metagenomics September 12-15, 2016 | Pune, INDIA PUNE UNIT Abstracts - Opening Address - Keynotes Abstract Book | BISMiS-2016 | Pune, India Opening Address TAXONOMY OF PROKARYOTES - NEW CHALLENGES IN A GLOBAL WORLD Peter Kämpfer* Justus-Liebig-University Giessen, HESSEN, Germany Email: [email protected] Systematics can be considered as a comprehensive science, because in science it is an essential aspect in comparing any two or more elements, whether they are genes or genomes, proteins or proteomes, biochemical pathways or metabolomes (just to list a few examples), or whole organisms. The development of high throughput sequencing techniques has led to an enormous amount of data (genomic and other “omic” data) and has also revealed an extensive diversity behind these data. These data are more and more used also in systematics and there is a strong trend to classify and name the taxonomic units in prokaryotic systematics preferably on the basis of sequence data. Unfortunately, the knowledge of the meaning behind the sequence data does not keep up with the tremendous increase of generated sequences. The extent of the accessory genome in any given cell, and perhaps the infinite extent of the pan-genome (as an aggregate of all the accessory genomes) is fascinating but it is an open question if and how these data should be used in systematics. Traditionally the polyphasic approach in bacterial systematics considers methods including both phenotype and genotype. And it is the phenotype that is (also) playing an essential role in driving the evolution.
    [Show full text]
  • Mycoplasma Pneumoniae Terminal Organelle
    MYCOPLASMA PNEUMONIAE TERMINAL ORGANELLE DEVELOPMENT AND GLIDING MOTILITY by BENJAMIN MICHAEL HASSELBRING (Under the Direction of Duncan Charles Krause) ABSTRACT With a minimal genome containing less than 700 open reading frames and a cell volume < 10% of that of model prokaryotes, Mycoplasma pneumoniae is considered among the smallest and simplest organisms capable of self-replication. And yet, this unique wall-less bacterium exhibits a remarkable level of cellular complexity with a dynamic cytoskeleton and a morphological asymmetry highlighted by a polar, membrane-bound terminal organelle containing an elaborate macromolecular core. The M. pneumoniae terminal organelle functions in distinct, and seemingly disparate cellular processes that include cytadherence, cell division, and presumably gliding motility, as individual cells translocate over surfaces with the cell pole harboring the structure engaged as the leading end. While recent years have witnessed a dramatic increase in the knowledge of protein interactions required for core stability and adhesin trafficking, the mechanism of M. pneumoniae gliding has not been defined nor have interdependencies between the various terminal organelle functions been assessed. The studies presented in the current volume describe the first genetic and molecular investigations into the location, components, architecture, and regulation of the M. pneumoniae gliding machinery. The data indicate that cytadherence and gliding motility are separable properties, and identify a subset of M. pneumoniae proteins contributing directly to the latter process. Characterizations of novel gliding-deficient mutants confirm that the terminal organelle contains the molecular gliding machinery, revealing that with the loss of a single terminal organelle cytoskeletal element, protein P41, terminal organelles detach from the cell body but retain gliding function.
    [Show full text]
  • Characterization of Antibiotic Resistance Genes in the Species of the Rumen Microbiota
    ARTICLE https://doi.org/10.1038/s41467-019-13118-0 OPEN Characterization of antibiotic resistance genes in the species of the rumen microbiota Yasmin Neves Vieira Sabino1, Mateus Ferreira Santana1, Linda Boniface Oyama2, Fernanda Godoy Santos2, Ana Júlia Silva Moreira1, Sharon Ann Huws2* & Hilário Cuquetto Mantovani 1* Infections caused by multidrug resistant bacteria represent a therapeutic challenge both in clinical settings and in livestock production, but the prevalence of antibiotic resistance genes 1234567890():,; among the species of bacteria that colonize the gastrointestinal tract of ruminants is not well characterized. Here, we investigate the resistome of 435 ruminal microbial genomes in silico and confirm representative phenotypes in vitro. We find a high abundance of genes encoding tetracycline resistance and evidence that the tet(W) gene is under positive selective pres- sure. Our findings reveal that tet(W) is located in a novel integrative and conjugative element in several ruminal bacterial genomes. Analyses of rumen microbial metatranscriptomes confirm the expression of the most abundant antibiotic resistance genes. Our data provide insight into antibiotic resistange gene profiles of the main species of ruminal bacteria and reveal the potential role of mobile genetic elements in shaping the resistome of the rumen microbiome, with implications for human and animal health. 1 Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. 2 Institute for Global Food Security, School of Biological
    [Show full text]
  • 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.
    [Show full text]