DOCSLIB.ORG

WO 2014/121301 Al 7 August 2014 (07.08.2014) P O P C T

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
WO 2014/121301 Al 7 August 2014 (07.08.2014) 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 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.
Load more

Recommended publications
  • Uncovering the Trimethylamine-Producing Bacteria of the Human Gut Microbiota Silke Rath1, Benjamin Heidrich1,2, Dietmar H
    Rath et al. Microbiome (2017) 5:54 DOI 10.1186/s40168-017-0271-9 RESEARCH Open Access Uncovering the trimethylamine-producing bacteria of the human gut microbiota Silke Rath1, Benjamin Heidrich1,2, Dietmar H. Pieper1 and Marius Vital1* Abstract Background: Trimethylamine (TMA), produced by the gut microbiota from dietary quaternary amines (mainly choline and carnitine), is associated with atherosclerosis and severe cardiovascular disease. Currently, little information on the composition of TMA producers in the gut is available due to their low abundance and the requirement of specific functional-based detection methods as many taxa show disparate abilities to produce that compound. Results: In order to examine the TMA-forming potential of microbial communities, we established databases for the key genes of the main TMA-synthesis pathways, encoding choline TMA-lyase (cutC) and carnitine oxygenase (cntA), using a multi-level screening approach on 67,134 genomes revealing 1107 and 6738 candidates to exhibit cutC and cntA, respectively. Gene-targeted assays enumerating the TMA-producing community by quantitative PCR and characterizing its composition via Illumina sequencing were developed and applied on human fecal samples (n =50) where all samples contained potential TMA producers (cutC was detected in all individuals, whereas only 26% harbored cntA) constituting, however, only a minor part of the total community (below 1% in most samples). Obtained cutC amplicons were associated with various taxa, in particular with Clostridium XIVa strains and Eubacterium sp. strain AB3007, though a bulk of sequences displayed low nucleotide identities to references (average 86% ± 7%) indicating that key human TMA producers are yet to be isolated.
    [Show full text]
  • Tratamiento Biológico Aerobio Para Aguas Residuales Con Elevada Conductividad Y Concentración De Fenoles
    PROGRAMA DE DOCTORADO EN INGENIERÍA Y PRODUCCIÓN INDUSTRIAL Tratamiento biológico aerobio para aguas residuales con elevada conductividad y concentración de fenoles TESIS DOCTORAL Presentada por: Eva Ferrer Polonio Dirigida por: Dr. José Antonio Mendoza Roca Dra. Alicia Iborra Clar Valencia Mayo 2017 AGRADECIMIENTOS La sabiduría popular, a la cual recurro muchas veces, dice: “Es de bien nacido ser agradecido”… pues sigamos su consejo, aquí van los míos. En primer lugar quiero agradecer a mis directores la confianza depositada en mí y a Depuración de Aguas del Mediterráneo, especialmente a Laura Pastor y Silvia Doñate, la dedicación e ilusión puestas en el proyecto. Durante el desarrollo de esta Tesis Doctoral he tenido la inmensa suerte de contar con un grupo de personas de las que he aprendido muchísimo y que de forma desinteresada han colaborado en este trabajo, enriqueciéndolo enormemente. Gracias al Dr. Jaime Primo Millo, del Instituto Agroforestal Mediterráneo de la Universitat Politècnica de València, por el asesoramiento recibido y por permitirme utilizar los equipos de cromatografía de sus instalaciones. También quiero dar un agradecimiento especial a una de las personas de su equipo de investigación, ya que sin su ayuda, tiempo y enseñanzas en los primeros análisis realizados con esta técnica, no me hubiera sido posible llevar a cabo esta tarea con tanta facilidad…gracias Dra. Nuria Cabedo Escrig. Otra de las personas con las que he tenido la suerte de colaborar ha sido la Dra. Blanca Pérez Úz, del Departamento de Microbiología III de la Facultad de Ciencias Biológicas de la Universidad Complutense de Madrid. Blanca, aunque no nos conocemos personalmente, tu profesionalidad y dedicación han permitido superar las barreras de la distancia…gracias.
    [Show full text]
  • The Isolation of Novel Lachnospiraceae Strains and the Evaluation of Their Potential Roles in Colonization Resistance Against Clostridium Difficile
    The isolation of novel Lachnospiraceae strains and the evaluation of their potential roles in colonization resistance against Clostridium difficile Diane Yuan Wang Honors Thesis in Biology Department of Ecology and Evolutionary Biology College of Literature, Science, & the Arts University of Michigan, Ann Arbor April 1st, 2014 Sponsor: Vincent B. Young, M.D., Ph.D. Associate Professor of Internal Medicine Associate Professor of Microbiology and Immunology Medical School Co-Sponsor: Aaron A. King, Ph.D. Associate Professor of Ecology & Evolutionary Associate Professor of Mathematics College of Literature, Science, & the Arts Reader: Blaise R. Boles, Ph.D. Assistant Professor of Molecular, Cellular and Developmental Biology College of Literature, Science, & the Arts 1 Table of Contents Abstract 3 Introduction 4 Clostridium difficile 4 Colonization Resistance 5 Lachnospiraceae 6 Objectives 7 Materials & Methods 9 Sample Collection 9 Bacterial Isolation and Selective Growth Conditions 9 Design of Lachnospiraceae 16S rRNA-encoding gene primers 9 DNA extraction and 16S ribosomal rRNA-encoding gene sequencing 10 Phylogenetic analyses 11 Direct inhibition 11 Bile salt hydrolase (BSH) detection 12 PCR assay for bile acid 7α-dehydroxylase detection 12 Tables & Figures Table 1 13 Table 2 15 Table 3 21 Table 4 25 Figure 1 16 Figure 2 19 Figure 3 20 Figure 4 24 Figure 5 26 Results 14 Isolation of novel Lachnospiraceae strains 14 Direct inhibition 17 Bile acid physiology 22 Discussion 27 Acknowledgments 33 References 34 2 Abstract Background: Antibiotic disruption of the gastrointestinal tract’s indigenous microbiota can lead to one of the most common nosocomial infections, Clostridium difficile, which has an annual cost exceeding $4.8 billion dollars.
    [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]
  • Clostridium Hathewayi Strain from a Continuous-flow Exclusion Chemostat Culture Derived from the Cecal Contents of a Feral Pig
    ARTICLE IN PRESS Anaerobe 13 (2007) 153–160 www.elsevier.com/locate/anaerobe Veterinary anaerobes and diseases Characterization of an antibiotic resistant Clostridium hathewayi strain from a continuous-flow exclusion chemostat culture derived from the cecal contents of a feral pig N. Ramlachana, R.C. Andersona,Ã, K. Andrewsa, G. Labanb,c, D.J. Nisbeta aUnited States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Food & Feed Safety Research Unit, 2881 F&B Road, College Station, TX 77845, USA bDepartment of Forestry and Natural Resources, Pfender Hall, 715 W State Street Purdue University, West Lafayette, IN, USA cCenter for the Environment, 503 Northwestern Avenue, Purdue University, West Lafayette, IN 47907, USA Received 8 March 2007; accepted 14 March 2007 Available online 23 March 2007 Abstract The chemostat model has been an important tool in studying intestinal microflora. To date, several competitive exclusion products have been developed from such studies as prophylactic treatment against pathogenic bacteria. A continuous-flow chemostat model of a feral pig was developed using inocula from the cecal contents of a wild boar caught in East Texas. Several strains of antibiotic-sensitive bacteria were isolated including Bacteroides, Lactobacillus, Enterococcus and Clostridium sp. This study reports on the characterization of a multidrug-resistant Clostridum hathewayi strain that was isolated from this feral pig’s cecal contents maintained in a continuous-flow chemostat system showing high resistance to carbapenems and macrolides (including the growth promoter tylosin). Clostridium hathewayi has been documented to be pathogenic to both humans and animals. Feral pigs may be an important source of pathogenic and antibiotic resistant bacteria and may pose potential risk to domestic species.
    [Show full text]
  • Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update
    GBE Revisiting the Evolution and Taxonomy of Clostridia,a Phylogenomic Update Pablo Cruz-Morales1,3, Camila A. Orellana1,GeorgeMoutafis2, Glenn Moonen2, Gonzalo Rincon2, Lars K. Nielsen1, and Esteban Marcellin1,* 1Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia 2Zoetis, Parkville, Victoria, Australia 3Present address: Joint BioEnergy Institute, Emeryville, CA *Corresponding author: E-mail: [email protected]. Accepted: May 6, 2019 Abstract Clostridium is a large genus of obligate anaerobes belonging to the Firmicutes phylum of bacteria, most of which have a Gram-positive cell wall structure. The genus includes significant human and animal pathogens, causative of potentially deadly diseases such as tetanus and botulism. Despite their relevance and many studies suggesting that they are not a monophyletic group, the taxonomy of the group has largely been neglected. Currently, species belonging to the genus are placed in the unnatural order defined as Clostridiales, which includes the class Clostridia. Here, we used genomic data from 779 strains to study the taxonomy and evolution of the group. This analysis allowed us to 1) confirm that the group is composed of more than one genus, 2) detect major differences between pathogens classified as a single species within the group of authentic Clostridium spp. (sensu stricto), 3) identify inconsistencies between taxonomy and toxin evolution that reflect on the pervasive misclassification of strains, and 4) identify differential traits within central metabolism of members of what has been defined earlier and confirmed by us as cluster I. Our analysis shows that the current taxonomic classification of Clostridium species hinders the prediction of functions and traits, suggests a new classification for this fascinating class of bacteria, and highlights the importance of phylogenomics for taxonomic studies.
    [Show full text]
  • Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks
    Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks Orland Gonzalez M¨unchen, 2009 Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks Orland Gonzalez Dissertation an der Fakult¨at f¨ur Mathematik, Informatik und Statistik der Ludwig-Maximilians-Universit¨at M¨unchen vorgelegt von Orland Gonzalez aus Manila M¨unchen, den 02.03.2009 Erstgutachter: Prof. Dr. Ralf Zimmer Zweitgutachter: Prof. Dr. Dieter Oesterhelt Tag der m¨undlichen Pr¨ufung: 21.01.2009 Contents Summary xiii Zusammenfassung xvi 1 Introduction 1 2 The Halophilic Archaea 9 2.1NaturalEnvironments............................. 9 2.2Taxonomy.................................... 11 2.3PhysiologyandMetabolism.......................... 14 2.3.1 Osmoadaptation............................ 14 2.3.2 NutritionandTransport........................ 16 2.3.3 Motility and Taxis ........................... 18 2.4CompletelySequencedGenomes........................ 19 2.5DynamicsofBlooms.............................. 20 2.6Motivation.................................... 21 3 The Metabolism of Halobacterium salinarum 23 3.1TheModelArchaeon.............................. 24 3.1.1 BacteriorhodopsinandOtherRetinalProteins............ 24 3.1.2 FlexibleBioenergetics......................... 26 3.1.3 Industrial Applications ......................... 27 3.2IntroductiontoMetabolicReconstructions.................. 27 3.2.1 MetabolismandMetabolicPathways................. 27 3.2.2 MetabolicReconstruction....................... 28 3.3Methods....................................
    [Show full text]
  • Clostridium Clostridioforme Reveals Species-Specific Genomic Properties and Numerous Putative Antibiotic Resistance Determinants
    Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants. Pierre Dehoux, Jean Christophe Marvaud, Amr Abouelleil, Ashlee M Earl, Thierry Lambert, Catherine Dauga To cite this version: Pierre Dehoux, Jean Christophe Marvaud, Amr Abouelleil, Ashlee M Earl, Thierry Lambert, et al.. Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species- specific genomic properties and numerous putative antibiotic resistance determinants.. BMCGe- nomics, BioMed Central, 2016, 17 (1), pp.819. 10.1186/s12864-016-3152-x. pasteur-01441074 HAL Id: pasteur-01441074 https://hal-pasteur.archives-ouvertes.fr/pasteur-01441074 Submitted on 19 Jan 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Dehoux et al. BMC Genomics (2016) 17:819 DOI 10.1186/s12864-016-3152-x RESEARCHARTICLE Open Access Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants Pierre Dehoux1, Jean Christophe Marvaud2, Amr Abouelleil3, Ashlee M. Earl3, Thierry Lambert2,4 and Catherine Dauga1,5* Abstract Background: Clostridium bolteae and Clostridium clostridioforme, previously included in the complex C.
    [Show full text]
  • Bacteria 1 Bacteria
    Bacteria 1 Bacteria Bacteria Escherichia coli aumentada 15.000 veces. Clasificación científica Dominio: Bacteria Filos Acidobacteria Actinobacteria Aquificae Bacteroidetes Chlamydiae Chlorobi Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres Firmicutes Fusobacteria Gemmatimonadetes Lentisphaerae Nitrospirae Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Verrucomicrobia Las bacterias son microorganismos unicelulares que presentan un tamaño de unos pocos micrómetros (entre 0,5 y 5 μm, por lo general) y diversas formas incluyendo esferas (cocos), barras (bacilos) y hélices (espirilos). Las bacterias son procariotas y, por lo tanto, a diferencia de las células eucariotas (de animales, plantas, hongos, etc.), no tienen el núcleo definido ni presentan, en general, orgánulos membranosos internos. Generalmente poseen una pared celular compuesta de peptidoglicano. Muchas bacterias disponen de flagelos o de otros sistemas de desplazamiento y son móviles. Del estudio de las bacterias se encarga la bacteriología, una rama de la microbiología. Las bacterias son los organismos más abundantes del planeta. Son ubicuas, se encuentran en todos los hábitats terrestres y acuáticos; crecen hasta en los más extremos como en los manantiales de aguas calientes y ácidas, en desechos radioactivos,[1] en las profundidades tanto del mar como de la corteza terrestre. Algunas bacterias pueden incluso sobrevivir en las condiciones extremas del espacio exterior. Se estima que se pueden encontrar en torno a 40 Bacteria 2 millones de células bacterianas en un gramo de tierra y un millón de células bacterianas en un mililitro de agua dulce. En total, se calcula que hay aproximadamente 5×1030 bacterias en el mundo.[2] Las bacterias son imprescindibles para el reciclaje de los elementos, pues muchos pasos importantes de los ciclos biogeoquímicos dependen de éstas.
    [Show full text]
  • Bacterial Communities Associated With
    BACTERIAL COMMUNITIES ASSOCIATED WITH NATURAL AND ANTHROPOGENIC PETROLEUM IMPACTED ANAEROBIC ENVIRONMENTS By JAMES PAUL DAVIS Bachelor of Science in Microbiology University of Oklahoma Norman, Oklahoma 2006 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY December, 2012 BACTERIAL COMMUNITIES ASSOCIATED WITH NATURAL AND ANTHROPOGENIC PETROLEUM IMPACTED ANAEROBIC ENVIRONMENTS Dissertation Approved: Dr. Mostafa S. Elshahed Dissertation Adviser Dr. Robert V. Miller Dr. Wouter D. Hoff Dr. Babu Z. Fathepure Dr. Ulrich Melcher Outside Committee Member Dr. Sheryl A. Tucker Dean of the Graduate College ii TABLE OF CONTENTS Table of contents .......................................................................................................... iii List of Tables .................................................................................................................v List of Figures .............................................................................................................. vi Preface ......................................................................................................................... vii Chapter Page I. CULTURE-INDEPENDENT MOLECULAR BIOLOGICAL APPROACHES IN MICROBIAL ECOLOGY .......................................................................................1 Microbial Ecology ...................................................................................................2 The
    [Show full text]
  • BMC Veterinary Research
    BMC Veterinary Research This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Effect of stoned olive pomace on rumen microbial communities and polyunsaturated fatty acids biohydrogenation: an in vitro study BMC Veterinary Research 2014, 10:271 doi:10.1186/s12917-014-0271-y Grazia Pallara ([email protected]) Arianna Buccioni ([email protected]) Roberta Pastorelli ([email protected]) Sara Minieri ([email protected]) Marcello Mele ([email protected]) Stefano Rapaccini ([email protected]) Anna Messini ([email protected]) Mariano Pauselli ([email protected]) Maurizio Servili ([email protected]) Luciana Giovannetti ([email protected]) Carlo Viti ([email protected]) Sample ISSN 1746-6148 Article type Research article Submission date 4 March 2014 Acceptance date 6 November 2014 Article URL http://www.biomedcentral.com/1746-6148/10/271 Like all articles in BMC journals, this peer-reviewed article can be downloaded, printed and distributed freely for any purposes (see copyright notice below). Articles in BMC journals are listed in PubMed and archived at PubMed Central. For information about publishing your research in BMC journals or any BioMed Central journal, go to http://www.biomedcentral.com/info/authors/ © Pallara et al.; licensee BioMed Central Ltd This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
    [Show full text]
  • 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.
    [Show full text]