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High-Quality Draft Genome Sequences of Five Anaerobic Oral Bacteria and Description of Peptoanaerobacter Stomatis Gen
Sizova et al. Standards in Genomic Sciences (2015) 10:37 DOI 10.1186/s40793-015-0027-8 EXTENDED GENOME REPORT Open Access High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae Maria V. Sizova1, Amanda Chilaka1, Ashlee M. Earl2, Sebastian N. Doerfert1, Paul A. Muller1, Manolito Torralba3, Jamison M. McCorrison3, A. Scott Durkin3, Karen E. Nelson3 and Slava S. Epstein1* Abstract Here we report a summary classification and the features of five anaerobic oral bacteria from the family Peptostreptococcaceae. Bacterial strains were isolated from human subgingival plaque. Strains ACC19a, CM2, CM5, and OBRC8 represent the first known cultivable members of “yet uncultured” human oral taxon 081; strain AS15 belongs to “cultivable” human oral taxon 377. Based on 16S rRNA gene sequence comparisons, strains ACC19a, CM2, CM5, and OBRC8 are distantly related to Eubacterium yurii subs. yurii and Filifactor alocis, with 93.2 – 94.4 % and 85.5 % of sequence identity, respectively. The genomes of strains ACC19a, CM2, CM5, OBRC8 and AS15 are 2,541,543; 2,312,592; 2,594,242; 2,553,276; and 2,654,638 bp long. The genomes are comprised of 2277, 1973, 2325, 2277, and 2308 protein-coding genes and 54, 57, 54, 36, and 28 RNA genes, respectively. Based on the distinct characteristics presented here, we suggest that strains ACC19a, CM2, CM5, and OBRC8 represent a novel genus and species within the family Peptostreptococcaceae, for which we propose the name Peptoanaerobacter stomatis gen. nov., sp. nov. The type strain is strain ACC19aT (=HM-483T; =DSM 28705T;=ATCC BAA-2665T). -
Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis
International Journal of Molecular Sciences Review Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis David Johane Machate 1, Priscila Silva Figueiredo 2 , Gabriela Marcelino 2 , Rita de Cássia Avellaneda Guimarães 2,*, Priscila Aiko Hiane 2 , Danielle Bogo 2, Verônica Assalin Zorgetto Pinheiro 2, Lincoln Carlos Silva de Oliveira 3 and Arnildo Pott 1 1 Graduate Program in Biotechnology and Biodiversity in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] (D.J.M.); [email protected] (A.P.) 2 Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; pri.fi[email protected] (P.S.F.); [email protected] (G.M.); [email protected] (P.A.H.); [email protected] (D.B.); [email protected] (V.A.Z.P.) 3 Chemistry Institute, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-67-3345-7416 Received: 9 March 2020; Accepted: 27 March 2020; Published: 8 June 2020 Abstract: Long-term high-fat dietary intake plays a crucial role in the composition of gut microbiota in animal models and human subjects, which affect directly short-chain fatty acid (SCFA) production and host health. This review aims to highlight the interplay of fatty acid (FA) intake and gut microbiota composition and its interaction with hosts in health promotion and obesity prevention and its related metabolic dysbiosis. -
Sporulation Evolution and Specialization in Bacillus
bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Research article From root to tips: sporulation evolution and specialization in Bacillus subtilis and the intestinal pathogen Clostridioides difficile Paula Ramos-Silva1*, Mónica Serrano2, Adriano O. Henriques2 1Instituto Gulbenkian de Ciência, Oeiras, Portugal 2Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal *Corresponding author: Present address: Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands Phone: 0031 717519283 Email: [email protected] (Paula Ramos-Silva) Running title: Sporulation from root to tips Keywords: sporulation, bacterial genome evolution, horizontal gene transfer, taxon- specific genes, Bacillus subtilis, Clostridioides difficile 1 bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Abstract Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of a highly resistant, dormant spore. Spores allow environmental persistence, dissemination and for pathogens, are infection vehicles. In both the model Bacillus subtilis, an aerobic species, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. -
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. -
A Survey of Carbon Fixation Pathways Through a Quantitative Lens
Journal of Experimental Botany, Vol. 63, No. 6, pp. 2325–2342, 2012 doi:10.1093/jxb/err417 Advance Access publication 26 December, 2011 REVIEW PAPER A survey of carbon fixation pathways through a quantitative lens Arren Bar-Even, Elad Noor and Ron Milo* Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel * To whom correspondence should be addressed. E-mail: [email protected] Received 15 August 2011; Revised 4 November 2011; Accepted 8 November 2011 Downloaded from Abstract While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it http://jxb.oxfordjournals.org/ has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures at Weizmann Institute of Science on July 3, 2016 of yet unknown carbon fixation pathways are suggested and discussed. -
Genetics of Human Gut Microbiome Composition
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.26.173724; this version posted June 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Genetics of human gut microbiome composition Authors: Alexander Kurilshikov1,†, Carolina Medina-Gomez2,3,†, Rodrigo Bacigalupe4,5,†, Djawad Radjabzadeh2,†, Jun Wang4,5,6,†, Ayse Demirkan1,7§, Caroline I. Le Roy8,§, Juan Antonio 5 Raygoza Garay9,10,§, Casey T. Finnicum11,§, Xingrong Liu12,§, Daria V. Zhernakova1,§, Marc Jan Bonder1,§, Tue H. Hansen13, Fabian Frost14, Malte C. Rühlemann15, Williams Turpin9,10, Jee- Young Moon16, Han-Na Kim17,18, Kreete Lüll19, Elad Barkan20, Shiraz A. Shah21, Myriam Fornage22,23, Joanna Szopinska-Tokov24, Zachary D. Wallen25, Dmitrii Borisevich13, Lars Agreus26, Anna Andreasson27, Corinna Bang15, Larbi Bedrani9, Jordana T. Bell8, Hans 10 Bisgaard21, Michael Boehnke28, Dorret I. Boomsma29, Robert D. Burk16,30,31, Annique Claringbould1, Kenneth Croitoru9,10, Gareth E. Davies11,29, Cornelia M. van Duijn32,33, Liesbeth Duijts3,34, Gwen Falony4,5, Jingyuan Fu1,35, Adriaan van der Graaf1, Torben Hansen13, Georg Homuth36, David A. Hughes37,38, Richard G. Ijzerman39, Matthew A. Jackson7,40, Vincent W.V. Jaddoe3,32, Marie Joossens4,5, Torben Jørgensen41, Daniel Keszthelyi42,43, Rob Knight44,45,46, 15 Markku Laakso47, Matthias Laudes48, Lenore J. Launer49, Wolfgang Lieb50, Aldons J. Lusis51,52, Ad A.M. Masclee42,43, Henriette A. Moll34, Zlatan Mujagic42,43, Qi Qibin16, Daphna Rothschild20, Hocheol Shin53,54, Søren J. Sørensen55, Claire J. -
UK Standards for Microbiology Investigations
UK Standards for Microbiology Investigations Identification of Anaerobic Cocci Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 14 | Issue no: 3 | Issue date: 04.02.15 | Page: 1 of 29 © Crown copyright 2015 Identification of Anaerobic Cocci Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website https://www.gov.uk/uk- standards-for-microbiology-investigations-smi-quality-and-consistency-in-clinical- laboratories. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for-microbiology-investigations- steering-committee). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories UK Standards for Microbiology Investigations are produced in association with: Logos correct at time of publishing. Bacteriology – Identification | ID 14 | Issue no: 3 | Issue date: 04.02.15 | Page: 2 of 29 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Anaerobic Cocci Contents ACKNOWLEDGMENTS ......................................................................................................... -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge; -
MICRO-ORGANISMS and RUMINANT DIGESTION: STATE of KNOWLEDGE, TRENDS and FUTURE PROSPECTS Chris Mcsweeney1 and Rod Mackie2
BACKGROUND STUDY PAPER NO. 61 September 2012 E Organización Food and Organisation des Продовольственная и cельскохозяйственная de las Agriculture Nations Unies Naciones Unidas Organization pour организация para la of the l'alimentation Объединенных Alimentación y la United Nations et l'agriculture Наций Agricultura COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE MICRO-ORGANISMS AND RUMINANT DIGESTION: STATE OF KNOWLEDGE, TRENDS AND FUTURE PROSPECTS Chris McSweeney1 and Rod Mackie2 The content of this document is entirely the responsibility of the authors, and does not necessarily represent the views of the FAO or its Members. 1 Commonwealth Scientific and Industrial Research Organisation, Livestock Industries, 306 Carmody Road, St Lucia Qld 4067, Australia. 2 University of Illinois, Urbana, Illinois, United States of America. This document is printed in limited numbers to minimize the environmental impact of FAO's processes and contribute to climate neutrality. Delegates and observers are kindly requested to bring their copies to meetings and to avoid asking for additional copies. Most FAO meeting documents are available on the Internet at www.fao.org ME992 BACKGROUND STUDY PAPER NO.61 2 Table of Contents Pages I EXECUTIVE SUMMARY .............................................................................................. 5 II INTRODUCTION ............................................................................................................ 7 Scope of the Study ........................................................................................................... -
Xylella Fastidiosa Biologia I Epidemiologia
Xylella fastidiosa Biologia i epidemiologia Emili Montesinos Seguí Catedràtic de Producció Vegetal (Patologia Vegetal) Universitat de Girona [email protected] www.youtube.com/watch?v=sur5VzJslcM Xylella fastidiosa, un patogen que no és nou Newton B. Pierce (1890s, USA) Agrobacterium tumefaciens Chlamydiae Proteobacteria Bartonella bacilliformis Campylobacter coli Bartonella henselae CDC Chlamydophila psittaci Campylobacter fetus Bartonella quintana Bacteroides fragilis CDC Brucella melitensis Bacteroidetes Chlamydophila pneumoniae Campylobacter hyointestinalis Bacteroides thetaiotaomicron Campylobacter jejuni CDC Brucella melitensis biovar Abortus CDC Chlamydia trachomatis Capnocytophaga canimorus Campylobacter lari CDC Brucella melitensis biovar Canis Chryseobacterium meningosepticum Parachlamydia acanthamoebae Campylobacter upsaliensis CDC Brucella melitensis biovar Suis Helicobacter pylori Candidatus Liberibacter africanus CDC Candidatus Liberibacter asiaticus Borrelia burgdorferi Epsilon Borrelia hermsii CDC Anaplasma phagocytophilum Borrelia recurrentis Alpha CDC Ehrlichia canis Spirochetes Borrelia turicatae CDC Ehrlichia chaffeensis Eikenella corrodens Leptospira interrogans CDC Ehrlichia ewingii CDC CDC Neisseria gonorrhoeae Treponema pallidum Ehrlichia ruminantium CDC Neisseria meningitidis CDC Neorickettsia sennetsu Spirillum minus Orientia tsutsugamushi Fusobacterium necrophorum Beta Fusobacteria CDC Bordetella pertussis Rickettsia conorii Streptobacillus moniliformis Burkholderia cepacia Rickettsia -
C. Difficile: Trials, Treatments and New Guidelines
C. difficile: trials, treatments and new guidelines CONTENTS REVIEW: Vulnerability of long-term care facility residents to Clostridium difficile infection due to microbiome disruptions FUTURE MICROBIOLOGY Vol. 13, No. 13 INTERVIEW: The gut microbiome and the potentials of probiotics: an interview with Simon Gaisford FUTURE MICROBIOLOGY Vol. 14, No. 4 REVIEW: Clostridioides (Clostridium) difficile infection: current and alternative therapeutic strategies FUTURE MICROBIOLOGY Vol. 13, No. 4 EDITORIAL: Microbiome therapeutics – the pipeline for C. difficile infection INTERVIEW: Updates on C. difficile: from clinical trials and guidelines – an interview with Yoav Golan NEWS ARTICLE: Could common painkillers promote C. difficile infection? Review For reprint orders, please contact: [email protected] Vulnerability of long-term care facility residents to Clostridium difficile infection due to microbiome disruptions Beth Burgwyn Fuchs*,1, Nagendran Tharmalingam1 & Eleftherios Mylonakis**,1 1Rhode Island Hospital, Alpert Medical School & Brown University, Providence, Rhode Island 02903 *Author for correspondence: Tel.: +401 444 7309; Fax: +401 606 5624; Helen [email protected]; **Author for correspondence: Tel.: +401 444 7845; Fax: +401 444 8179; [email protected] Aging presents a significant risk factor for Clostridium difficile infection (CDI). A disproportionate number of CDIs affect individuals in long-term care facilities compared with the general population, likely due to the vulnerable nature of the residents and shared environment. Review of the literature cites a number of underlying medical conditions such as the use of antibiotics, proton pump inhibitors, chemotherapy, renal disease and feeding tubes as risk factors. These conditions alter the intestinal environment through direct bacterial killing, changes to pH that influence bacterial stabilities or growth, or influence nutrient availability that direct population profiles. -
The Clostridioides Difficile Species Problem: Global Phylogenomic 2 Analysis Uncovers Three Ancient, Toxigenic, Genomospecies
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.21.307223; this version posted September 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 The Clostridioides difficile species problem: global phylogenomic 2 analysis uncovers three ancient, toxigenic, genomospecies 3 Daniel R. Knight1, Korakrit Imwattana2,3, Brian Kullin4, Enzo Guerrero-Araya5,6, Daniel Paredes- 4 Sabja5,6,7, Xavier Didelot8, Kate E. Dingle9, David W. Eyre10, César Rodríguez11, and Thomas V. 5 Riley1,2,12,13* 6 1 Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia. 2 School of 7 Biomedical Sciences, the University of Western Australia, Nedlands, Western Australia, Australia. 3 Department of 8 Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand. 4 Department of Pathology, University 9 of Cape Town, Cape Town, South Africa. 5 Microbiota-Host Interactions and Clostridia Research Group, Facultad de 10 Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile. 6 Millenium Nucleus in the Biology of Intestinal 11 Microbiota, Santiago, Chile. 7Department of Biology, Texas A&M University, College Station, TX, 77843, USA. 8 School 12 of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK. 9 Nuffield Department of Clinical 13 Medicine, University of Oxford, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical 14 Research Centre, John Radcliffe Hospital, Oxford, UK. 10 Big Data Institute, Nuffield Department of Population Health, 15 University of Oxford, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, 16 John Radcliffe Hospital, Oxford, UK.