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11 results on '"MESH: Classification"'

1. SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

Author

Pierre Lechat, Laurence Motreff, Amine Ghozlane, Stevenn Volant, Christophe Malabat, Perrine Woringer, Pascal Campagne, Sean Kennedy, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Pôle Biomics (C2RT), Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris] (IP)-Institut Pasteur [Paris] (IP), Institut Pasteur, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]-Institut Pasteur [Paris]

Subjects
Source code, Computer science, Statistics as Topic, Biochemistry, Workflow, MESH: Body Fluids, Feces, User-Computer Interface, 0302 clinical medicine, Structural Biology, RNA, Ribosomal, 16S, lcsh:QH301-705.5, media_common, Visualization, 0303 health sciences, Applied Mathematics, Microbiota, MESH: Feces, Classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Body Fluids, MESH: RNA, Ribosomal, 16S, MESH: Classification, MESH: Internet, 030220 oncology & carcinogenesis, Child, Preschool, Web application, lcsh:R858-859.7, DNA microarray, MESH: Metagenomics, media_common.quotation_subject, education, Differential analysis, lcsh:Computer applications to medicine. Medical informatics, Set (abstract data type), MESH: Workflow, 03 medical and health sciences, MESH: Software, Humans, MESH: Microbiota, Microbiome, Molecular Biology, MESH: Statistics as Topic, 030304 developmental biology, MESH: User-Computer Interface, User Friendly, Internet, Information retrieval, MESH: Humans, MESH: Child, Preschool, MESH: Metagenome, 16S ribosomal RNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, lcsh:Biology (General), Metagenomics, Container (abstract data type), Metagenome, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software
Abstract

Background Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills. Results Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at http://shaman.pasteur.fr/, and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at https://github.com/aghozlane/shaman. Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis. Conclusions With SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.

Published
2020
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2. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)

Author

Walker, Peter J, Siddell, Stuart G, Lefkowitz, Elliot J, Mushegian, Arcady R, Adriaenssens, Evelien M, Alfenas-Zerbini, Poliane, Davison, Andrew J, Dempsey, Donald M, Dutilh, Bas E, García, María Laura, Harrach, Balázs, Harrison, Robert L, Hendrickson, R Curtis, Junglen, Sandra, Knowles, Nick J, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Łobocka, Małgorzata, Nibert, Max L, Oksanen, Hanna M, Orton, Richard J, Robertson, David L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B, Suzuki, Nobuhiro, Van Dooerslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Zerbini, Francisco Murilo, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Instituto de Higiene e Medicina Tropical (IHMT), Global Health and Tropical Medicine (GHTM), TB, HIV and opportunistic diseases and pathogens (THOP), University of Queensland [Brisbane], University of Bristol [Bristol], University of Alabama at Birmingham [ Birmingham] (UAB), National Science Foundation [Arlington] (NSF), Quadram Institute Biosciences, Universidade Federal de Vicosa (UFV), MRC - University of Glasgow Centre for Virus Research, Utrecht University [Utrecht], Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Institute for Veterinary Medical Research [Budapest] (AOTI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Invasive Insect Biocontrol and Behavior Laboratory [Beltsville, USA], USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Institute for Animal Health, the Pirbright Institute, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Centers for Disease Control and Prevention, Polish Academy of Sciences (PAN), Harvard Medical School [Boston] (HMS), University of Helsinki, Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), UOS Torino, Mississippi State University [Mississippi], University of Oxford [Oxford], Okayama University, University of Arizona, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Arizona State University [Tempe] (ASU), E.M.A. gratefully acknowledges funding by the U.K. Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. A.J.D. is supported by the U.K. Medical Research Council (MC_UU_12014/3). B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004. B.H. is supported by the National Research, Development and Innovation Office—NKFIH (NN128309). N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. A.R.M. is a Program Director at the U.S. National Science Foundation (NSF), the statements and opinions expressed herein are made in a personal capacity and do not constitute endorsement by NSF or the government of the United States. H.M.O was supported by the University of Helsinki and Academy of Finland by funding for FINStruct and Instruct Centre FI, part of Biocenter Finland and Instruct-ERIC. D.L.R. is supported by the U.K. Medical Research Council (MC_UU_1201412). R.J.O. and D.B.S. are supported by the Wellcome Trust (WT108418AIA). S.S. acknowledges partial support from the Special Research Initiative (MAFES), Mississippi State University, and from the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. Except for Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton and Donald B. Smith, the authors were members of the ICTV Executive Committee during the relevant period. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services, or of the institutions and companies affiliated with the authors., Sub Bioinformatics, Theoretical Biology and Bioinformatics, Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), The Pirbright Institute, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), University of Oxford, and Molecular and Integrative Biosciences Research Programme

Subjects
International Cooperation, education, virus, Viroids/classification, Viruses, Unclassified/classification, MESH: Viruses, ICTV, 03 medical and health sciences, SDG 17 - Partnerships for the Goals, SDG 3 - Good Health and Well-being, Virology, Taverne, SDG 14 - Life Below Water, MESH: Phylogeny, Phylogeny, Taxonomy, 030304 developmental biology, SDG 15 - Life on Land, 11832 Microbiology and virology, 0303 health sciences, Unclassified/classification, Code, 030306 microbiology, Viruses/classification, General Medicine, Classification, Viroids, 3. Good health, MESH: Viroids, MESH: Classification, MESH: International Cooperation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viruses, MESH: Viruses, Unclassified, Viruses, Unclassified, Classification/methods
Abstract

Funding Information: E.M.A. gratefully acknowledges funding by the U.K. Biotechnology and Biological Sciences Research Council (BBSRC); this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. A.J.D. is supported by the U.K. Medical Research Council (MC_UU_12014/3). B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004. B.H. is supported by the National Research, Development and Innovation Office—NKFIH (NN128309). N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. A.R.M. is a Program Director at the U.S. National Science Foundation (NSF); the statements and opinions expressed herein are made in a personal capacity and do not constitute endorsement by NSF or the government of the United States. H.M.O was supported by the University of Helsinki and Academy of Finland by funding for FINStruct and Instruct Centre FI, part of Biocenter Finland and Instruct-ERIC. D.L.R. is supported by the U.K. Medical Research Council (MC_UU_1201412). R.J.O. and D.B.S. are supported by the Wellcome Trust (WT108418AIA). S.S. acknowledges partial support from the Special Research Initiative (MAFES), Mississippi State University, and from the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. Except for Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton and Donald B. Smith, the authors were members of the ICTV Executive Committee during the relevant period. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services, or of the institutions and companies affiliated with the authors. Publisher Copyright: © 2021, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply. This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2021. The entire ICTV was invited to vote on 290 taxonomic proposals approved by the ICTV Executive Committee at its meeting in October 2020, as well as on the proposed revision of the International Code of Virus Classification and Nomenclature (ICVCN). All proposals and the revision were ratified by an absolute majority of the ICTV members. Of note, ICTV mandated a uniform rule for virus species naming, which will follow the binomial 'genus-species' format with or without Latinized species epithets. The Study Groups are requested to convert all previously established species names to the new format. ICTV has also abolished the notion of a type species, i.e., a species chosen to serve as a name-bearing type of a virus genus. The remit of ICTV has been clarified through an official definition of ‘virus’ and several other types of mobile genetic elements. The ICVCN and ICTV Statutes have been amended to reflect these changes. publishersversion inpress

Published
2021
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3. Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)

Author

Walker, Peter J, Siddell, Stuart G, Lefkowitz, Elliot J, Mushegian, Arcady R, Adriaenssens, Evelien M, Dempsey, Donald M, Dutilh, Bas E, Harrach, Balázs, Harrison, Robert L, Hendrickson, R Curtis, Junglen, Sandra, Knowles, Nick J, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Nibert, Max, Orton, Richard J, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B, Varsani, Arvind, Zerbini, Francisco Murilo, Davison, Andrew J, Sub Bioinformatics, Theoretical Biology and Bioinformatics, University of Queensland [Brisbane], University of Bristol [Bristol], University of Alabama at Birmingham [ Birmingham] (UAB), Division of Molecular and Cellular Biosciences [Alexandria, USA] (MCB), National Science Foundation [Arlington] (NSF), Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Utrecht University [Utrecht], Hungarian Academy of Sciences (MTA), United States Department of Agriculture (USDA), Humboldt University Of Berlin, The Pirbright Institute, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), National Institutes of Health [Bethesda] (NIH), Harvard Medical School [Boston] (HMS), MRC - University of Glasgow Centre for Virus Research, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], University of Oxford, Arizona State University [Tempe] (ASU), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), The authors declare no conflicts of interest. A.R.M. is a Program Director at the U.S. National Science Foundation (NSF), the statements and opinions expressed herein are made in a personal capacity and do not constitute endorsement by NSF or the government of the United States. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. This work was supported in part through Laulima Government Solutions, LLC’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 and European Research Council (ERC) Consolidator grant 865694: DiversiPHI. B.H. is partially supported by National Research, Development and Innovation Office – NKFIH, NN128309. S.S. acknowledges partial support from Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. E.M.A. was funded by the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. S.J. is supported by the Federal Ministry of Education and Research (BMBF) under project number 01KI1716 as part of the Research Network Zoonotic Infectious Diseases. FMZ is partially supported by CAPES (Finance Code 001). None of the work reported involved research on human participants or animals. All authors have contributed to this work and agreed to its publication. Except for Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton and Donald B. Smith, the authors were members of the ICTV Executive Committee during the relevant period., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), Sub Bioinformatics, Theoretical Biology and Bioinformatics, Humboldt University of Berlin, Institute for Animal Health, the Pirbright Institute, Institut Pasteur [Paris], Consiglio Nazionale delle Ricerche (CNR), University of Oxford [Oxford], and Universidade Federal de Vicosa (UFV)

Subjects
0303 health sciences, MESH: Terminology as Topic, 030306 microbiology, education, General Medicine, Biology, no key words, Virology, Executive committee, Statute, MESH: Viruses, 03 medical and health sciences, MESH: Classification, Law, Taverne, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Classification methods, Taxonomy (biology), Virus classification, health care economics and organizations, MESH: Virology, 030304 developmental biology
Abstract

International audience; This article reports the changes to virus classification and taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2020. The entire ICTV was invited to vote on 206 taxonomic proposals approved by the ICTV Executive Committee at its meeting in July 2019, as well as on the proposed revision of the ICTV Statutes. All proposals and the revision of the Statutes were approved by an absolute majority of the ICTV voting membership. Of note, ICTV has approved a proposal that extends the previously established realm Riboviria to encompass nearly all RNA viruses and reverse-transcribing viruses, and approved three separate proposals to establish three realms for viruses with DNA genomes.

Published
2020
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4. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Author

Simon Roux, J. Rodney Brister, Ho Bin Jang, Olivier Zablocki, Mart Krupovic, Jens H. Kuhn, Evelien M. Adriaenssens, Matthew B. Sullivan, Andrew M. Kropinski, Rob Lavigne, Dann Turner, Benjamin Bolduc, Ohio State University [Columbus] (OSU), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), DOE Joint Genome Institute [Walnut Creek], U.S. Department of Energy [Washington] (DOE), Institute of Integrative Biology [Liverpool, UK], University of Liverpool, Quadram Institute, National Center for Biotechnology Information (NCBI), National Institutes of Health [Bethesda] (NIH), Ontario Veterinary College [Univ. Guelph, Canada], University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Faculty of BioScience Engineering [KU Leuven, Belgium], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of the West of England [Bristol] (UWE Bristol), High-performance computational support was provided as an award from the Ohio Supercomputer Center to M.B.S. Funding was provided in part by the Department of Energy’s Genome Sciences Program Soil Microbiome Scientific Focus Area award (no. SCW1632) to Lawrence Livermore National Laboratory, NSF Biological Oceanography awards (OCE no. 1536989 and OCE no. 1756314), and a Gordon and Betty Moore Foundation Investigator Award (no. 3790) to M.B.S. Funding was provided to J.R.B. by the Intramural Research Program of the National Institutes of Health (NIH) National Library of Medicine. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract DE-AC02-05CH11231 to S.R. This work was funded in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract no. HHSN272200700016I to J.H.K. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors., We thank L. Bollinger, G. Trubl and I. Tolstoy for their comments on improving the manuscript, as well as Z.-Q. You for helping push the network analytics., Biotechnology and Biological Sciences Research Council (BBSRC), and Institut Pasteur [Paris] (IP)

Subjects
MESH: Genome, Viral/genetics, Classification and taxonomy, MESH: Viruses/classification, MESH: Gene Regulatory Networks/genetics, Applied Microbiology and Biotechnology, Genome, 0302 clinical medicine, RefSeq, TOOL, Bacteriophages, Gene Regulatory Networks, Viral, MESH: Phylogeny, Phylogeny, 0303 health sciences, MESH: Metagenomics, Classification, MESH: Classification, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Molecular Medicine, ICTV BACTERIAL, POPULATIONS, Taxonomy (biology), MESH: Prokaryotic Cells/virology, MESH: Viruses/genetics, Centre for Research in Biosciences, MESH: Bacteriophages/genetics, Life Sciences & Biomedicine, Biotechnology, Biomedical Engineering, Bioengineering, PHAGE, Computational biology, Genome, Viral, Biology, CLASSIFICATION, 03 medical and health sciences, MD Multidisciplinary, Human virome, Virus classification, 030304 developmental biology, virus classification, archaeal and bacterial virus taxonomy, scalable framework, gene-sharing networks, Science & Technology, ARCHAEAL VIRUSES, Hierarchical clustering, Computational biology and bioinformatics, Prokaryotic Cells, MESH: Metagenome/genetics, Biotechnology & Applied Microbiology, Metagenomics, EVOLUTIONARY, Metagenome, UPDATE, ECOGENOMICS, Bacterial virus, 030217 neurology & neurosurgery, Software, GENERATION
Abstract

Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification. ispartof: NATURE BIOTECHNOLOGY vol:37 issue:6 pages:632-+ ispartof: location:United States status: published

Published
2019
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5. The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

Author

Simonetta Gribaldo, Vincent Daubin, Anthony M. Poole, Patrick Forterre, Céline Brochier-Armanet, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Stockholm University, University of Canterbury [Christchurch], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), A.M.P. is a Royal Swedish Academy of Sciences Research Fellow supported by a grant from the Knut and Alice Wallenberg Foundation. V.D. is supported by the grants 'Phylariane', 'Ecogenome' and 'Living Deep' from the French ANR (National Agency for Research). C.B.A. is supported by an Action Thématique et Incitative sur Programme (ATIP) of the French Centre National de la Recherche Scientifique (CNRS)., ANR-08-BLAN-0090,EcoGenome,From a genomic species definition toward an Ecological Species Concept for bacteria(2008), ANR-10-BLAN-1725,Living Deep,Bases génomiques et moléculaires de la piézophilie chez Pyrococcus yayanosii CH1, un piézophile obligatoire(2010), and Institut Pasteur [Paris] (IP)

Subjects
0303 health sciences, General Immunology and Microbiology, 030306 microbiology, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Lineage (evolution), Tree of life (biology), MESH: Biological Evolution, Context (language use), Biology, biology.organism_classification, Microbiology, MESH: Bacteria, MESH: Classification, MESH: Eukaryota, 03 medical and health sciences, Infectious Diseases, Evolutionary biology, MESH: Archaea, MESH: Genome, 030304 developmental biology, Ancestor, Archaea
Abstract

The origin of eukaryotes and their evolutionary relationship with the Archaea is a major biological question and the subject of intense debate. In the context of the classical view of the universal tree of life, the Archaea and the Eukarya have a common ancestor, the nature of which remains undetermined. Alternative views propose instead that the Eukarya evolved directly from a bona fide archaeal lineage. Several recent large-scale phylogenomic studies using an array of approaches are divided in supporting either one or the other scenario, despite analysing largely overlapping data sets of universal genes. We examine the reasons for such a lack of consensus and consider how alternative approaches may enable progress in answering this fascinating and as-yet-unresolved question.

Published
2010
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6. Four years of DNA barcoding: Current advances and prospects

Author

Lise Frézal, Raphaël Leblois, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Populations, École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), and École Pratique des Hautes Études (EPHE)

Subjects
0106 biological sciences, MESH: Sequence Analysis, DNA, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Barcode, 01 natural sciences, DNA barcoding, law.invention, law, MESH: DNA Fingerprinting, Species identification, MESH: Animals, DNA taxonomy, 0303 health sciences, Animal life, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Classification, DNA Barcoding, MESH: Classification, Infectious Diseases, Cytochrome c oxidase, Microbiology (medical), Cytochrome C Oxidase Subunit 1, Zoology, Biology, DNA, Mitochondrial, International species databank, 010603 evolutionary biology, Microbiology, COI, 03 medical and health sciences, Species Specificity, DNA barcode, Genetics, Animals, MESH: Species Specificity, Dna taxonomy, Animal species, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Electronic Data Processing, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], MESH: DNA, Mitochondrial, Sequence Analysis, DNA, DNA Fingerprinting, Evolutionary biology, Classification methods, MESH: Automatic Data Processing, BOLD
Abstract

International audience; Research using cytochrome c oxidase barcoding techniques on zoological specimens was initiated by Hebert et al. [Hebert, P.D.N., Ratnasingham, S., deWaard, J.R., 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. B 270, S96-S99]. By March 2004, the Consortium for the Barcode of Life started to promote the use of a standardized DNA barcoding approach, consisting of identifying a specimen as belonging to a certain animal species based on a single universal marker: the DNA barcode sequence. Over the last 4 years, this approach has become increasingly popular and advances as well as limitations have clearly emerged as increasing amounts of organisms have been studied. Our purpose is to briefly expose DNA Barcode of Life principles, pros and cons, relevance and universality. The initially proposed Barcode of life framework has greatly evolved, giving rise to a flexible description of DNA barcoding and a larger range of applications.

Published
2008
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7. Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae

Author

John M. Dye, Sergey V. Netesov, Janusz T. Paweska, Mark S. Lever, Travis K. Warren, Peter B. Jahrling, Jean L. Patterson, Stephan Becker, Alexander Bukreyev, Jens H. Kuhn, Lisa E. Hensley, Kartik Chandran, Eric M. Leroy, Sophie J. Smither, J. Rodney Brister, Erica Ollmann Saphire, Victoria Wahl-Jensen, Yiming Bao, Steven B. Bradfute, Manfred Weidmann, Robert Swanepoel, Karl M. Johnson, Jonathan S. Towner, Gene G. Olinger, Viktor E. Volchkov, Olga Dolnik, Anna N. Honko, Louise Pitt, Sina Bavari, Gary P. Kobinger, Guido van der Groen, Sheli R. Radoshitzky, Gustavo Palacios, Robert A. Davey, Sven Enterlein, Elke Mühlberger, Stuart T. Nichol, Institut für Virologie, Philipps University, Centre International de Recherches Médicales de Franceville (CIRMF), National Institute for Communicable Diseases [Johannesburg] (NICD), University of Göttingen - Georg-August-Universität Göttingen, Centers for Disease Control and Prevention [Atlanta] (CDC), and Centers for Disease Control and Prevention

Subjects
MESH: Terminology as Topic, [SDV]Life Sciences [q-bio], Filoviridae, Computational biology, medicine.disease_cause, Article, 03 medical and health sciences, Virology, MESH: Filoviridae Infections, medicine, MESH: Animals, Nomenclature, Virus classification, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Ebola virus, MESH: Humans, biology, 030306 microbiology, General Medicine, Genome project, biology.organism_classification, 3. Good health, Gene nomenclature, MESH: Classification, MESH: Filoviridae, Homo sapiens, Taxonomy (biology)
Abstract

The task of international expert groups is to recommend the classification and naming of viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and nomenclature for filoviruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length virus names (such as “Ebola virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the virus (e.g., Ebola virus), isolation host (e.g., members of the species Homo sapiens), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzavirus nomenclature and the nomenclature recently proposed for rotaviruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this nomenclature would increase the general understanding of filovirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.

Published
2013
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8. Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

Author

Virginia P. Edgcomb, William D. Orsi, Anke Behnke, Thorsten Stoeck, Maria J. Rodriguez-Mora, Andrei Y. Chistoserdov, Richard Christen, Linda A. Amaral-Zettler, Dept of Ecology, University of Kaiserslautern, Dpt of Ecology, Institut de signalisation, biologie du développement et cancer (ISBDC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Josephine Bay Paul Center, Marine Biological Laboratory, University of Louisiana, Northeastern University [Boston], and Woods Hole Oceanographic Institution (WHOI)

Subjects
MESH: Sequence Analysis, DNA, Library, Physiology, Plant Science, Genome, Structural Biology, MESH: Animals, Taxonomic rank, [SDV.BDD]Life Sciences [q-bio]/Development Biology, lcsh:QH301-705.5, MESH: Bacteria, Anaerobic, Sequence Tagged Sites, Sanger sequencing, 0303 health sciences, Agricultural and Biological Sciences(all), Ecology, Eukaryota, Biodiversity, Classification, MESH: Classification, MESH: Eukaryota, symbols, General Agricultural and Biological Sciences, Biotechnology, Research Article, DNA, Bacterial, Rare biosphere, Biology, MESH: Biodiversity, General Biochemistry, Genetics and Molecular Biology, Sequence-tagged site, 03 medical and health sciences, symbols.namesake, Bacteria, Anaerobic, MESH: Sequence Tagged Sites, MESH: Ciliophora, Animals, Seawater, 14. Life underwater, Ciliophora, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Biochemistry, Genetics and Molecular Biology(all), 030306 microbiology, MESH: Seawater, Cell Biology, Sequence Analysis, DNA, MESH: DNA, Bacterial, lcsh:Biology (General), Evolutionary biology, Pyrosequencing, Species richness, Developmental Biology
Abstract

Background Recent advances in sequencing strategies make possible unprecedented depth and scale of sampling for molecular detection of microbial diversity. Two major paradigm-shifting discoveries include the detection of bacterial diversity that is one to two orders of magnitude greater than previous estimates, and the discovery of an exciting 'rare biosphere' of molecular signatures ('species') of poorly understood ecological significance. We applied a high-throughput parallel tag sequencing (454 sequencing) protocol adopted for eukaryotes to investigate protistan community complexity in two contrasting anoxic marine ecosystems (Framvaren Fjord, Norway; Cariaco deep-sea basin, Venezuela). Both sampling sites have previously been scrutinized for protistan diversity by traditional clone library construction and Sanger sequencing. By comparing these clone library data with 454 amplicon library data, we assess the efficiency of high-throughput tag sequencing strategies. We here present a novel, highly conservative bioinformatic analysis pipeline for the processing of large tag sequence data sets. Results The analyses of ca. 250,000 sequence reads revealed that the number of detected Operational Taxonomic Units (OTUs) far exceeded previous richness estimates from the same sites based on clone libraries and Sanger sequencing. More than 90% of this diversity was represented by OTUs with less than 10 sequence tags. We detected a substantial number of taxonomic groups like Apusozoa, Chrysomerophytes, Centroheliozoa, Eustigmatophytes, hyphochytriomycetes, Ichthyosporea, Oikomonads, Phaeothamniophytes, and rhodophytes which remained undetected by previous clone library-based diversity surveys of the sampling sites. The most important innovations in our newly developed bioinformatics pipeline employ (i) BLASTN with query parameters adjusted for highly variable domains and a complete database of public ribosomal RNA (rRNA) gene sequences for taxonomic assignments of tags; (ii) a clustering of tags at k differences (Levenshtein distance) with a newly developed algorithm enabling very fast OTU clustering for large tag sequence data sets; and (iii) a novel parsing procedure to combine the data from individual analyses. Conclusion Our data highlight the magnitude of the under-sampled 'protistan gap' in the eukaryotic tree of life. This study illustrates that our current understanding of the ecological complexity of protist communities, and of the global species richness and genome diversity of protists, is severely limited. Even though 454 pyrosequencing is not a panacea, it allows for more comprehensive insights into the diversity of protistan communities, and combined with appropriate statistical tools, enables improved ecological interpretations of the data and projections of global diversity.

Published
2009
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9. AutoClass@IJM: a powerful tool for Bayesian classification of heterogeneous data in biology

Author

Fiona Achcar, Denis Mestivier, Jean-Michel Camadro, Institut Jacques Monod (IJM (UMR_7592)), and Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Bayes Theorem, MESH: Algorithms, Biology, Machine learning, computer.software_genre, Computational resource, Bioinformatics, 03 medical and health sciences, Upload, Naive Bayes classifier, User-Computer Interface, MESH: Gene Expression Profiling, MESH: Software, 0302 clinical medicine, Computer cluster, Genetics, Cluster Analysis, Relevance (information retrieval), Cluster analysis, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, MESH: User-Computer Interface, 0303 health sciences, Internet, business.industry, Gene Expression Profiling, Bayes Theorem, Articles, Missing data, Classification, MESH: Cluster Analysis, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Classification, MESH: Internet, MESH: Oligonucleotide Array Sequence Analysis, Artificial intelligence, User interface, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, 030217 neurology & neurosurgery, Algorithms, Software
Abstract

International audience; Recently, several theoretical and applied studies have shown that unsupervised Bayesian classification systems are of particular relevance for biological studies. However, these systems have not yet fully reached the biological community mainly because there are few freely available dedicated computer programs, and Bayesian clustering algorithms are known to be time consuming, which limits their usefulness when using personal computers. To overcome these limitations, we developed AutoClass@IJM, a computational resource with a web interface to AutoClass, a powerful unsupervised Bayesian classification system developed by the Ames Research Center at N.A.S.A. AutoClass has many powerful features with broad applications in biological sciences: (i) it determines the number of classes automatically, (ii) it allows the user to mix discrete and real valued data, (iii) it handles missing values. End users upload their data sets through our web interface; computations are then queued in our cluster server. When the clustering is completed, an URL to the results is sent back to the user by e-mail. AutoClass@IJM is freely available at: http://ytat2.ijm.univ-paris-diderot.fr/AutoclassAtIJM.html.

Published
2009
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10. Diversity of Wolbachia isolated from the Cubitermes sp. affinis subarquatus complex of species (Termitidae), revealed by multigene phylogenies

Author

Virginie Roy, Myriam Harry, Biodiversité et fonctionnement du sol (BIOSOL), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)

Subjects
MESH: Sequence Analysis, DNA, MESH: Cytoskeletal Proteins, MESH: Isoptera, Genus, RNA, Ribosomal, 16S, MESH: Animals, MESH: Phylogeny, MESH: Bacterial Proteins, Phylogeny, reproductive and urinary physiology, Recombination, Genetic, 0303 health sciences, biology, Classification, Eusociality, Bacterial Typing Techniques, MESH: RNA, Ribosomal, 16S, Termitidae, MESH: Classification, MESH: Wolbachia, Wolbachia, MESH: Recombination, Genetic, MESH: Genes, Bacterial, Bacterial Outer Membrane Proteins, Zoology, Isoptera, Microbiology, MESH: Bacterial Typing Techniques, 03 medical and health sciences, Bacterial Proteins, Phylogenetics, Botany, parasitic diseases, Genetics, Animals, Molecular Biology, 030304 developmental biology, 030306 microbiology, Host (biology), MESH: Bacterial Outer Membrane Proteins, Sequence Analysis, DNA, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, 16S ribosomal RNA, Cytoskeletal Proteins, Genes, Bacterial, bacteria, Arthropod, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Wolbachia are endosymbiotic bacteria that may alter the reproductive mechanisms of arthropod hosts. Eusocial termites provide considerable scope for Wolbachia studies owing to their ancient origin, their great diversity and their considerable ecological, biological and behavioral plasticity. This article describes the phylogenetic distribution of Wolbachia infecting termites of the Cubitermes genus, which are particularly abundant soil-feeders in equatorial Africa. Fourteen colonies of the Cubitermes sp. affinis subarquatus complex of species were screened using five bacterial genes (wsp, ftsZ, coxA, fbpA and 16S rRNA genes) and a striking diversity of Wolbachia strains was identified within these closely related species. In the host complex, three Wolbachia variants were found that were not in the super groups usually reported for termites (F and H), each infecting one or two Cubitermes species.

Published
2007
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11. Taxonomic position and geographical distribution of the common sheep G1 and camel G6 strains of Echinococcus granulosus in three African countries

Author

Jean-Mathieu Bart, P. Koskei, Renaud Piarroux, S. Maillard, Jenny Knapp, M. C. Benchikh-Elfegoun, Bruno Gottstein, Institut de l'Ouest : Droit et Europe (IODE), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institute of Parasitology, University of Bern, Infections Parasitaires : Transmission, Physiopathologie et Thérapeutiques (IP-TPT), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Service de Santé des Armées, Institut de l'Ouest : Droit et Europe ( IODE ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Infections Parasitaires : Transmission, Physiopathologie et Thérapeutiques ( IP-TPT ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Assistance Publique - Hôpitaux de Marseille ( APHM ) -Service de Santé des Armées-Université de Montpellier ( UM ), Millon, Laurence, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), and Service de Santé des Armées-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)

Subjects
MESH : Algeria, MESH : Classification, MESH : Echinococcosis, MESH: Echinococcus granulosus, Animal Diseases, 030308 mycology & parasitology, 0302 clinical medicine, MESH: Demography, MESH : Mauritania, MESH: Animals, Echinococcus granulosus, MESH: Phylogeny, Phylogeny, 0303 health sciences, 630 Agriculture, Phylogenetic tree, biology, MESH : Animal Diseases, Mauritania, MESH: Camels, General Medicine, Classification, MESH: Classification, Infectious Diseases, Taxonomy (biology), MESH: Algeria, MESH : Ethiopia, MESH: Mauritania, MESH : Demography, Camelus, 030231 tropical medicine, Cestoda, Zoology, MESH: Sheep, MESH: Ethiopia, Bovidae, MESH : Sheep, [ SDV.EE.SANT ] Life Sciences [q-bio]/Ecology, environment/Health, 03 medical and health sciences, MESH: Echinococcosis, Echinococcosis, Phylogenetics, parasitic diseases, Animals, Humans, Helminths, [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, Demography, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Sheep, MESH: Humans, General Veterinary, MESH : Camels, MESH : Echinococcus granulosus, MESH : Humans, MESH : Phylogeny, biology.organism_classification, MESH: Animal Diseases, Echinococcus, Algeria, Insect Science, Parasitology, Ethiopia, MESH : Animals
Abstract

International audience; The taxonomic and phylogenetic status of Echinococcus granulosus strains are still controversial and under discussion. In the present study, we investigated the genetic polymorphism of E. granulosus isolates originating from three countries of Africa, including a region of Algeria, where the common G1 sheep and the camel G6 strains coexist sympatrically. Seventy-one hydatid cysts were collected from sheep, cattle, camels, and humans. Two mitochondrial markers (cox1 and nad1) were used for strain identification. Two nuclear markers (actII and hbx2) were used to study the possible occurrence of cross-fertilization. Despite the heterogeneity observed among the G1 isolates, they were all localized within one robust cluster. A second strong cluster was also observed containing all of the G6 isolates. Both strains appeared as two distinct groups, and no cases of interbreeding were found. Thus, the attribution of a species rank can be suggested. We also found the Tasmanian sheep G2 strain for the first time in Africa. Because of the slight variations observed between the common sheep and the Tasmanian sheep strains, further studies should be carried out to elucidate the epidemiological relevance of this genetic discrimination.

Published
2007
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