Roadmap for naming uncultivated Archaea and Bacteria View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2020-06-08

AUTHORS

Alison E. Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T. Konstantinidis, Christopher E. Lane, R. Thane Papke, Donovan H. Parks, Ramon Rossello-Mora, Matthew B. Stott, Iain C. Sutcliffe, J. Cameron Thrash, Stephanus N. Venter, William B. Whitman, Silvia G. Acinas, Rudolf I. Amann, Karthik Anantharaman, Jean Armengaud, Brett J. Baker, Roman A. Barco, Helge B. Bode, Eric S. Boyd, Carrie L. Brady, Paul Carini, Patrick S. G. Chain, Daniel R. Colman, Kristen M. DeAngelis, Maria Asuncion de los Rios, Paulina Estrada-de los Santos, Christopher A. Dunlap, Jonathan A. Eisen, David Emerson, Thijs J. G. Ettema, Damien Eveillard, Peter R. Girguis, Ute Hentschel, James T. Hollibaugh, Laura A. Hug, William P. Inskeep, Elena P. Ivanova, Hans-Peter Klenk, Wen-Jun Li, Karen G. Lloyd, Frank E. Löffler, Thulani P. Makhalanyane, Duane P. Moser, Takuro Nunoura, Marike Palmer, Victor Parro, Carlos Pedrós-Alió, Alexander J. Probst, Theo H. M. Smits, Andrew D. Steen, Emma T. Steenkamp, Anja Spang, Frank J. Stewart, James M. Tiedje, Peter Vandamme, Michael Wagner, Feng-Ping Wang, Pablo Yarza, Brian P. Hedlund, Anna-Louise Reysenbach

ABSTRACT

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity. More... »

PAGES

987-994

References to SciGraph publications

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  • Journal

    TITLE

    Nature Microbiology

    ISSUE

    8

    VOLUME

    5

    Author Affiliations

  • Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
  • Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
  • Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
  • Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
  • Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
  • Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
  • School of Civil and Environmental Engineering, Georgia Tech, Atlanta, GA, USA
  • Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
  • Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
  • Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
  • School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
  • Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
  • Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
  • Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
  • Department of Microbiology, University of Georgia, Athens, GA, USA
  • Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
  • Max Planck Institute for Marine Microbiology, Bremen, Germany
  • Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
  • CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
  • Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
  • Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
  • Senckenberg Society for Nature Research, Frankfurt am Main, Germany
  • Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
  • University of the West of England, Bristol, England
  • Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
  • Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
  • Microbiology Department, University of Massachusetts, Amherst, MA, USA
  • National Museum of Natural Sciences, CSIC, Madrid, Spain
  • Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
  • National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
  • Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
  • Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
  • Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
  • LS2N, Université de Nantes, CNRS, Nantes, France
  • Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
  • GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
  • Department of Marine Sciences, University of Georgia, Athens, GA, USA
  • Department of Biology, University of Waterloo, Waterloo, Canada
  • Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
  • School of Science, RMIT University, Melbourne, Victoria, Australia
  • School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
  • School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
  • Department of Microbiology, University of Tennessee, Knoxville, TN, USA
  • Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
  • Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
  • Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
  • Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
  • School of Life Sciences, University of Nevada, Las Vegas, NV, USA
  • Astrobiology Center (CSIC-INTA), Madrid, Spain
  • National Biotechnology Center, Cantoblanco, Madrid, Spain
  • Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
  • Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
  • Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
  • Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
  • Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
  • Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
  • Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
  • International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
  • Ribocon GmbH, Bremen, Germany
  • Biology Department, Portland State University, Portland, OR, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41564-020-0733-x

    DOI

    http://dx.doi.org/10.1038/s41564-020-0733-x

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1128290503

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/32514073


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