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Journal article

Roadmap for naming uncultivated Archaea and Bacteria.

  • Murray AE Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA. alison.murray@dri.edu.
  • Freudenstein J Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.
  • Gribaldo S Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France.
  • Hatzenpichler R Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
  • Hugenholtz P Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
  • Kämpfer P Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany.
  • Konstantinidis KT School of Civil and Environmental Engineering, Georgia Tech, Atlanta, GA, USA.
  • Lane CE Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA.
  • Papke RT Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA.
  • Parks DH Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
  • Rossello-Mora R Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain.
  • Stott MB School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
  • Sutcliffe IC Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK.
  • Thrash JC Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
  • Venter SN Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
  • Whitman WB Department of Microbiology, University of Georgia, Athens, GA, USA.
  • Acinas SG Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain.
  • Amann RI Max Planck Institute for Marine Microbiology, Bremen, Germany.
  • Anantharaman K Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
  • Armengaud J CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France.
  • Baker BJ Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA.
  • Barco RA Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA.
  • Bode HB Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.
  • Boyd ES Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.
  • Brady CL University of the West of England, Bristol, England.
  • Carini P Department of Environmental Science, University of Arizona, Tuscon, AZ, USA.
  • Chain PSG Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
  • Colman DR Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.
  • DeAngelis KM Microbiology Department, University of Massachusetts, Amherst, MA, USA.
  • de Los Rios MA National Museum of Natural Sciences, CSIC, Madrid, Spain.
  • Estrada-de Los Santos P Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.
  • Dunlap CA National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA.
  • Eisen JA Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA.
  • Emerson D Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
  • Ettema TJG Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
  • Eveillard D LS2N, Université de Nantes, CNRS, Nantes, France.
  • Girguis PR Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
  • Hentschel U GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany.
  • Hollibaugh JT Department of Marine Sciences, University of Georgia, Athens, GA, USA.
  • Hug LA Department of Biology, University of Waterloo, Waterloo, Canada.
  • Inskeep WP Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.
  • Ivanova EP School of Science, RMIT University, Melbourne, Victoria, Australia.
  • Klenk HP School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.
  • Li WJ School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
  • Lloyd KG Department of Microbiology, University of Tennessee, Knoxville, TN, USA.
  • Löffler FE Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.
  • Makhalanyane TP Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
  • Moser DP Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA.
  • Nunoura T Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
  • Palmer M School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
  • Parro V Astrobiology Center (CSIC-INTA), Madrid, Spain.
  • Pedrós-Alió C National Biotechnology Center, Cantoblanco, Madrid, Spain.
  • Probst AJ Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany.
  • Smits THM Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland.
  • Steen AD Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA.
  • Steenkamp ET Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
  • Spang A Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.
  • Stewart FJ Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.
  • Tiedje JM Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
  • Vandamme P Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium.
  • Wagner M Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
  • Wang FP International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
  • Yarza P Ribocon GmbH, Bremen, Germany.
  • Hedlund BP School of Life Sciences, University of Nevada, Las Vegas, NV, USA. brian.hedlund@unlv.edu.
  • Reysenbach AL Biology Department, Portland State University, Portland, OR, USA. bwar@pdx.edu.
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  • 2020-06-10
Published in:
  • Nature microbiology. - 2020
English 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.
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https://sonar.ch/global/documents/145438
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