Roadmap for naming uncultivated Archaea and Bacteria.,Nature Microbiology

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Roadmap for naming uncultivated Archaea and Bacteria.
Nature Microbiology ( IF 28.3 ) Pub Date : 2020-06-08 , DOI: 10.1038/s41564-020-0733-x
Alison E Murray ₁ , John Freudenstein ₂ , Simonetta Gribaldo ₃ , Roland Hatzenpichler ₄ , Philip Hugenholtz ₅ , Peter Kämpfer ₆ , Konstantinos T Konstantinidis ₇ , Christopher E Lane ₈ , R Thane Papke ₉ , Donovan H Parks ₅ , Ramon Rossello-Mora ₁₀ , Matthew B Stott ₁₁ , Iain C Sutcliffe ₁₂ , J Cameron Thrash ₁₃ , Stephanus N Venter ₁₄ , William B Whitman ₁₅ , Silvia G Acinas ₁₆ , Rudolf I Amann ₁₇ , Karthik Anantharaman ₁₈ , Jean Armengaud ₁₉ , Brett J Baker ₂₀ , Roman A Barco ₂₁ , Helge B Bode _{22,

23} , Eric S Boyd ₂₄ , Carrie L Brady ₂₅ , Paul Carini ₂₆ , Patrick S G Chain ₂₇ , Daniel R Colman ₂₄ , Kristen M DeAngelis ₂₈ , Maria Asuncion de Los Rios ₂₉ , Paulina Estrada-de Los Santos ₃₀ , Christopher A Dunlap ₃₁ , Jonathan A Eisen ₃₂ , David Emerson ₃₃ , Thijs J G Ettema ₃₄ , Damien Eveillard ₃₅ , Peter R Girguis ₃₆ , Ute Hentschel ₃₇ , James T Hollibaugh ₃₈ , Laura A Hug ₃₉ , William P Inskeep ₄₀ , Elena P Ivanova ₄₁ , Hans-Peter Klenk ₄₂ , Wen-Jun Li ₄₃ , Karen G Lloyd ₄₄ , Frank E Löffler _{45,

46} , Thulani P Makhalanyane ₄₇ , Duane P Moser ₄₈ , Takuro Nunoura ₄₉ , Marike Palmer ₅₀ , Victor Parro ₅₁ , Carlos Pedrós-Alió ₅₂ , Alexander J Probst ₅₃ , Theo H M Smits ₅₄ , Andrew D Steen ₅₅ , Emma T Steenkamp ₁₄ , Anja Spang _{56,

57} , Frank J Stewart ₂₄ , James M Tiedje ₅₈ , Peter Vandamme ₅₉ , Michael Wagner ₆₀ , Feng-Ping Wang ₆₁ , Pablo Yarza ₆₂ , Brian P Hedlund ₅₀ , Anna-Louise Reysenbach ₆₃

Affiliation

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.
Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.
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.
Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, 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 for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.
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.

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.

中文翻译：

命名未栽培的古细菌和细菌的路线图。

单扩增基因组（SAGs）和超基因组组装基因组（MAGs）的组装导致基于古细菌和细菌的成员的基于基因组的发现激增，因此有必要为未培养微生物的命名制定准则。国际原核生物命名法（ICNP）仅将文化视为“典型物质”，从而防止了未经培养的生物的命名。在此共识声明中，我们提出了两条解决该命名难题的潜在途径。一种选择是采用先前对ICNP提出的修改，以将DNA序列识别为可接受的类型材料。另一种选择是为未栽培的古细菌和细菌创建命名法，将来可能最终与ICNP合并。不管走什么路

更新日期：2020-06-08

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