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Journal Articles Nature Microbiology Year : 2020

Roadmap for naming uncultivated Archaea and Bacteria

1 DRI - Desert Research Institute
2 Ecology and Organismal Biology
3 Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell
4 MSU - Montana State University
5 UQ [All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations] - The University of Queensland
6 JLU - Justus-Liebig-Universität Gießen = Justus Liebig University
7 Botanical and Environmental Consultant
8 ICM - Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona]
9 LEP - Laboratoire Environnement Profond
10 LBSP - Laboratoire de Biochimie des Systèmes Perturbés
11 University of Texas at Austin [Austin]
12 BMLS - Buchmann Institute for Molecular Life Sciences [Frankfurt am Main]
13 ISAO - Istituto delle Scienze dell' Atmosfera e dell'Oceano [Bologna]
14 UNAM - Universidad Nacional Autónoma de México = National Autonomous University of Mexico
15 Bigelow Laboratory for Ocean Sciences
16 Uppsala University
17 LS2N - Laboratoire des Sciences du Numérique de Nantes
18 LS2N - équipe COMBI - Combinatoire et Bioinformatique
19 Department of Theoretical Mechanics
20 DSMZ - Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
21 SYSU - Sun Yat-sen University [Guangzhou]
22 PTB - Physikalisch-Technische Bundesanstalt [Braunschweig]
23 JAMSTEC - Japan Agency for Marine-Earth Science and Technology
24 EPS - Department of Earth and Planetary Science [UC Berkeley]
25 The Center for Microbial Ecology, Department of Microbiology and Molecular Genetics
26 UGENT - Universiteit Gent = Ghent University
27 Research and Development - SANOFI
28 WGU Nevada - University of Nevada [Las Vegas]
29 PSU - Portland State University [Portland]
Alison Murray
Konstantinos Konstantinidis
  • Function : Author
Christopher Lane
  • Function : Author
R. Thane Papke
  • Function : Author
Donovan Parks
  • Function : Author
Ramon Rossello-Mora
  • Function : Author
Matthew Stott
  • Function : Author
Iain Sutcliffe
  • Function : Author
J. Cameron Thrash
  • Function : Author
William Whitman
  • Function : Author
Rudolf Amann
Karthik Anantharaman
  • Function : Author
Roman Barco
  • Function : Author
Eric Boyd
  • Function : Author
Carrie Brady
  • Function : Author
Patrick Chain
  • Function : Author
Daniel Colman
  • Function : Author
Kristen Deangelis
  • Function : Author
Maria Asuncion de Los Rios
  • Function : Author
Christopher Dunlap
  • Function : Author
Jonathan Eisen
  • Function : Author
Thijs Ettema
Peter Girguis
  • Function : Author
Ute Hentschel
  • Function : Author
James Hollibaugh
  • Function : Author
Laura Hug
  • Function : Author
Wen-Jun Li
  • Function : Author
  • PersonId : 1005621
Karen Lloyd
  • Function : Author
Thulani Makhalanyane
  • Function : Author
Duane Moser
  • Function : Author
Marike Palmer
  • Function : Author
Victor Parro
  • Function : Author
Carlos Pedrós-Alió
  • Function : Author
Theo Smits
  • Function : Author
Andrew Steen
  • Function : Author
Emma Steenkamp
  • Function : Author
Anja Spang
Frank Stewart
  • Function : Author
Michael Wagner
  • Function : Author
Feng-Ping Wang
  • Function : Author
Pablo Yarza
  • Function : Author

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.
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hal-02863761 , version 1 (18-09-2020)
hal-02863761 , version 2 (16-02-2024)

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Alison Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, et al.. Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 2020, 5 (8), pp.987-994. ⟨10.1038/s41564-020-0733-x⟩. ⟨hal-02863761v2⟩
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