Roadmap for naming uncultivated Archaea and Bacteria

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 ArmengaudBrett 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, Brian P. Hedlund, Anna Louise Reysenbach

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

27 Citations (Scopus)
6 Downloads (Pure)

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.

Original languageEnglish
Pages (from-to)987-994
Number of pages8
JournalNature Microbiology
Volume5
Issue number8
Early online date8 Jun 2020
DOIs
Publication statusPublished - 1 Aug 2020

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