FABI | Forestry and Agricultural Biotechnology Institute

Roadmap for naming uncultivated Archaea and Bacteria

Murray AE,Freudenstein J,Gribaldo S,Hatzenpichler R,Hugenholtz P,Kämpfer P,Konstantinidis K,Lane CE,Papke RT,Parks DH,Rossello-Mora R,Stott MB,Sutcliffe IC,Thrash JC,Venter SN,Whitman WB,Acinas SG,Amann RI,Anantharaman K,Armengaud J,Baker BJ,Barco RA,Bode HB,Boyd ES,Brady CL,Carini P,Chain PSG,Colman DR,DeAngelis KM,de los Rios MA,Estrada-de los Santos P,Dunlap CA,Eisen JA,Emerson D,Ettema TJG,Eveillard D,Girguis PR,Hentschel U,HollibaughTJ,Hug LA,Inskeep WP,Ivanova EP,Klenk H,Li W,Lloyd KLG,Löffler FE,Makhalanyane TP,Moser DP,Palmer M,Parro V,Pedrós-Alió C,Probst AJ,Smits THM,Steen AD,Steenkamp ET,Spang A,Stewart FJ,Tiedje JM,Vandamme P,Wagner M,Wang F,Hedlund BP,Reysenbach A

Year2020

JournalNature Microbiology

DOI10.1038/s41564-020-0733-x

Abstract

AbstractThe 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.