Roadmap for naming uncultivated Archaea and Bacteria.
Alison E MurrayJohn FreudensteinSimonetta GribaldoRoland HatzenpichlerPhilip HugenholtzPeter KämpferKonstantinos T KonstantinidisChristopher E LaneR Thane PapkeDonovan H ParksRamon Rossello-MoraMatthew B StottIain C SutcliffeJ Cameron ThrashStephanus N VenterWilliam B WhitmanSilvia G AcinasRudolf I AmannKarthik AnantharamanJean ArmengaudBrett J BakerRoman A BarcoHelge B BodeEric S BoydCarrie L BradyPaul CariniPatrick S G ChainDaniel R ColmanKristen M DeAngelisMaria Asuncion de Los RiosPaulina Estrada-de Los SantosChristopher A DunlapJonathan A EisenDavid EmersonThijs J G EttemaDamien EveillardPeter R GirguisUte HentschelJames T HollibaughLaura A HugWilliam P InskeepElena P IvanovaHans-Peter KlenkWen-Jun LiKaren G LloydFrank E LöfflerThulani Peter MakhalanyaneDuane P MoserTakuro NunouraMarike PalmerVictor ParroCarlos Pedrós-AlióAlexander J ProbstTheo H M SmitsAndrew D SteenEmma T SteenkampAnja SpangFrank J StewartJames M TiedjePeter VandammeMichael WagnerFeng-Ping WangPablo YarzaBrian P HedlundAnna-Louise ReysenbachPublished in: Nature microbiology (2020)
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.