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 Armengaud; Brett 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

doi:10.1038/s41564-020-0733-x

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

Escuela Nacional de Ciencias Biológicas (ENCB)

Research output: Contribution to journal › Review article › peer-review

105 Scopus citations

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 language	English
Pages (from-to)	987-994
Number of pages	8
Journal	Nature Microbiology
Volume	5
Issue number	8
DOIs	https://doi.org/10.1038/s41564-020-0733-x
State	Published - 1 Aug 2020

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Murray, A. E., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., Kämpfer, P., Konstantinidis, K. T., Lane, C. E., Papke, R. T., Parks, D. H., Rossello-Mora, R., Stott, M. B., Sutcliffe, I. C., Thrash, J. C., Venter, S. N., Whitman, W. B., Acinas, S. G., Amann, R. I., Anantharaman, K., ... Reysenbach, A. L. (2020). Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5(8), 987-994. https://doi.org/10.1038/s41564-020-0733-x

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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 {\textquoteleft}type material{\textquoteright}, 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.",

author = "Murray, {Alison E.} and John Freudenstein and Simonetta Gribaldo and Roland Hatzenpichler and Philip Hugenholtz and Peter K{\"a}mpfer and Konstantinidis, {Konstantinos T.} and Lane, {Christopher E.} and Papke, {R. Thane} and Parks, {Donovan H.} and Ramon Rossello-Mora and Stott, {Matthew B.} and Sutcliffe, {Iain C.} and Thrash, {J. Cameron} and Venter, {Stephanus N.} and Whitman, {William B.} and Acinas, {Silvia G.} and Amann, {Rudolf I.} and Karthik Anantharaman and Jean Armengaud and Baker, {Brett J.} and Barco, {Roman A.} and Bode, {Helge B.} and Boyd, {Eric S.} and Brady, {Carrie L.} and Paul Carini and Chain, {Patrick S.G.} and Colman, {Daniel R.} and DeAngelis, {Kristen M.} and {de los Rios}, {Maria Asuncion} and {Estrada-de los Santos}, Paulina and Dunlap, {Christopher A.} and Eisen, {Jonathan A.} and David Emerson and Ettema, {Thijs J.G.} and Damien Eveillard and Girguis, {Peter R.} and Ute Hentschel and Hollibaugh, {James T.} and Hug, {Laura A.} and Inskeep, {William P.} and Ivanova, {Elena P.} and Klenk, {Hans Peter} and Li, {Wen Jun} and Lloyd, {Karen G.} and L{\"o}ffler, {Frank E.} and Makhalanyane, {Thulani P.} and Moser, {Duane P.} and Takuro Nunoura and Marike Palmer and Victor Parro and Carlos Pedr{\'o}s-Ali{\'o} and Probst, {Alexander J.} and Smits, {Theo H.M.} and Steen, {Andrew D.} and Steenkamp, {Emma T.} and Anja Spang and Stewart, {Frank J.} and Tiedje, {James M.} and Peter Vandamme and Michael Wagner and Wang, {Feng Ping} and Hedlund, {Brian P.} and Reysenbach, {Anna Louise}",

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Murray, AE, Freudenstein, J, Gribaldo, S, Hatzenpichler, R, Hugenholtz, P, Kämpfer, P, Konstantinidis, KT, 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, Hollibaugh, JT, Hug, LA, Inskeep, WP, Ivanova, EP, Klenk, HP, Li, WJ, Lloyd, KG, Löffler, FE, Makhalanyane, TP, Moser, DP, Nunoura, T, 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, FP, Hedlund, BP & Reysenbach, AL 2020, 'Roadmap for naming uncultivated Archaea and Bacteria', Nature Microbiology, vol. 5, no. 8, pp. 987-994. https://doi.org/10.1038/s41564-020-0733-x

TY - JOUR

T1 - Roadmap for naming uncultivated Archaea and Bacteria

AU - Murray, Alison E.

AU - Freudenstein, John

AU - Gribaldo, Simonetta

AU - Hatzenpichler, Roland

AU - Hugenholtz, Philip

AU - Kämpfer, Peter

AU - Konstantinidis, Konstantinos T.

AU - Lane, Christopher E.

AU - Papke, R. Thane

AU - Parks, Donovan H.

AU - Rossello-Mora, Ramon

AU - Stott, Matthew B.

AU - Sutcliffe, Iain C.

AU - Thrash, J. Cameron

AU - Venter, Stephanus N.

AU - Whitman, William B.

AU - Acinas, Silvia G.

AU - Amann, Rudolf I.

AU - Anantharaman, Karthik

AU - Armengaud, Jean

AU - Baker, Brett J.

AU - Barco, Roman A.

AU - Bode, Helge B.

AU - Boyd, Eric S.

AU - Brady, Carrie L.

AU - Carini, Paul

AU - Chain, Patrick S.G.

AU - Colman, Daniel R.

AU - DeAngelis, Kristen M.

AU - de los Rios, Maria Asuncion

AU - Estrada-de los Santos, Paulina

AU - Dunlap, Christopher A.

AU - Eisen, Jonathan A.

AU - Emerson, David

AU - Ettema, Thijs J.G.

AU - Eveillard, Damien

AU - Girguis, Peter R.

AU - Hentschel, Ute

AU - Hollibaugh, James T.

AU - Hug, Laura A.

AU - Inskeep, William P.

AU - Ivanova, Elena P.

AU - Klenk, Hans Peter

AU - Li, Wen Jun

AU - Lloyd, Karen G.

AU - Löffler, Frank E.

AU - Makhalanyane, Thulani P.

AU - Moser, Duane P.

AU - Nunoura, Takuro

AU - Palmer, Marike

AU - Parro, Victor

AU - Pedrós-Alió, Carlos

AU - Probst, Alexander J.

AU - Smits, Theo H.M.

AU - Steen, Andrew D.

AU - Steenkamp, Emma T.

AU - Spang, Anja

AU - Stewart, Frank J.

AU - Tiedje, James M.

AU - Vandamme, Peter

AU - Wagner, Michael

AU - Wang, Feng Ping

AU - Hedlund, Brian P.

AU - Reysenbach, Anna Louise

PY - 2020/8/1

Y1 - 2020/8/1

N2 - 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.

AB - 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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U2 - 10.1038/s41564-020-0733-x

DO - 10.1038/s41564-020-0733-x

M3 - Artículo de revisión

C2 - 32514073

SN - 2058-5276

VL - 5

SP - 987

EP - 994

JO - Nature Microbiology

JF - Nature Microbiology

IS - 8

ER -

Roadmap for naming uncultivated Archaea and Bacteria

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