Roadmap for naming uncultivated Archaea and Bacteria

被引：116

作者：

Murray, Alison E. ^{[1
]}

Freudenstein, John ^{[2
]}

Gribaldo, Simonetta ^{[3
]}

Hatzenpichler, Roland ^{[4
,5
]}

Hugenholtz, Philip ^{[6
]}

Kaempfer, Peter ^{[7
]}

Konstantinidis, Konstantinos T. ^{[8
]}

Lane, Christopher E. ^{[9
]}

Papke, R. Thane ^{[10
]}

Parks, Donovan H. ^{[6
]}

Rossello-Mora, Ramon ^{[11
]}

Stott, Matthew B. ^{[12
]}

Sutcliffe, Iain C. ^{[13
]}

Thrash, J. Cameron ^{[14
]}

Venter, Stephanus N. ^{[15
]}

Whitman, William B. ^{[16
]}

Acinas, Silvia G. ^{[17
]}

Amann, Rudolf, I ^{[18
]}

Anantharaman, Karthik ^{[19
]}

Armengaud, Jean ^{[20
]}

Baker, Brett J. ^{[21
]}

Barco, Roman A. ^{[22
]}

Bode, Helge B. ^{[23
,24
,25
]}

Boyd, Eric S. ^{[26
]}

Brady, Carrie L. ^{[27
]}

Carini, Paul ^{[28
]}

Chain, Patrick S. G. ^{[29
]}

Colman, Daniel R. ^{[26
]}

DeAngelis, Kristen M. ^{[30
]}

de los Rios, Maria Asuncion ^{[31
]}

Estrada-de los Santos, Paulina ^{[32
]}

Dunlap, Christopher A. ^{[33
]}

Eisen, Jonathan A. ^{[34
]}

Emerson, David ^{[35
]}

Ettema, Thijs J. G. ^{[36
]}

Eveillard, Damien ^{[37
]}

Girguis, Peter R. ^{[38
]}

Hentschel, Ute ^{[39
]}

Hollibaugh, James T. ^{[40
]}

Hug, Laura A. ^{[41
]}

Inskeep, William P. ^{[42
]}

Ivanova, Elena P. ^{[43
]}

Klenk, Hans-Peter ^{[44
]}

Li, Wen-Jun ^{[45
]}

Lloyd, Karen G. ^{[46
]}

Lffler, Frank E. ^{[47
,48
,49
]}

Makhalanyane, Thulani P. ^{[50
]}

Moser, Duane P. ^{[51
]}

Nunoura, Takuro ^{[52
]}

Palmer, Marike ^{[53
]}

机构：

[1] Desert Res Inst, Div Earth & Ecosyst Sci, Reno, NV 89512 USA

[2] Ohio State Univ, Dept Evolut Ecol & Organismal Biol, Columbus, OH 43210 USA

[3] Inst Pasteur, Evolutionary Biol Microbial Cell, Dept Microbiol, Paris, France

[4] Montana State Univ, Dept Chem & Biochem, Ctr Biofilm Engn, Bozeman, MT 59717 USA

[5] Montana State Univ, Thermal Biol Inst, Bozeman, MT 59717 USA

[6] Univ Queensland, Australian Ctr Ecogen, Sch Chem & Mol Biosci, Brisbane, Qld, Australia

[7] Justus Liebig Univ, Dept Appl Microbiol, Giessen, Germany

[8] Georgia Tech, Sch Civil & Environm Engn, Atlanta, GA USA

[9] Univ Rhode Isl, Dept Biol Sci, Kingston, RI 02881 USA

[10] Univ Connecticut, Dept Mol & Cellular Biol, Storrs, CT USA

[11] CSIC UIB, Mediterranean Inst Adv Studies, Illes Balears, Spain

[12] Univ Canterbury, Sch Biol Sci, Christchurch, New Zealand

[13] Northumbria Univ, Dept Appl Sci, Newcastle Upon Tyne, Tyne & Wear, England

[14] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA

[15] Univ Pretoria, Dept Biochem Genet & Microbiol, Pretoria, South Africa

[16] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA

[17] CSIC, Dept Marine Biol & Oceanog, Inst Ciences Mar, Barcelona, Spain

[18] Max Planck Inst Marine Microbiol, Bremen, Germany

[19] Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA

[20] CEA Pharmacol & Immunoanal Unit SPI, CEA Technol Innovat Detect & Diag Lab, Bagnols Sur Ceze, France

[21] Univ Texas Austin, Dept Marine Sci, Marine Sci Inst, Port Aransas, TX USA

[22] Univ Southern Calif, Dept Earth Sci, Los Angeles, CA 90007 USA

[23] Goethe Univ Frankfurt, Mol Biotechnol, Dept Biosci, Frankfurt, Germany

[24] Goethe Univ Frankfurt, Buchmann Inst Mol Life Sci BMLS, Frankfurt, Germany

[25] Senckenberg Soc Nat Res, Frankfurt, Germany

[26] Montana State Univ, Dept Microbiol & Immunol, Bozeman, MT 59717 USA

[27] Univ West England, Bristol, Avon, England

[28] Univ Arizona, Dept Environm Sci, Tucson, AZ USA

[29] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA

[30] Univ Massachusetts, Dept Microbiol, Amherst, MA 01003 USA

[31] CSIC, Natl Museum Nat Sci, Madrid, Spain

[32] Inst Politecn Nacl, Escuela Nacl Ciencias Biol, Mexico City, DF, Mexico

[33] Natl Ctr Agr Utilizat Res, Crop Bioprotect Res Unit, Peoria, IL USA

[34] Univ Calif Davis, Dept Evolut & Ecol, Dept Med Microbiol & Immunol, Davis, CA 95616 USA

[35] Bigelow Lab Ocean Sci, East Boothbay, ME USA

[36] Wageningen Univ & Res, Lab Microbiol, Wageningen, Netherlands

[37] Univ Nantes, CNRS, LS2N, Nantes, France

[38] Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA

[39] GEOMAR Helmholtz Ctr Ocean Res, RU Marine Microbiol, RD3 Marine Ecol, Kiel, Germany

[40] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA

[41] Univ Waterloo, Dept Biol, Waterloo, ON, Canada

[42] Montana State Univ, Dept Land Resources & Environm Sci, Bozeman, MT 59717 USA

[43] RMIT Univ, Sch Sci, Melbourne, Vic, Australia

[44] Newcastle Univ, Sch Nat & Environm Sci, Newcastle Upon Tyne, Tyne & Wear, England

[45] Sun Yat Sen Univ, Sch Life Sci, Guangzhou, Peoples R China

[46] Univ Tennessee, Dept Microbiol, Knoxville, TN 37996 USA

[47] Univ Tennessee, Ctr Environm Biotechnol, Dept Microbiol, Knoxville, TN 37932 USA

[48] Univ Tennessee, Ctr Environm Biotechnol, Dept Civil & Environm Engn, Knoxville, TN 37932 USA

[49] Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA

[50] Univ Pretoria, Ctr Microbial Ecol & Genom, Dept Biochem Genet & Microbiol, Pretoria, South Africa

来源：

NATURE MICROBIOLOGY | 2020年 / 5卷 / 08期

基金：

美国国家科学基金会;

关键词：

AD-HOC COMMITTEE; MICROBES; TAXONOMY; GENOME; NEED;

D O I：

10.1038/s41564-020-0733-x

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

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. In this Consensus Statement, the authors discuss the issue of naming uncultivated prokaryotic microorganisms, which currently do not have a formal nomenclature system due to a lack of type material or cultured representatives, and propose two recommendations including the recognition of DNA sequences as type material.

引用

页码：987 / 994

页数：8

共 50 条

[1] Roadmap for naming uncultivated Archaea and Bacteria
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