Genomic encyclopedia of bacteria and archaea

sequencing a myriad of type strains

Nikos C. Kyrpides, Philip Hugenholtz, Jonathan A Eisen, Tanja Woyke, Markus Göker, Charles T. Parker, Rudolf Amann, Brian J. Beck, Patrick S G Chain, Jongsik Chun, Rita R. Colwell, Antoine Danchin, Peter Dawyndt, Tom Dedeurwaerdere, Edward F. DeLong, John C. Detter, Paul De Vos, Timothy J. Donohue, Xiu Zhu Dong, Dusko S. Ehrlich & 44 others Claire Fraser, Richard Gibbs, Jack Gilbert, Paul Gilna, Frank O liver Glöckner, Janet K. Jansson, Jay D. Keasling, Rob Knight, David Labeda, Alla Lapidus, Jung Sook Lee, Wen Jun Li, Juncai Ma, Victor Markowitz, Edward R B Moore, Mark Morrison, Folker Meyer, Karen E. Nelson, Moriya Ohkuma, Christos A. Ouzounis, Norman Pace, Julian Parkhill, Nan Qin, Ramon Rossello-Mora, Johannes Sikorski, David Smith, Mitch Sogin, Rick Stevens, Uli Stingl, Ken Ichiro Suzuki, Dorothea Taylor, Jim M. Tiedje, Brian Tindall, Michael Wagner, George Weinstock, Jean Weissenbach, Owen White, Jun Wang, Lixin Zhang, Yu Guang Zhou, Dawn Field, William B. Whitman, George M. Garrity, Hans Peter Klenk

Research output: Contribution to journalArticle

109 Citations (Scopus)

Abstract

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

Original languageEnglish (US)
Pages (from-to)e1001920
JournalPLoS Biology
Volume12
Issue number8
DOIs
StatePublished - Aug 1 2014

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Encyclopedias
Planets
Archaea
Bacteria
Microbial Genetics
Genes
Global Warming
microbial genetics
genomics
genetic variation
bacteria
Genetic Association Studies
pressing
Microbial Drug Resistance
funding
antibiotic resistance
global warming
Names
genes
Global warming

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Kyrpides, N. C., Hugenholtz, P., Eisen, J. A., Woyke, T., Göker, M., Parker, C. T., ... Klenk, H. P. (2014). Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biology, 12(8), e1001920. https://doi.org/10.1371/journal.pbio.1001920

Genomic encyclopedia of bacteria and archaea : sequencing a myriad of type strains. / Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A; Woyke, Tanja; Göker, Markus; Parker, Charles T.; Amann, Rudolf; Beck, Brian J.; Chain, Patrick S G; Chun, Jongsik; Colwell, Rita R.; Danchin, Antoine; Dawyndt, Peter; Dedeurwaerdere, Tom; DeLong, Edward F.; Detter, John C.; De Vos, Paul; Donohue, Timothy J.; Dong, Xiu Zhu; Ehrlich, Dusko S.; Fraser, Claire; Gibbs, Richard; Gilbert, Jack; Gilna, Paul; Glöckner, Frank O liver; Jansson, Janet K.; Keasling, Jay D.; Knight, Rob; Labeda, David; Lapidus, Alla; Lee, Jung Sook; Li, Wen Jun; Ma, Juncai; Markowitz, Victor; Moore, Edward R B; Morrison, Mark; Meyer, Folker; Nelson, Karen E.; Ohkuma, Moriya; Ouzounis, Christos A.; Pace, Norman; Parkhill, Julian; Qin, Nan; Rossello-Mora, Ramon; Sikorski, Johannes; Smith, David; Sogin, Mitch; Stevens, Rick; Stingl, Uli; Suzuki, Ken Ichiro; Taylor, Dorothea; Tiedje, Jim M.; Tindall, Brian; Wagner, Michael; Weinstock, George; Weissenbach, Jean; White, Owen; Wang, Jun; Zhang, Lixin; Zhou, Yu Guang; Field, Dawn; Whitman, William B.; Garrity, George M.; Klenk, Hans Peter.

In: PLoS Biology, Vol. 12, No. 8, 01.08.2014, p. e1001920.

Research output: Contribution to journalArticle

Kyrpides, NC, Hugenholtz, P, Eisen, JA, Woyke, T, Göker, M, Parker, CT, Amann, R, Beck, BJ, Chain, PSG, Chun, J, Colwell, RR, Danchin, A, Dawyndt, P, Dedeurwaerdere, T, DeLong, EF, Detter, JC, De Vos, P, Donohue, TJ, Dong, XZ, Ehrlich, DS, Fraser, C, Gibbs, R, Gilbert, J, Gilna, P, Glöckner, FOL, Jansson, JK, Keasling, JD, Knight, R, Labeda, D, Lapidus, A, Lee, JS, Li, WJ, Ma, J, Markowitz, V, Moore, ERB, Morrison, M, Meyer, F, Nelson, KE, Ohkuma, M, Ouzounis, CA, Pace, N, Parkhill, J, Qin, N, Rossello-Mora, R, Sikorski, J, Smith, D, Sogin, M, Stevens, R, Stingl, U, Suzuki, KI, Taylor, D, Tiedje, JM, Tindall, B, Wagner, M, Weinstock, G, Weissenbach, J, White, O, Wang, J, Zhang, L, Zhou, YG, Field, D, Whitman, WB, Garrity, GM & Klenk, HP 2014, 'Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains', PLoS Biology, vol. 12, no. 8, pp. e1001920. https://doi.org/10.1371/journal.pbio.1001920
Kyrpides, Nikos C. ; Hugenholtz, Philip ; Eisen, Jonathan A ; Woyke, Tanja ; Göker, Markus ; Parker, Charles T. ; Amann, Rudolf ; Beck, Brian J. ; Chain, Patrick S G ; Chun, Jongsik ; Colwell, Rita R. ; Danchin, Antoine ; Dawyndt, Peter ; Dedeurwaerdere, Tom ; DeLong, Edward F. ; Detter, John C. ; De Vos, Paul ; Donohue, Timothy J. ; Dong, Xiu Zhu ; Ehrlich, Dusko S. ; Fraser, Claire ; Gibbs, Richard ; Gilbert, Jack ; Gilna, Paul ; Glöckner, Frank O liver ; Jansson, Janet K. ; Keasling, Jay D. ; Knight, Rob ; Labeda, David ; Lapidus, Alla ; Lee, Jung Sook ; Li, Wen Jun ; Ma, Juncai ; Markowitz, Victor ; Moore, Edward R B ; Morrison, Mark ; Meyer, Folker ; Nelson, Karen E. ; Ohkuma, Moriya ; Ouzounis, Christos A. ; Pace, Norman ; Parkhill, Julian ; Qin, Nan ; Rossello-Mora, Ramon ; Sikorski, Johannes ; Smith, David ; Sogin, Mitch ; Stevens, Rick ; Stingl, Uli ; Suzuki, Ken Ichiro ; Taylor, Dorothea ; Tiedje, Jim M. ; Tindall, Brian ; Wagner, Michael ; Weinstock, George ; Weissenbach, Jean ; White, Owen ; Wang, Jun ; Zhang, Lixin ; Zhou, Yu Guang ; Field, Dawn ; Whitman, William B. ; Garrity, George M. ; Klenk, Hans Peter. / Genomic encyclopedia of bacteria and archaea : sequencing a myriad of type strains. In: PLoS Biology. 2014 ; Vol. 12, No. 8. pp. e1001920.
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