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; Claire Fraser; Richard Gibbs; Jack Gilbert; Paul Gilna; Frank Oliver 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 J. Smith; Mitch Sogin; Rick Stevens; Ulrich 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

doi:10.1371/journal.pbio.1001920

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. EhrlichClaire Fraser, Richard Gibbs, Jack Gilbert, Paul Gilna, Frank Oliver 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 J. Smith, Mitch Sogin, Rick Stevens, Ulrich 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

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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 language	English (US)
Pages (from-to)	e1001920
Journal	PLoS Biology
Volume	12
Issue number	8
DOIs	https://doi.org/10.1371/journal.pbio.1001920
State	Published - Aug 5 2014

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Kyrpides, N. C., Hugenholtz, P., Eisen, J. A., Woyke, T., Göker, M., Parker, C. T., Amann, R., Beck, B. J., Chain, P. S. G., Chun, J., Colwell, R. R., Danchin, A., Dawyndt, P., Dedeurwaerdere, T., DeLong, E. F., Detter, J. C., De Vos, P., Donohue, T. J., Dong, X.-Z., ... 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

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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.",

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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, X-Z, Ehrlich, DS, Fraser, C, Gibbs, R, Gilbert, J, Gilna, P, Glöckner, FO, Jansson, JK, Keasling, JD, Knight, R, Labeda, D, Lapidus, A, Lee, J-S, Li, W-J, 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, DJ, Sogin, M, Stevens, R, Stingl, U, Suzuki, K, Taylor, D, Tiedje, JM, Tindall, B, Wagner, M, Weinstock, G, Weissenbach, J, White, O, Wang, J, Zhang, L, Zhou, Y-G, 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

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T1 - Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

AU - Kyrpides, Nikos C.

AU - Hugenholtz, Philip

AU - Eisen, Jonathan A.

AU - Woyke, Tanja

AU - Göker, Markus

AU - Parker, Charles T.

AU - Amann, Rudolf

AU - Beck, Brian J.

AU - Chain, Patrick S. G.

AU - Chun, Jongsik

AU - Colwell, Rita R.

AU - Danchin, Antoine

AU - Dawyndt, Peter

AU - Dedeurwaerdere, Tom

AU - DeLong, Edward F.

AU - Detter, John C.

AU - De Vos, Paul

AU - Donohue, Timothy J.

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AU - Ehrlich, Dusko S.

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AU - Gibbs, Richard

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AU - Gilna, Paul

AU - Glöckner, Frank Oliver

AU - Jansson, Janet K.

AU - Keasling, Jay D.

AU - Knight, Rob

AU - Labeda, David

AU - Lapidus, Alla

AU - Lee, Jung-Sook

AU - Li, Wen-Jun

AU - MA, Juncai

AU - Markowitz, Victor

AU - Moore, Edward R. B.

AU - Morrison, Mark

AU - Meyer, Folker

AU - Nelson, Karen E.

AU - Ohkuma, Moriya

AU - Ouzounis, Christos A.

AU - Pace, Norman

AU - Parkhill, Julian

AU - Qin, Nan

AU - Rossello-Mora, Ramon

AU - Sikorski, Johannes

AU - Smith, David J.

AU - Sogin, Mitch

AU - Stevens, Rick

AU - Stingl, Ulrich

AU - Suzuki, Ken-ichiro

AU - Taylor, Dorothea

AU - Tiedje, Jim M.

AU - Tindall, Brian

AU - Wagner, Michael

AU - Weinstock, George

AU - Weissenbach, Jean

AU - White, Owen

AU - Wang, Jun

AU - Zhang, Lixin

AU - Zhou, Yu-Guang

AU - Field, Dawn

AU - Whitman, William B.

AU - Garrity, George M.

AU - Klenk, Hans Peter

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PY - 2014/8/5

Y1 - 2014/8/5

N2 - 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.

AB - 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.

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UR - https://dx.plos.org/10.1371/journal.pbio.1001920

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SP - e1001920

JO - PLoS Biology

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ER -

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

Abstract

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