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Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

(2014) PLOS BIOLOGY. 12(8).
Author
Organization
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.
Keywords
TREE, MICROORGANISMS, PROJECT, STANDARDS, PHYLOGENY, MINIMUM INFORMATION, MICROBIAL DIVERSITY, NOMENCLATURE, PUBLICATION, PROKARYOTES

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Please use this url to cite or link to this publication:

MLA
Kyrpides, Nikos C et al. “Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains.” PLOS BIOLOGY 2014 : n. pag. Print.
APA
Kyrpides, N. C., Hugenholtz, P., Eisen, J. A., Woyke, T., Göker, M., Parker, C. T., Amann, R., et al. (2014). Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLOS BIOLOGY.
Chicago author-date
Kyrpides, Nikos C, Philip Hugenholtz, Jonathan A Eisen, Tanja Woyke, Markus Göker, Charles T Parker, Rudolf Amann, et al. 2014. “Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains.” Plos Biology.
Chicago author-date (all authors)
Kyrpides, Nikos C, Philip Hugenholtz, Jonathan A Eisen, Tanja Woyke, Markus Göker, Charles T Parker, Rudolf Amann, Brian J Beck, Patrick SG 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 RB 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, and Hans-Peter Klenk. 2014. “Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains.” Plos Biology.
Vancouver
1.
Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, et al. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLOS BIOLOGY. 2014.
IEEE
[1]
N. C. Kyrpides et al., “Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains,” PLOS BIOLOGY, vol. 12, no. 8. 2014.
@misc{5917706,
  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.},
  articleno    = {e1001920},
  author       = {Kyrpides, Nikos C and Hugenholtz, Philip and Eisen, Jonathan A and Woyke, Tanja and Göker, Markus and Parker, Charles T and Amann, Rudolf and Beck, Brian J and Chain, Patrick SG and Chun, Jongsik and Colwell, Rita R and Danchin, Antoine and Dawyndt, Peter and Dedeurwaerdere, Tom and DeLong, Edward F and Detter, John C and De Vos, Paul and Donohue, Timothy J and Dong, Xiu-Zhu and Ehrlich, Dusko S and Fraser, Claire and Gibbs, Richard and Gilbert, Jack and Gilna, Paul and Glöckner, Frank Oliver and Jansson, Janet K and Keasling, Jay D and Knight, Rob and Labeda, David and Lapidus, Alla and Lee, Jung-Sook and Li, Wen-Jun and Ma, Juncai and Markowitz, Victor and Moore, Edward RB and Morrison, Mark and Meyer, Folker and Nelson, Karen E and Ohkuma, Moriya and Ouzounis, Christos A and Pace, Norman and Parkhill, Julian and Qin, Nan and Rossello-Mora, Ramon and Sikorski, Johannes and Smith, David and Sogin, Mitch and Stevens, Rick and Stingl, Uli and Suzuki, Ken-ichiro and Taylor, Dorothea and Tiedje, Jim M and Tindall, Brian and Wagner, Michael and Weinstock, George and Weissenbach, Jean and White, Owen and Wang, Jun and Zhang, Lixin and Zhou, Yu-Guang and Field, Dawn and Whitman, William B and Garrity, George M and Klenk, Hans-Peter},
  issn         = {1545-7885},
  keywords     = {TREE,MICROORGANISMS,PROJECT,STANDARDS,PHYLOGENY,MINIMUM INFORMATION,MICROBIAL DIVERSITY,NOMENCLATURE,PUBLICATION,PROKARYOTES},
  language     = {eng},
  number       = {8},
  pages        = {7},
  series       = {PLOS BIOLOGY},
  title        = {Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains},
  url          = {http://dx.doi.org/10.1371/journal.pbio.1001920},
  volume       = {12},
  year         = {2014},
}

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