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

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.
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7] ;  [8] ;  [9] ;  [10] ;  [11] ;  [12] ;  [13] ;  [14] ;  [15] ;  [9] ;  [13] ;  [16] ;  [17] ;  [18] more »;  [19] ;  [20] ;  [21] ;  [22] ;  [23] ;  [24] ;  [25] ;  [26] ;  [27] ;  [28] ;  [29] ;  [30] ;  [17] ;  [31] ;  [32] ;  [2] ;  [21] ;  [33] ;  [34] ;  [35] ;  [26] ;  [36] ;  [37] ;  [38] ;  [5] ;  [39] ;  [40] ;  [21] ;  [41] ;  [42] ;  [6] ;  [43] ;  [5] ;  [44] ;  [45] ;  [46] ;  [19] ;  [47] ;  [17] ;  [17] ;  [48] ;  [49] ;  [43] ;  [5] « less
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  2. Univ. of Queensland, Brisbane, QLD (Australia)
  3. Univ. of California, Davis, CA (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig (Germany)
  6. NamesforLife, LLC, East Lansing, MI (United States)
  7. Max Planck Inst. for Marine Microbiology, Bremen (Germany)
  8. American Type Culture Collection (ATCC), Manassas, VA (United States)
  9. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  10. Seoul National Univ. (Korea, Republic of)
  11. Univ. of Maryland, College Park, MD (United States); Johns Hopkins Univ., Baltimore, MD (United States)
  12. AMAbiotics SAS, Evry (France)
  13. Ghent Univ. (Belgium)
  14. Univ. catholique de Louvain, Louvain-la-Neuve (Belgium)
  15. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
  16. Univ. of Wisconsin, Madison, WI (United States)
  17. Chinese Academy of Sciences (CAS), Beijing (China)
  18. National Inst. of Agricultural Research (INRA), Jouy-en-Josas (France)
  19. Univ. of Maryland School of Medicine, Baltimore, MD (United States)
  20. Baylor College of Medicine, Houston, TX (United States)
  21. Argonne National Lab. (ANL), Argonne, IL (United States)
  22. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  23. Max Planck Inst. for Marine Microbiology, Bremen (Germany); Jacobs Univ. Bremen (Germany)
  24. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  25. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  26. Univ. of Colorado, Boulder, CO (United States)
  27. USDA ARS National Center for Agricultural Utilization Research, Peoria, IL (United States)
  28. St. Petersburg State Univ. (Russian Federation); St. Petersburg Academic Univ. (Russian Federation)
  29. Korea Research Inst. of Bioscience and Biotechnology (KRIBB), Daejeon (Korea, Republic of)
  30. The Key Lab. for Microbial Resources of the Ministry of Education, Kunming (China)
  31. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  32. Univ. of Gothenburg (Sweden)
  33. The J. Craig Venter Inst., Rockville, MD (United States)
  34. Japan Collection of Microorganisms, Wako (Japan)
  35. Centre for Research & Technology, Thessalonica (Greece)
  36. The Wellcome Trust Sanger Institute, Cambridge (United Kingdom)
  37. Zhejiang Univ., Hangzhou (China)
  38. Institut Mediterrani d'Estudis Avancats (IMEDEA, CSIC-UIB), Illes Balears (Spain)
  39. CABI, Surrey (United Kingdom)
  40. Josephine Bay Paul Center for Comparative Evolution and Molecular Biology, Woods Hole, MA (United States)
  41. King Abdullah Univ. of Science and Technology (KAUST), Thuwal (Kingdom of Saudi Arabia)
  42. NITE Biological Resource Center (NBRC), Chiba (Japan)
  43. Michigan State Univ., East Lansing, MI (United States)
  44. Univ. of Vienna,Vienna (Austria)
  45. The Jackson Lab. for Genomic Medicine, Farmington, CT (United States)
  46. Commissariat a l'Energie Atomique (CEA), Evry (France)
  47. Univ. of Copenhagen, Copenhagen (Denmark)
  48. U.K. Natural Environment Research Council (NERC), Environmental Bioinformatics Centre, Oxford (United Kingdom)
  49. Univ. of Georgia, Athens, GA (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
PLoS biology (Online)
Additional Journal Information:
Journal Name: PLoS biology (Online); Journal Volume: 12; Journal Issue: 8; Journal ID: ISSN 1545-7885
Publisher:
Public Library of Science
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
genome sequencing; archaea; bacteria; genomic medicine; bacterial genomics; genomic libraries; phylogenetics; comparative genomics
OSTI Identifier:
1407248

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 Oliver, 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., and Klenk, Hans -Peter. Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains. United States: N. p., Web. doi: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 Oliver, 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. United States. doi: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 Oliver, 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., and Klenk, Hans -Peter. 2014. "Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains". United States. doi:10.1371/journal.pbio.1001920. https://www.osti.gov/servlets/purl/1407248.
@article{osti_1407248,
title = {Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains},
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 S. G. 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 R. B. 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},
abstractNote = {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.},
doi = {10.1371/journal.pbio.1001920},
journal = {PLoS biology (Online)},
number = 8,
volume = 12,
place = {United States},
year = {2014},
month = {8}
}

Works referenced in this record:

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  • Shih, P. M.; Wu, D.; Latifi, A.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 3, p. 1053-1058
  • DOI: 10.1073/pnas.1217107110