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

Journal Article · · PLoS Biology (Online)
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  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)
+ Show Author Affiliations

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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1407248
Journal Information:
PLoS Biology (Online), Journal Name: PLoS Biology (Online) Journal Issue: 8 Vol. 12; ISSN 1545-7885
Publisher:
Public Library of ScienceCopyright Statement
Country of Publication:
United States
Language:
English

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Figures / Tables (3)

Table 1(p. 4)table Table 1
Figure 1(p. 5)figure Figure 1
Figure 2(p. 5)figure Figure 2

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
archaea
bacteria
bacterial genomics
comparative genomics
genome sequencing
genomic libraries
genomic medicine
phylogenetics