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PLoS Biol. 2014 Aug 5;12(8):e1001920. doi: 10.1371/journal.pbio.1001920. eCollection 2014.

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

Author information

  • 1DOE-Joint Genome Institute, Walnut Creek, California, United States of America; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
  • 2Australian Centre for Ecogenomics Research, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
  • 3University of California, Davis, Davis, California, United States of America.
  • 4DOE-Joint Genome Institute, Walnut Creek, California, United States of America.
  • 5DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
  • 6NamesforLife, LLC, East Lansing, Michigan, United States of America.
  • 7Max Planck Institute for Marine Microbiology, Bremen, Germany.
  • 8American Type Culture Collection (ATCC), Manassas, Virginia, United States of America.
  • 9Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, United States of America.
  • 10School of Biological Sciences and Chunlab Inc., Seoul National University, Seoul, Korea.
  • 11University of Maryland, College Park, College Park, Maryland, United States of America; Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America.
  • 12AMAbiotics SAS, Genopole, Evry, France.
  • 13Ghent University, Department of Applied Mathematics and Computer Science, Ghent, Belgium.
  • 14Centre for Philosophy of Law, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
  • 15Department of Civil and Environmental Engineering and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
  • 16Ghent University, Department of Applied Mathematics and Computer Science, Ghent, Belgium; Ghent University, BCCM/LMG Bacteria collection, Laboratory of Microbiology, Ghent, Belgium.
  • 17University of Wisconsin-Madison, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America.
  • 18Bioresource Center (BRC) of Institute of Microbiology, Chinese Academy of Sciences, P. R. China.
  • 19Institut National de la Recherche Agronomique, Jouy en Josas, France.
  • 20Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
  • 21Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America.
  • 22Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois, United States of America.
  • 23BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Knoxville, Tennessee, United States of America.
  • 24Max Planck Institute for Marine Microbiology, Bremen, Germany; Jacobs University Bremen gGmbH, Bremen, Germany.
  • 25Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
  • 26Lawrence Berkeley National Laboratory, Berkeley, California, United States of America; Joint BioEnergy Institute (JBEI), Berkeley, California, United States of America.
  • 27Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America.
  • 28ARS, USDA, National Center for Agricultural Utilization Research, Peoria, Illinois, United States of America.
  • 29Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
  • 30Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon, Korea.
  • 31The Key Laboratory for Microbial Resources of the Ministry of Education, Kunming, People's Republic of China.
  • 32China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
  • 33DOE-Joint Genome Institute, Walnut Creek, California, United States of America; Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
  • 34CCUG - Culture Collection University of Gothenburg, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.
  • 35Diamantina Institute, The University of Queensland, St Lucia, Queensland, Australia.
  • 36Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America.
  • 37The J. Craig Venter Institute, Rockville, Maryland, United States of America.
  • 38Riken Bioresource Center, Japan Collection of Microorganisms, Hirosawa, Wako, Saitama, Japan.
  • 39Chemical Process & Energy Resources Institute, Centre for Research & Technology, Thessalonica, Greece; Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
  • 40Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America.
  • 41The Pathogen Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
  • 42State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
  • 43Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Illes Balears, Spain.
  • 44CABI, Bakeham Lane, Egham, Surrey, United Kingdom.
  • 45Josephine Bay Paul Center for Comparative Evolution and Molecular Biology, MBL, Woods Hole, Massachusetts, United States of America.
  • 46Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
  • 47NITE Biological Resource Center (NBRC), Kisarazu-shi, Chiba, Japan.
  • 48Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America.
  • 49Department of Microbial Ecology, University of Vienna, Vienna, Austria.
  • 50The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.
  • 51Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, France.
  • 52State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark.
  • 53Bioresource Center (BRC) of Institute of Microbiology, Chinese Academy of Sciences, P. R. China; Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
  • 54U.K. Natural Environment Research Council (NERC), Environmental Bioinformatics Centre, Oxford, United Kingdom.
  • 55Department of Microbiology, University of Georgia, Athens, Georgia, United States of America.
  • 56NamesforLife, LLC, East Lansing, Michigan, United States of America; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America.

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.

PMID:
25093819
[PubMed - indexed for MEDLINE]
PMCID:
PMC4122341
Free PMC Article
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