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

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

Author information

1
DOE-Joint Genome Institute, Walnut Creek, California, United States of America; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
2
Australian Centre for Ecogenomics Research, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
3
University of California, Davis, Davis, California, United States of America.
4
DOE-Joint Genome Institute, Walnut Creek, California, United States of America.
5
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
6
NamesforLife, LLC, East Lansing, Michigan, United States of America.
7
Max Planck Institute for Marine Microbiology, Bremen, Germany.
8
American Type Culture Collection (ATCC), Manassas, Virginia, United States of America.
9
Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, United States of America.
10
School of Biological Sciences and Chunlab Inc., Seoul National University, Seoul, Korea.
11
University 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.
12
AMAbiotics SAS, Genopole, Evry, France.
13
Ghent University, Department of Applied Mathematics and Computer Science, Ghent, Belgium.
14
Centre for Philosophy of Law, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
15
Department of Civil and Environmental Engineering and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
16
Ghent University, Department of Applied Mathematics and Computer Science, Ghent, Belgium; Ghent University, BCCM/LMG Bacteria collection, Laboratory of Microbiology, Ghent, Belgium.
17
University of Wisconsin-Madison, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America.
18
Bioresource Center (BRC) of Institute of Microbiology, Chinese Academy of Sciences, P. R. China.
19
Institut National de la Recherche Agronomique, Jouy en Josas, France.
20
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
21
Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America.
22
Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois, United States of America.
23
BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Knoxville, Tennessee, United States of America.
24
Max Planck Institute for Marine Microbiology, Bremen, Germany; Jacobs University Bremen gGmbH, Bremen, Germany.
25
Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
26
Lawrence Berkeley National Laboratory, Berkeley, California, United States of America; Joint BioEnergy Institute (JBEI), Berkeley, California, United States of America.
27
Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America.
28
ARS, USDA, National Center for Agricultural Utilization Research, Peoria, Illinois, United States of America.
29
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
30
Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon, Korea.
31
The Key Laboratory for Microbial Resources of the Ministry of Education, Kunming, People's Republic of China.
32
China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
33
DOE-Joint Genome Institute, Walnut Creek, California, United States of America; Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
34
CCUG - Culture Collection University of Gothenburg, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.
35
Diamantina Institute, The University of Queensland, St Lucia, Queensland, Australia.
36
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America.
37
The J. Craig Venter Institute, Rockville, Maryland, United States of America.
38
Riken Bioresource Center, Japan Collection of Microorganisms, Hirosawa, Wako, Saitama, Japan.
39
Chemical Process & Energy Resources Institute, Centre for Research & Technology, Thessalonica, Greece; Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
40
Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America.
41
The Pathogen Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
42
State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
43
Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Illes Balears, Spain.
44
CABI, Bakeham Lane, Egham, Surrey, United Kingdom.
45
Josephine Bay Paul Center for Comparative Evolution and Molecular Biology, MBL, Woods Hole, Massachusetts, United States of America.
46
Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
47
NITE Biological Resource Center (NBRC), Kisarazu-shi, Chiba, Japan.
48
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America.
49
Department of Microbial Ecology, University of Vienna, Vienna, Austria.
50
The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.
51
Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, France.
52
State 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.
53
Bioresource 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.
54
U.K. Natural Environment Research Council (NERC), Environmental Bioinformatics Centre, Oxford, United Kingdom.
55
Department of Microbiology, University of Georgia, Athens, Georgia, United States of America.
56
NamesforLife, 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
PMCID:
PMC4122341
DOI:
10.1371/journal.pbio.1001920
[Indexed for MEDLINE]
Free PMC Article

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