ArticlePLoS biology2014
Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.
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Article in PLoS biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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115citing papers in PubMed
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Who cites it
115 citing papers in PubMed.
- Taxonomic Resolution of 16S rRNA, FastANI, Mash, and FastAAI across 30,495 Prokaryotic Type-Strain Genomes.bioRxiv : the preprint server for biology · 2026Article
- Prokaryotic assemblages recovered by sedimentary DNA record natural and human-driven disturbances over the past 13 500 years in a cultural landscape.The ISME journal · 2026Article
- Towards a phylogenetically informed approach to solving protein-protein interactions.Biochemical Society transactions · 2025Review
- A metagenomic perspective on the microbial prokaryotic genome census.Science advances · 2025Article
- Optimal Representative Strain selector-a comprehensive pipeline for selecting next-generation reference strains of bacterial species.NAR genomics and bioinformatics · 2024Article
- Profile of Bacterial Communities in Copper Mine Tailings Revealed through High-Throughput Sequencing.Microorganisms · 2024Article
- The complete genomic sequence of the type strainMicrobiology resource announcements · 2024Article
- Why and how to use the SeqCode.mLife · 2024Article
- pyPGCF: A Python Software for Phylogenomic Analysis, Species Demarcation, Identification of Core, and Fingerprint Proteins of Bacterial Genomes That Are Important for Plants.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A comparative genome analysis of theMicrobial genomics · 2023Article
- Thermophilic Carboxylesterases from Hydrothermal Vents of the Volcanic Island of Ischia Active on Synthetic and Biobased Polymers and Mycotoxins.Applied and environmental microbiology · 2023Article
- Expanding the genomic encyclopedia ofCell genomics · 2022Article
- Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach.Environmental microbiology · 2022Article
- A Comparative Analysis of the Core Proteomes within and among theMicroorganisms · 2022Article
- Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data.Microbial genomics · 2022Article
- Leveraging multiomics approaches for producing lignocellulose degrading enzymes.Cellular and molecular life sciences : CMLS · 2022Review
- Unveiling the genomic potential ofMicrobial genomics · 2022Article
- Genotype-phenotype correlations within theFrontiers in microbiology · 2022Article
- EvaluatingMicrobiology spectrum · 2021Article
- Identification of Two Variants of Acinetobacter baumannii Strain ATCC 17978 with Distinct Genotypes and Phenotypes.Infection and immunity · 2021Article
55 more citing papers are in PubMed but not listed here.
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Authors and funding
64 authors.
Nikos C KyrpidesDOE-Joint Genome Institute, Walnut Creek, California, United States of America; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
Philip HugenholtzAustralian Centre for Ecogenomics Research, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
Jonathan A EisenUniversity of California, Davis, Davis, California, United States of America.
Tanja WoykeDOE-Joint Genome Institute, Walnut Creek, California, United States of America.
Markus GökerDSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
Charles T ParkerNamesforLife, LLC, East Lansing, Michigan, United States of America.
Rudolf AmannMax Planck Institute for Marine Microbiology, Bremen, Germany.
Brian J BeckAmerican Type Culture Collection (ATCC), Manassas, Virginia, United States of America.
Patrick S G ChainLos Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, United States of America.
Jongsik ChunSchool of Biological Sciences and Chunlab Inc., Seoul National University, Seoul, Korea.
Rita R ColwellUniversity 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.
Antoine DanchinAMAbiotics SAS, Genopole, Evry, France.
Peter DawyndtGhent University, Department of Applied Mathematics and Computer Science, Ghent, Belgium.
Tom DedeurwaerdereCentre for Philosophy of Law, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
Edward F DeLongDepartment of Civil and Environmental Engineering and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
John C DetterLos Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, United States of America.
Paul De VosGhent University, Department of Applied Mathematics and Computer Science, Ghent, Belgium; Ghent University, BCCM/LMG Bacteria collection, Laboratory of Microbiology, Ghent, Belgium.
Timothy J DonohueUniversity of Wisconsin-Madison, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America.
Xiu-Zhu DongBioresource Center (BRC) of Institute of Microbiology, Chinese Academy of Sciences, P. R. China.
Dusko S EhrlichInstitut National de la Recherche Agronomique, Jouy en Josas, France.
Claire FraserInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
Richard GibbsHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America.
Jack GilbertInstitute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois, United States of America.
Paul GilnaBioEnergy Science Center (BESC), Oak Ridge National Laboratory, Knoxville, Tennessee, United States of America.
Frank Oliver GlöcknerMax Planck Institute for Marine Microbiology, Bremen, Germany; Jacobs University Bremen gGmbH, Bremen, Germany.
Janet K JanssonLawrence Berkeley National Laboratory, Berkeley, California, United States of America.
Jay D KeaslingLawrence Berkeley National Laboratory, Berkeley, California, United States of America; Joint BioEnergy Institute (JBEI), Berkeley, California, United States of America.
Rob KnightHoward Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America.
David LabedaARS, USDA, National Center for Agricultural Utilization Research, Peoria, Illinois, United States of America.
Alla LapidusTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
Jung-Sook LeeKorean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon, Korea.
Wen-Jun LiThe Key Laboratory for Microbial Resources of the Ministry of Education, Kunming, People's Republic of China.
Juncai MaChina General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
Victor MarkowitzDOE-Joint Genome Institute, Walnut Creek, California, United States of America; Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
Edward R B MooreCCUG - Culture Collection University of Gothenburg, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.
Mark MorrisonDiamantina Institute, The University of Queensland, St Lucia, Queensland, Australia.
Folker MeyerMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America.
Karen E NelsonThe J. Craig Venter Institute, Rockville, Maryland, United States of America.
Moriya OhkumaRiken Bioresource Center, Japan Collection of Microorganisms, Hirosawa, Wako, Saitama, Japan.
Christos A OuzounisChemical Process & Energy Resources Institute, Centre for Research & Technology, Thessalonica, Greece; Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Norman PaceDepartment of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America.
Julian ParkhillThe Pathogen Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
Nan QinState Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
Ramon Rossello-MoraInstitut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Illes Balears, Spain.
Johannes SikorskiDSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
David SmithCABI, Bakeham Lane, Egham, Surrey, United Kingdom.
Mitch SoginJosephine Bay Paul Center for Comparative Evolution and Molecular Biology, MBL, Woods Hole, Massachusetts, United States of America.
Rick StevensMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America.
Uli StinglRed Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
Ken-Ichiro SuzukiNITE Biological Resource Center (NBRC), Kisarazu-shi, Chiba, Japan.
Dorothea TaylorNamesforLife, LLC, East Lansing, Michigan, United States of America.
Jim M TiedjeDepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America.
Brian TindallDSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
Michael WagnerDepartment of Microbial Ecology, University of Vienna, Vienna, Austria.
George WeinstockThe Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.
Jean WeissenbachCommissariat à l'Energie Atomique (CEA), Genoscope, Evry, France.
Owen WhiteInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
Jun WangState 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.
Lixin ZhangBioresource 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.
Yu-Guang ZhouChina General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
Dawn FieldU.K. Natural Environment Research Council (NERC), Environmental Bioinformatics Centre, Oxford, United Kingdom.
William B WhitmanDepartment of Microbiology, University of Georgia, Athens, Georgia, United States of America.
George M GarrityNamesforLife, LLC, East Lansing, Michigan, United States of America; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America.
Hans-Peter KlenkDSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
GenomicsSequence Analysis, DNAArchaeaBacteriaDatabases, GeneticGenome, ArchaealGenome, BacterialPhylogeny
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