A synthesis of bacterial and archaeal phenotypic trait data.

Archaea / genetics Bacteria / genetics Ecosystem Genome, Archaeal Genome, Bacterial Phenotype

Journal

Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192

Informations de publication

Date de publication:
05 06 2020
Historique:
received: 15 04 2019
accepted: 20 04 2020
entrez: 7 6 2020
pubmed: 7 6 2020
medline: 5 11 2020
Statut: epublish

Résumé

A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients.

Identifiants

DOI: 10.1038/s41597-020-0497-4 PMID: 32503990 PMC: PMC7275036
pubmed: 32503990
doi: 10.1038/s41597-020-0497-4
pii: 10.1038/s41597-020-0497-4
pmc: PMC7275036
doi:

Types de publication

Dataset Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

170

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Auteurs

Joshua S Madin (JS)

Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA. jmadin@hawaii.edu.
ORCID: 0000-0002-5005-6227

Daniel A Nielsen (DA)

Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
ORCID: 0000-0001-6678-5937

Maria Brbic (M)

Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia.
Department of Computer Science, Stanford University, Stanford, CA, USA.

Ross Corkrey (R)

Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, 7005, Australia.

David Danko (D)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.

Kyle Edwards (K)

Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.

Martin K M Engqvist (MKM)

Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
ORCID: 0000-0003-2174-2225

Noah Fierer (N)

Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.

Jemma L Geoghegan (JL)

Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
ORCID: 0000-0003-0970-0153

Michael Gillings (M)

Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
ORCID: 0000-0002-4043-4351

Nikos C Kyrpides (NC)

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Energy, Joint Genome Institute, Berkeley, CA, 94720, USA.
ORCID: 0000-0002-6131-0462

Elena Litchman (E)

Kellogg Biological Station and Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA.

Christopher E Mason (CE)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
ORCID: 0000-0002-1850-1642

Lisa Moore (L)

Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
ORCID: 0000-0002-4114-1518

Søren L Nielsen (SL)

Department of Science and Environment, Roskilde University, Roskilde, Denmark.
ORCID: 0000-0003-4309-5153

Ian T Paulsen (IT)

Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.

Nathan D Price (ND)

Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA.
ORCID: 0000-0002-4157-0267

T B K Reddy (TBK)

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Energy, Joint Genome Institute, Berkeley, CA, 94720, USA.

Matthew A Richards (MA)

Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA.

Eduardo P C Rocha (EPC)

Microbial Evolutionary Genomics, Institut Pasteur, CNRS UMR3525, 28 rue Dr. Roux, 75015, Paris, France.

Thomas M Schmidt (TM)

Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.

Heba Shaaban (H)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.

Maulik Shukla (M)

Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA.

Fran Supek (F)

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain.
Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain.
ORCID: 0000-0002-7811-6711

Sasha G Tetu (SG)

Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
ORCID: 0000-0002-8943-3499

Sara Vieira-Silva (S)

Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
ORCID: 0000-0002-4616-7602

Alice R Wattam (AR)

Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, 22904, USA.

David A Westfall (DA)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.

Mark Westoby (M)

Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
ORCID: 0000-0001-7690-4530

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Classifications MeSH

questionsmedicales.fr › Archéobactéries › A synthesis of bacterial and archaeal...
questionsmedicales.fr › Bactéries › A synthesis of bacterial and archaeal...
questionsmedicales.fr › Environnement et santé publique › Environnement › Écosystème › A synthesis of bacterial and archaeal...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome d'archéobactérie › A synthesis of bacterial and archaeal...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › A synthesis of bacterial and archaeal...
questionsmedicales.fr › Phénomènes génétiques › Phénotype › A synthesis of bacterial and archaeal...