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A synthesis of bacterial and archaeal phenotypic trait data.
Madin, Joshua S; Nielsen, Daniel A; Brbic, Maria; Corkrey, Ross; Danko, David; Edwards, Kyle; Engqvist, Martin K M; Fierer, Noah; Geoghegan, Jemma L; Gillings, Michael; Kyrpides, Nikos C; Litchman, Elena; Mason, Christopher E; Moore, Lisa; Nielsen, Søren L; Paulsen, Ian T; Price, Nathan D; Reddy, T B K; Richards, Matthew A; Rocha, Eduardo P C; Schmidt, Thomas M; Shaaban, Heba; Shukla, Maulik; Supek, Fran; Tetu, Sasha G; Vieira-Silva, Sara; Wattam, Alice R; Westfall, David A; Westoby, Mark.
Affiliation
  • Madin JS; Hawai'i Institute of Marine Biology, University of Hawai'i at Manoa, Kane'ohe, HI, 96744, USA. jmadin@hawaii.edu.
  • Nielsen DA; Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
  • Brbic M; Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia.
  • Corkrey R; Department of Computer Science, Stanford University, Stanford, CA, USA.
  • Danko D; Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, 7005, Australia.
  • Edwards K; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
  • Engqvist MKM; Department of Oceanography, University of Hawai'i at Manoa, Honolulu, HI, 96822, USA.
  • Fierer N; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
  • Geoghegan JL; Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
  • Gillings M; Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
  • Kyrpides NC; Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
  • Litchman E; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Mason CE; Department of Energy, Joint Genome Institute, Berkeley, CA, 94720, USA.
  • Moore L; Kellogg Biological Station and Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA.
  • Nielsen SL; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
  • Paulsen IT; Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
  • Price ND; Department of Science and Environment, Roskilde University, Roskilde, Denmark.
  • Reddy TBK; Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
  • Richards MA; Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA.
  • Rocha EPC; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
  • Schmidt TM; Department of Energy, Joint Genome Institute, Berkeley, CA, 94720, USA.
  • Shaaban H; Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA.
  • Shukla M; Microbial Evolutionary Genomics, Institut Pasteur, CNRS UMR3525, 28 rue Dr. Roux, 75015, Paris, France.
  • Supek F; Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
  • Tetu SG; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
  • Vieira-Silva S; Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA.
  • Wattam AR; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain.
  • Westfall DA; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain.
  • Westoby M; Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
Sci Data ; 7(1): 170, 2020 06 05.
Article in En | MEDLINE | ID: mdl-32503990
ABSTRACT
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Phenotype / Bacteria / Archaea Language: En Journal: Sci Data Year: 2020 Document type: Article Affiliation country: Estados Unidos
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Phenotype / Bacteria / Archaea Language: En Journal: Sci Data Year: 2020 Document type: Article Affiliation country: Estados Unidos