A synthesis of bacterial and archaeal phenotypic trait data
Journal article, 2020
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.
Author
Joshua S. Madin
Hawaiʻi Institute of Marine Biology
Daniel A. Nielsen
Macquarie University
Maria Brbic
Ruder Boskovic Institute
Stanford University
Ross Corkrey
University of Tasmania
David Danko
Weill Cornell Medical College
Kyle Edwards
University of Hawaii
Martin Engqvist
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Noah Fierer
University of Colorado at Boulder
Jemma L. Geoghegan
Macquarie University
Michael R. Gillings
Macquarie University
Nikos C. Kyrpides
DOE Joint Genome Institute
Lawrence Berkeley National Laboratory
Elena Litchman
Michigan State University
Christopher E. Mason
Weill Cornell Medical College
Lisa Moore
Macquarie University
Søren L. Nielsen
Roskilde University (RUC)
Ian T. Paulsen
Macquarie University
Nathan D. Price
Institute for Systems Biology
T. B.K. Reddy
Lawrence Berkeley National Laboratory
DOE Joint Genome Institute
Matthew A. Richards
Institute for Systems Biology
Eduardo P.C. Rocha
Centre national de la recherche scientifique (CNRS)
Thomas M. Schmidt
University of Michigan
Heba Shaaban
Weill Cornell Medical College
Maulik Shukla
Argonne National Laboratory
Fran Supek
Catalan Institution for Research and Advanced Studies
IRB Barcelona - Institute for Research in Biomedicine
Sasha G. Tetu
Macquarie University
Sara Vieira-Silva
KU Leuven
Alice R. Wattam
University of Virginia
David A. Westfall
Weill Cornell Medical College
Mark Westoby
Macquarie University
Scientific data
2052-4463 (eISSN)
Vol. 7 1 170Subject Categories
Evolutionary Biology
Botany
Ecology
DOI
10.1038/s41597-020-0497-4
PubMed
32503990