A synthesis of bacterial and archaeal phenotypic trait data

Joshua S. Madin (1) , Daniel A. Nielsen (2) , Maria Brbic (3) , Ross Corkrey (4) , David Danko (5) , Kyle Edwards (1) , Martin Engqvist (6) , Noah Fierer (7) , Jemma L Geoghegan (2) , Michael Gillings (2) , Nikos Kyrpides (8) , Elena Litchman (9) , Christopher Mason (5) , Lisa Moore (2) , Søren Nielsen (10) , Ian Paulsen (2) , Nathan D Price (11) , T. B. K. Reddy (8) , Matthew A Richards (11) , Eduardo P. C. Rocha (12) , Thomas M Schmidt (13) , Heba Shaaban (5) , Maulik Shukla (14) , Fran Supek (15) , Sasha Tetu (2) , Sara Vieira-Silva (16) , Alice Wattam (17) , David Westfall (5) , Mark Westoby (2)

1 UHM - University of Hawai‘i [Mānoa]
2 Macquarie University [Sydney]
3 Rudjer Boskovic Institute [Zagreb]
4 UTAS - University of Tasmania [Hobart, Australia]
5 Weill Cornell Medicine [New York]
6 Chalmers University of Technology [Gothenburg, Sweden]
7 University of Colorado [Boulder]
8 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
9 Michigan State University [East Lansing]
10 Roskilde University
11 ISB - Institute for Systems Biology [Seattle]
12 Génomique évolutive des Microbes / Microbial Evolutionary Genomics
13 University of Michigan [Ann Arbor]
14 ANL - Argonne National Laboratory [Lemont]
15 IRB - Institute for Research in Biomedicine [Barcelona, Spain]
16 Rega Institute for Medical Research [Leuven, België]
17 University of Virginia

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.

Domains: Life Sciences [q-bio]; Microbiology and Parasitology; Bacteriology; Life Sciences [q-bio]; Genetics; Populations and Evolution [q-bio.PE]; Life Sciences [q-bio]; Quantitative Methods [q-bio.QM]; Life Sciences [q-bio]; Biochemistry, Molecular Biology; Genomics [q-bio.GN]; Life Sciences [q-bio]; Biodiversity; Populations and Evolution [q-bio.PE]; Computer Science [cs]; Bioinformatics [q-bio.QM]

Joshua S. Madin, Daniel A. Nielsen, Maria Brbic, Ross Corkrey, David Danko, et al.. A synthesis of bacterial and archaeal phenotypic trait data. Scientific Data , 2020, 7 (1), pp.170. ⟨10.1038/s41597-020-0497-4⟩. ⟨pasteur-03015782⟩