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Journal articles
A synthesis of bacterial and archaeal phenotypic trait data
Joshua Madin
1
Daniel Nielsen
2
Maria Brbic
3
Ross Corkrey
4
David Danko
5
Kyle Edwards
1
Martin Engqvist
6
Noah Fierer
7
Jemma Geoghegan
2
Michael Gillings
2
Nikos Kyrpides
8
Elena Litchman
9
Christopher Mason
5
Lisa Moore
2
Søren Nielsen
10
Ian Paulsen
2
Nathan Price
11
T. B. K. Reddy
8
Matthew Richards
11
Eduardo Rocha
12
Thomas 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
Jemma L Geoghegan 2
Author
Michael Gillings 2
Author
Nikos Kyrpides 8
Author
Elena Litchman 9
Author
Nathan D Price 11
Author
T. B. K. Reddy 8
Author
Matthew A Richards 11
Author
Eduardo P. C. Rocha 12
Author IdHAL : epcrocha ORCID : https://orcid.org/0000-0001-7704-822X
Mark Westoby 2
Author
1
UHM - University of Hawai‘i [Mānoa] (1890 East-West Rd, Honolulu, HI 96822
University of Hawaii at Manoa - United States)
2
Macquarie University [Sydney] (Sydney, NSW, 2109, Australia - Australia)
3
Rudjer Boskovic Institute [Zagreb] ( Bijenicka cesta 54, HR-10002 Zagreb - Croatia)
4
UTAS - University of Tasmania [Hobart, Australia] (Hobart TAS 7005, Australie - Australia)
5
Weill Cornell Medicine [New York] (1300 York Avenue
New York, NY 10065 - United States)
6
Chalmers University of Technology [Gothenburg, Sweden] (SE-412 96 GOTHENBURG, SWEDEN - Sweden)
7
University of Colorado [Boulder] (Boulder, Colorado 80309 - United States)
8
LBNL - Lawrence Berkeley National Laboratory [Berkeley] (1 Cyclotron Rd. MS 50A-1148, Berkeley, CA 94720 - United States)
9
Michigan State University [East Lansing] (220 Trowbridge Rd
East Lansing, MI 48824 - United States)
- Michigan State University System (Michigan - United States)
10
Roskilde University (Roskilde University
Universitetsvej 1, P.O. Box 260
DK-4000 Roskilde - Denmark)
11
ISB - Institute for Systems Biology [Seattle] (Seattle, WA 98109 - United States)
12
Génomique évolutive des Microbes / Microbial Evolutionary Genomics (Département Génomes et Génétique - 25-28 rue du docteur Roux, F-75724 Paris Cedex 15 - France)
- Institut Pasteur [Paris] (25-28, rue du docteur Roux, 75724 Paris cedex 15 - France)
- CNRS - Centre National de la Recherche Scientifique : UMR3525 (France)
13
University of Michigan [Ann Arbor] (500 Church Street Ann Arbor, MI 48109-1090 - United States)
- University of Michigan System (Michigan - United States)
14
ANL - Argonne National Laboratory [Lemont] (9700 S Cass Ave B109, Lemont, IL, 60439 - United States)
15
IRB - Institute for Research in Biomedicine [Barcelona, Spain] (Parc Científic de Barcelona C/ Baldiri Reixac 10 08028 Barcelona - Spain)
- University of Barcelona (Gran Via de les Corts Catalanes, 585, 08007 Barcelona - Spain)
- BIST - Barcelona Institute of Science and Technology (Carrer Comte d'Urgell, 187, 08036 Barcelona, Espagne - Spain)
16
Rega Institute for Medical Research [Leuven, België] (Minderbroedersstraat 10, B 3000 Leuven - Belgium)
- KU Leuven - Catholic University of Leuven - Katholieke Universiteit Leuven (Oude Markt 13 - bus 5005, 3000 Leuven - Belgium)
17
University of Virginia [Charlottesville] (P.O. Box 400229, Charlottesville, VA 22904-4229 - United States)
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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Journal articles
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https://hal-pasteur.archives-ouvertes.fr/pasteur-03015782
Contributor : Rocha Eduardo <>
Submitted on : Friday, November 20, 2020 - 9:28:48 AM
Last modification on : Wednesday, November 25, 2020 - 3:27:05 AM
Contributor : Rocha Eduardo <>
Submitted on : Friday, November 20, 2020 - 9:28:48 AM
Last modification on : Wednesday, November 25, 2020 - 3:27:05 AM
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Madin-2020-A-synthesis-of-bact...
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Distributed under a Creative Commons Attribution 4.0 International License
Identifiers
- HAL Id : pasteur-03015782, version 1
- DOI : 10.1038/s41597-020-0497-4
- PUBMED : 32503990
- PUBMEDCENTRAL : PMC7275036
Citation
Joshua Madin, Daniel Nielsen, Maria Brbic, Ross Corkrey, David Danko, et al.. A synthesis of bacterial and archaeal phenotypic trait data. Scientific Data , Nature Publishing Group, 2020, 7 (1), pp.170. ⟨10.1038/s41597-020-0497-4⟩. ⟨pasteur-03015782⟩
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