A synthesis of bacterial and archaeal phenotypic trait data

Joshua S. Madin; Daniel A. Nielsen; Maria Brbic; Ross Corkrey; David Danko; Kyle Edwards; Martin K.M. Engqvist; Noah Fierer; Jemma L. Geoghegan; Michael Gillings; Nikos C. Kyrpides; Elena Litchman; Christopher E. Mason; Lisa Moore; Søren L. Nielsen; Ian T. Paulsen; Nathan D. Price; T. B.K. Reddy; Matthew A. Richards; Eduardo P.C. Rocha; Thomas M. Schmidt; Heba Shaaban; Maulik Shukla; Fran Supek; Sasha G. Tetu; Sara Vieira-Silva; Alice R. Wattam; David A. Westfall; Mark Westoby

doi:10.1038/s41597-020-0497-4

A synthesis of bacterial and archaeal phenotypic trait data

Joshua S. Madin, Daniel A. Nielsen, Maria Brbic, Ross Corkrey, David Danko, Kyle Edwards, Martin K.M. Engqvist, Noah Fierer, Jemma L. Geoghegan, Michael Gillings, Nikos C. Kyrpides, Elena Litchman, Christopher E. Mason, Lisa Moore, Søren L. Nielsen, Ian T. Paulsen, Nathan D. Price, T. B.K. Reddy, Matthew A. Richards, Eduardo P.C. RochaThomas M. Schmidt, Heba Shaaban, Maulik Shukla, Fran Supek, Sasha G. Tetu, Sara Vieira-Silva, Alice R. Wattam, David A. Westfall, Mark Westoby

School of Medicine

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

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.

Original language	English (US)
Article number	170
Journal	Scientific Data
Volume	7
Issue number	1
DOIs	https://doi.org/10.1038/s41597-020-0497-4
State	Published - Dec 1 2020

ASJC Scopus subject areas

Statistics and Probability
Information Systems
Education
Computer Science Applications
Statistics, Probability and Uncertainty
Library and Information Sciences

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10.1038/s41597-020-0497-4

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Madin, J. S., Nielsen, D. A., Brbic, M., Corkrey, R., Danko, D., Edwards, K., Engqvist, M. K. M., Fierer, N., Geoghegan, J. L., Gillings, M., Kyrpides, N. C., Litchman, E., Mason, C. E., Moore, L., Nielsen, S. L., Paulsen, I. T., Price, N. D., Reddy, T. B. K., Richards, M. A., ... Westoby, M. (2020). A synthesis of bacterial and archaeal phenotypic trait data. Scientific Data, 7(1), Article 170. https://doi.org/10.1038/s41597-020-0497-4

Madin, JS, Nielsen, DA, Brbic, M, Corkrey, R, Danko, D, Edwards, K, Engqvist, MKM, Fierer, N, Geoghegan, JL, Gillings, M, Kyrpides, NC, Litchman, E, Mason, CE, Moore, L, Nielsen, SL, Paulsen, IT, Price, ND, Reddy, TBK, Richards, MA, Rocha, EPC, Schmidt, TM, Shaaban, H, Shukla, M, Supek, F, Tetu, SG, Vieira-Silva, S, Wattam, AR, Westfall, DA & Westoby, M 2020, 'A synthesis of bacterial and archaeal phenotypic trait data', Scientific Data, vol. 7, no. 1, 170. https://doi.org/10.1038/s41597-020-0497-4

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A synthesis of bacterial and archaeal phenotypic trait data

Abstract

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