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

^*Corresponding author for this work

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

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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
Article number	170
Pages (from-to)	170
Number of pages	8
Journal	Scientific Data
Volume	7
DOIs	https://doi.org/10.1038/s41597-020-0497-4
Publication status	Published - 5 Jun 2020

Bibliographical note

Copyright the Author(s) 2020. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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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, 170. Article 170. https://doi.org/10.1038/s41597-020-0497-4

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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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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, 170, pp. 170. https://doi.org/10.1038/s41597-020-0497-4

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AU - Tetu, Sasha G.

AU - Vieira-Silva, Sara

AU - Wattam, Alice R.

AU - Westfall, David A.

AU - Westoby, Mark

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VL - 7

SP - 170

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ER -

A synthesis of bacterial and archaeal phenotypic trait data

Abstract

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A synthesis of bacterial and archaeal phenotypic trait data

Abstract

Bibliographical note

Access to Document

Other files and links

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Projects

Toxic Oceans: how do anthropogenic pollutants impact vital marine microbes?

Building virtual cyanobacteria: moving beyond the genomics era

Cite this