A synthesis of bacterial and archaeal phenotypic trait data

Joshua Madin; Daniel Nielsen; Maria Brbic; Ross Corkrey; David Danko; Kyle Edwards; Martin Engqvist; Noah Fierer; Jemma Geoghegan; Michael Gillings; Nikos Kyrpides; Elena Litchman; Cristopher Mason; Lisa Moore; Søren Laurentius Nielsen; Ian Paulsen; Nathan Price; T.B.K. Reddy; Matt Richards; Eduardo Rocha; Thomas Schmidt; Heba Shaaba; Maulik Shukla; Fran Supek; Sasha Tetu; Sara Vieira-Silva; Alice Wattam; David Westfall; Mark Westoby

doi:10.1038/s41597-020-0497-4

A synthesis of bacterial and archaeal phenotypic trait data

Joshua Madin^*, Daniel Nielsen, Maria Brbic, Ross Corkrey, David Danko, Kyle Edwards, Martin Engqvist, Noah Fierer, Jemma Geoghegan, Michael Gillings, Nikos Kyrpides, Elena Litchman, Cristopher Mason, Lisa Moore, Søren Laurentius Nielsen, Ian Paulsen, Nathan Price, T.B.K. Reddy, Matt Richards, Eduardo RochaThomas Schmidt, Heba Shaaba, Maulik Shukla, Fran Supek, Sasha Tetu, Sara Vieira-Silva, Alice Wattam, David Westfall, Mark Westoby

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › Research › peer-review

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
Journal	Scientific Data
Volume	7
Issue number	1
Number of pages	8
ISSN	2052-4463
DOIs	https://doi.org/10.1038/s41597-020-0497-4
Publication status	Published - 5 Jun 2020

Link to document

10.1038/s41597-020-0497-4

s41597-020-0497-4Final published version, 2.98 MBLicence: CC BY

Cite this

Madin, J., Nielsen, D., Brbic, M., Corkrey, R., Danko, D., Edwards, K., Engqvist, M., Fierer, N., Geoghegan, J., Gillings, M., Kyrpides, N., Litchman, E., Mason, C., Moore, L., Nielsen, S. L., Paulsen, I., Price, N., Reddy, T. B. K., Richards, M., ... 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

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title = "A synthesis of bacterial and archaeal phenotypic trait data",

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.",

author = "Joshua Madin and Daniel Nielsen and Maria Brbic and Ross Corkrey and David Danko and Kyle Edwards and Martin Engqvist and Noah Fierer and Jemma Geoghegan and Michael Gillings and Nikos Kyrpides and Elena Litchman and Cristopher Mason and Lisa Moore and Nielsen, {S{\o}ren Laurentius} and Ian Paulsen and Nathan Price and T.B.K. Reddy and Matt Richards and Eduardo Rocha and Thomas Schmidt and Heba Shaaba and Maulik Shukla and Fran Supek and Sasha Tetu and Sara Vieira-Silva and Alice Wattam and David Westfall and Mark Westoby",

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Madin, J, Nielsen, D, Brbic, M, Corkrey, R, Danko, D, Edwards, K, Engqvist, M, Fierer, N, Geoghegan, J, Gillings, M, Kyrpides, N, Litchman, E, Mason, C, Moore, L, Nielsen, SL, Paulsen, I, Price, N, Reddy, TBK, Richards, M, Rocha, E, Schmidt, T, Shaaba, H, Shukla, M, Supek, F, Tetu, S, Vieira-Silva, S, Wattam, A, Westfall, D & 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

TY - JOUR

T1 - A synthesis of bacterial and archaeal phenotypic trait data

AU - Madin, Joshua

AU - Nielsen, Daniel

AU - Brbic, Maria

AU - Corkrey, Ross

AU - Danko, David

AU - Edwards, Kyle

AU - Engqvist, Martin

AU - Fierer, Noah

AU - Geoghegan, Jemma

AU - Gillings, Michael

AU - Kyrpides, Nikos

AU - Litchman, Elena

AU - Mason, Cristopher

AU - Moore, Lisa

AU - Nielsen, Søren Laurentius

AU - Paulsen, Ian

AU - Price, Nathan

AU - Reddy, T.B.K.

AU - Richards, Matt

AU - Rocha, Eduardo

AU - Schmidt, Thomas

AU - Shaaba, Heba

AU - Shukla, Maulik

AU - Supek, Fran

AU - Tetu, Sasha

AU - Vieira-Silva, Sara

AU - Wattam, Alice

AU - Westfall, David

AU - Westoby, Mark

PY - 2020/6/5

Y1 - 2020/6/5

N2 - 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.

AB - 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.

U2 - 10.1038/s41597-020-0497-4

DO - 10.1038/s41597-020-0497-4

M3 - Journal article

SN - 2052-4463

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ER -