Qiita: rapid, web-enabled microbiome meta-analysis

Antonio Gonzalez; Jose A. Navas-Molina; Tomasz Kosciolek; Daniel McDonald; Yoshiki Vázquez-Baeza; Gail Ackermann; Jeff DeReus; Stefan Janssen; Austin D. Swafford; Stephanie B. Orchanian; Jon G. Sanders; Joshua Shorenstein; Hannes Holste; Semar Petrus; Adam Robbins-Pianka; Colin J. Brislawn; Mingxun Wang; Jai Ram Rideout; Evan Bolyen; Matthew Dillon; J. Gregory Caporaso; Pieter C. Dorrestein; Rob Knight

doi:10.1038/s41592-018-0141-9

Qiita: rapid, web-enabled microbiome meta-analysis

Antonio Gonzalez, Jose A. Navas-Molina, Tomasz Kosciolek, Daniel McDonald, Yoshiki Vázquez-Baeza, Gail Ackermann, Jeff DeReus, Stefan Janssen, Austin D. Swafford, Stephanie B. Orchanian, Jon G. Sanders, Joshua Shorenstein, Hannes Holste, Semar Petrus, Adam Robbins-Pianka, Colin J. Brislawn, Mingxun Wang, Jai Ram Rideout, Evan Bolyen, Matthew DillonJ. Gregory Caporaso, Pieter C. Dorrestein, Rob Knight

Informatics, Computing, and Cyber Systems, School of

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

247 Scopus citations

Abstract

Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.

Original language	English (US)
Pages (from-to)	796-798
Number of pages	3
Journal	Nature Methods
Volume	15
Issue number	10
DOIs	https://doi.org/10.1038/s41592-018-0141-9
State	Published - Oct 1 2018

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Gonzalez, A., Navas-Molina, J. A., Kosciolek, T., McDonald, D., Vázquez-Baeza, Y., Ackermann, G., DeReus, J., Janssen, S., Swafford, A. D., Orchanian, S. B., Sanders, J. G., Shorenstein, J., Holste, H., Petrus, S., Robbins-Pianka, A., Brislawn, C. J., Wang, M., Rideout, J. R., Bolyen, E., ... Knight, R. (2018). Qiita: rapid, web-enabled microbiome meta-analysis. Nature Methods, 15(10), 796-798. https://doi.org/10.1038/s41592-018-0141-9

Gonzalez, A, Navas-Molina, JA, Kosciolek, T, McDonald, D, Vázquez-Baeza, Y, Ackermann, G, DeReus, J, Janssen, S, Swafford, AD, Orchanian, SB, Sanders, JG, Shorenstein, J, Holste, H, Petrus, S, Robbins-Pianka, A, Brislawn, CJ, Wang, M, Rideout, JR, Bolyen, E, Dillon, M, Caporaso, JG, Dorrestein, PC & Knight, R 2018, 'Qiita: rapid, web-enabled microbiome meta-analysis', Nature Methods, vol. 15, no. 10, pp. 796-798. https://doi.org/10.1038/s41592-018-0141-9

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title = "Qiita: rapid, web-enabled microbiome meta-analysis",

abstract = "Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.",

author = "Antonio Gonzalez and Navas-Molina, {Jose A.} and Tomasz Kosciolek and Daniel McDonald and Yoshiki V{\'a}zquez-Baeza and Gail Ackermann and Jeff DeReus and Stefan Janssen and Swafford, {Austin D.} and Orchanian, {Stephanie B.} and Sanders, {Jon G.} and Joshua Shorenstein and Hannes Holste and Semar Petrus and Adam Robbins-Pianka and Brislawn, {Colin J.} and Mingxun Wang and Rideout, {Jai Ram} and Evan Bolyen and Matthew Dillon and Caporaso, {J. Gregory} and Dorrestein, {Pieter C.} and Rob Knight",

note = "Funding Information: We are grateful to J. Debelius, J. Jansson, D. Bazaldua, and J. Kuczynski for their help in improving Qiita via suggestion, code changes, and contributed datasets, or during the preparation of this manuscript; and to J. Gordon and his laboratory for helpful discussions. This work was supported in part by the Alfred P. Sloan Foundation (2017-9838 and 2015-13933 (R.K.)), the NIH/NIDDK (P01DK078669 (R.K.)), the NSF (DBI-1565057 and 1565100 (J.G.C. and R.K.)), the Office of Naval Research (ONR; N00014-15-1-2809 (R.K.)), and the US Army (CDMRP W81XWH-15-1-0653 (R.K.)). Publisher Copyright: {\textcopyright} 2018, The Author(s), under exclusive licence to Springer Nature America, Inc.",

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AU - Vázquez-Baeza, Yoshiki

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AU - DeReus, Jeff

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AU - Swafford, Austin D.

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AU - Shorenstein, Joshua

AU - Holste, Hannes

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AU - Robbins-Pianka, Adam

AU - Brislawn, Colin J.

AU - Wang, Mingxun

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AU - Bolyen, Evan

AU - Dillon, Matthew

AU - Caporaso, J. Gregory

AU - Dorrestein, Pieter C.

AU - Knight, Rob

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Qiita: rapid, web-enabled microbiome meta-analysis

Abstract

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