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

Nat Methods. 2018 Oct;15(10):796-798. doi: 10.1038/s41592-018-0141-9. Epub 2018 Oct 1.

Authors

Antonio Gonzalez¹, Jose A Navas-Molina^{1 2 3}, Tomasz Kosciolek¹, Daniel McDonald¹, Yoshiki Vázquez-Baeza¹, Gail Ackermann¹, Jeff DeReus¹, Stefan Janssen¹, Austin D Swafford⁴, Stephanie B Orchanian⁴, Jon G Sanders¹, Joshua Shorenstein^{1 5}, Hannes Holste^{1 2}, Semar Petrus⁶, Adam Robbins-Pianka⁷, Colin J Brislawn⁸, Mingxun Wang⁹, Jai Ram Rideout¹⁰, Evan Bolyen¹⁰, Matthew Dillon¹⁰, J Gregory Caporaso^{10 11}, Pieter C Dorrestein^{1 4 9}, Rob Knight^{12 13 14}

Affiliations

¹ Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
² Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
³ Google LLC, Mountain View, CA, USA.
⁴ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
⁵ Inscripta, Inc., Boulder, CO, USA.
⁶ Department of Biology, University of California, San Diego, La Jolla, CA, USA.
⁷ Department of Computer Science, University of Colorado, Boulder, Boulder, CO, USA.
⁸ Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
⁹ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
¹⁰ Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
¹¹ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
¹² Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
¹³ Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
¹⁴ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. robknight@ucsd.edu.

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.

Publication types

Meta-Analysis
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computational Biology / methods*
Humans
Internet*
Metagenomics*
Microbiota*
Software*
User-Computer Interface

Abstract

Publication types

MeSH terms

Grants and funding