QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

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1 Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
2 Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
3 Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
4 Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
5 Department of Population Health and Reproduction, University of California, Davis, CA, USA
6 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
7 Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
8 University of Copenhagen, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Copenhagen, Denmark
9 Centre for Integrative Biology, University of Trento, Trento, Italy
10 State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
11 Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China
12 University of Chinese Academy of Sciences, Beijing, China
13 Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
14 Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
15 Hepatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
16 Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
17 Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
18 Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA
19 Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
20 Collaborative mass spectrometry innovation center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
21 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
22 Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
23 Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada
24 A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA
25 Department of Biology, University of British Columbia Okanagan, Okanagan, BC, Canada
26 Computational Bioscience Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
27 Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
28 Irving K. Barber School of Arts and Sciences, Department of Biology, The University of British Columbia, Kelowna, BC, Canada
29 Department of Medicine, The University of British Columbia, Kelowna, BC, Canada
30 Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
31 Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
32 Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
33 Stanford University, Statistics Department, Palo Alto, CA, USA
34 Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
35 Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
36 Broad Institute of MIT and Harvard, Cambridge, MA, USA
37 Research School of Biology, The Australian National University, Canberra, ACT, Australia
38 Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany
39 Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
40 College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
41 San Diego State University, Department of Biology, San Diego, CA, USA
42 Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA
43 Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
44 Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
45 Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA
46 Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
47 Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
48 Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
49 Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
50 Department of Statistics, University of Washington, Seattle, WA, USA
51 Department of Animal Science, Colorado State University, Fort Collins, CO, USA
52 Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, BC, Canada
53 Mountain View, Google LLC, Mountain View, CA, USA
54 Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
55 School of Information Studies, Syracuse University, Syracuse, NY, USA
56 School of STEM, University of Washington Bothell, Bothell, WA, USA
57 Department of Biological Sciences, Webster University, St Louis, MO, USA
58 Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA
59 College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
60 Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
61 Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
62 Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA
63 Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
64 Department of Biology, San Diego State University, San Diego, CA, USA
65 Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
66 Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
67 Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
68 Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
69 Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
70 Department of Mathematics, University of Arizona, Tucson, AZ, USA
71 National Laboratory Service, Environment Agency, Starcross, UK
72 College of Agriculture and Life Sciences, University of Florida, Gainesville, FL, USA
73 Department of Biostatistics, University of Washington, Seattle, WA, USA
74 University of Washington Bothell, School of STEM, Division of Biological Sciences, Bothell, WA, USA
75 Merck & Co. Inc., Kenilworth, NJ, USA
76 Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
DOI
10.7287/peerj.preprints.27295v2
Published
Accepted
Subject Areas
Bioinformatics, Ecology, Microbiology, Data Science
Keywords
microbiome, bioinformatics, data science, software, microbial ecology, reproducibility
Copyright
© 2018 Bolyen et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope E, Da Silva R, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley G, Janssen S, Jarmusch AK, Jiang L, Kaehler B, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MG, Lee J, Ley R, Liu Y, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton J, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson, II MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CH, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. 2018. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ Preprints 6:e27295v2

Abstract

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.

Author Comment

This version integrates editor feedback received prior to peer review at another journal. It adds discussion of other tools being used for microbiome data science, worked examples illustrating how QIIME 2 works (Supplementary File 2), and feedback on QIIME 2 from 15 users (Supplementary File 3).

Supplemental Information

Supplementary File 1 contains the QIIME 2 .qzv files corresponding to Figure 1a-d

These are also accessible at https://github.com/qiime2/paper1 and can be viewed using QIIME 2 View ( https://view.qiime2.org ) where readers can interact with the results, and explore the methods used to generate them (see the Provenance tab after loading a .qzv file with QIIME 2 View).

DOI: 10.7287/peerj.preprints.27295v2/supp-1