Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (original) (raw)

Data availability

Data for the analyses presented in Fig. 1 are available as follows: Earth Microbiome Project data in Fig. 1a were obtained from ftp://ftp.microbio.me/emp/release1, and the American Gut Project (AGP) data were obtained from Qiita (http://qiita.microbio.me) study ID 10317. Sequence data in Fig. 1b are available in Qiita under study ID 10249 and the EBI under accession number ERP016173. Sequence data in Fig. 1c are available in Qiita under study ID 925 and the EBI under accession number ERP022167. Data in Fig. 1d are available in the q2-ili GitHub repository (https://github.com/biocore/q2-ili). Interactive versions of the Fig. 1 visualizations can be accessed at https://github.com/qiime2/paper1.

Code availability

QIIME 2 is open source and free for all use, including commercial. It is licensed under a BSD three-clause license. Source code is available at https://github.com/qiime2. Help for QIIME 2 is provided at https://forum.qiime2.org.

Change history

• 09 August 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Acknowledgements

QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Sloan Foundation (J.G.C. and R.K.); ERCSTG project MetaPG (N.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (Y.B.); the Australian National Health and Medical Research Council APP1085372 (G.A.H., J.G.C., Von Bing Yap and R.K.); the Natural Sciences and Engineering Research Council (NSERC) to D.L.G.; and the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. All NCI coauthors were supported by the Intramural Research Program of the National Cancer Institute. S.M.G. and C. Diener were supported by the Washington Research Foundation Distinguished Investigator Award. Thanks to the Yellowstone Center for Resources for research permit no. 5664 to J.R.S. for Yellowstone access and sample collection. We thank P. J. McMurdie for helpful discussion on the relationships between QIIME 2 and phyloseq. We would like to thank the users of QIIME 1 and 2, whose invaluable feedback has shaped QIIME 2. In particular, we would like to thank A. Abdelfattah (Stockholm University, Sweden), R. C. T. Boutin (University of British Columbia, Canada), D. J. Bradshaw II (Florida Atlantic University Harbor Branch Oceanographic Institute, USA), L. Bullington (MPG Ranch, USA), J. W. Debelius (Karolinska Institutet, Sweden), C. Duvallet (Massachusetts Institute of Technology, USA), E. Korzune Ganda (Cornell University, USA), A. Mahnert (Medical University of Graz, Austria), M. C. Melendrez (St. Cloud State University, USA), D. O’Rourke (University of New Hampshire, USA), A. R. Rivers (USDA ARS, USA), B. Sen (Tianjin University, China), S. Tangedal (Haukeland University Hospital and University of Bergen, Norway), P. J. Torres (San Diego State University, USA) and J. Warren (National Laboratory Service, UK) for writing end-user reviews included in the Supplementary Methods.

Author information

Author notes

1. These authors contributed equally: Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich.

Authors and Affiliations

1. Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
   Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, John Chase, Emily K. Cope, Kestrel Gorlick, Christopher R. Keefe, Paul Keim, Jorden Kreps, Ahmad Turan Naimey, Talima Pearson, Arron Shiffer & J. Gregory Caporaso
2. Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
   Christian C. Abnet, Erikka Loftfield, Rashmi Sinha, Emily Vogtmann & Yunhu Wan
3. Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
   Gabriel A. Al-Ghalith
4. Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
   Harriet Alexander
5. Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA
   Harriet Alexander & C. Titus Brown
6. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
   Eric J. Alm & Claire Duvallet
7. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
   Eric J. Alm
8. Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
   Manimozhiyan Arumugam, Asker Brejnrod & Lasse Buur Rasmussen
9. Centre for Integrative Biology, University of Trento, Trento, Italy
   Francesco Asnicar & Nicola Segata
10. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
    Yang Bai & Yong-Xin Liu
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
    Yang Bai & Yong-Xin Liu
12. University of Chinese Academy of Sciences, Beijing, China
    Yang Bai
13. Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
    Jordan E. Bisanz
14. Division of Gastroenterology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
    Kyle Bittinger
15. Hepatology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
    Kyle Bittinger
16. Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
    Colin J. Brislawn
17. Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA
    Benjamin J. Callahan
18. Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
    Benjamin J. Callahan
19. Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
    Andrés Mauricio Caraballo-Rodríguez, Ricardo Da Silva, Pieter C. Dorrestein, Madeleine Ernst, Julia M. Gauglitz, Alan K. Jarmusch, Kyo Bin Kang, Irina Koester, Alexey V. Melnik, Louis Felix Nothias, Daniel Petras, Anupriya Tripathi & Mingxun Wang
20. Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
    Emily K. Cope & J. Gregory Caporaso
21. Institute for Systems Biology, Seattle, WA, USA
    Christian Diener & Sean M. Gibbons
22. Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
    Gavin M. Douglas
23. Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada
    Daniel M. Durall
24. A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA
    Christian F. Edwardson
25. Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
    Madeleine Ernst
26. Department of Biology, University of British Columbia Okanagan, Okanagan, British Columbia, Canada
    Mehrbod Estaki
27. Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
    Jennifer Fouquier & Michael Shaffer
28. Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
    Jennifer Fouquier, Catherine Lozupone, Elmar Pruesse & Michael Shaffer
29. eScience Institute, University of Washington, Seattle, WA, USA
    Sean M. Gibbons
30. Irving K. Barber School of Arts and Sciences, Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada
    Deanna L. Gibson
31. Department of Medicine, University of British Columbia, Kelowna, British Columbia, Canada
    Deanna L. Gibson
32. Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
    Antonio Gonzalez, Hannes Holste, Clarisse Marotz, Daniel McDonald, Jamie T. Morton, Jose A. Navas-Molina, Se Jin Song, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Zhenjiang Zech Xu, Qiyun Zhu & Rob Knight
33. Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
    Jiarong Guo
34. Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
    Benjamin Hillmann & Dan Knights
35. Statistics Department, Stanford University, Palo Alto, CA, USA
    Susan Holmes
36. Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
    Hannes Holste
37. Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
    Curtis Huttenhower & Lauren J. McIver
38. Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Curtis Huttenhower & Lauren J. McIver
39. Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
    Gavin A. Huttley & Benjamin D. Kaehler
40. Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany
    Stefan Janssen
41. Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
    Lingjing Jiang
42. School of Science, University of New South Wales, Canberra, Australian Capital Territory, Australia
    Benjamin D. Kaehler
43. College of Pharmacy, Sookmyung Women’s University, Seoul, Republic of Korea
    Kyo Bin Kang
44. Department of Biology, San Diego State University, San Diego, CA, USA
    Scott T. Kelley
45. Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA
    Dan Knights
46. Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
    Irina Koester
47. Department of Pediatrics, University of California San Diego, La Jolla, California, USA
    Tomasz Kosciolek
48. Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
    Morgan G. I. Langille
49. Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA
    Joslynn Lee
50. Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
    Ruth Ley & William Walters
51. Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
    Ruth Ley
52. Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
    Massoud Maher, Jamie T. Morton & Jose A. Navas-Molina
53. Department of Statistics, University of Washington, Seattle, WA, USA
    Bryan D. Martin
54. Department of Animal Science, Colorado State University, Fort Collins, CO, USA
    Jessica L. Metcalf
55. Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada
    Sydney C. Morgan
56. Google LLC, Mountain View, CA, USA
    Jose A. Navas-Molina
57. Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
    Stephanie B. Orchanian, Austin D. Swafford & Rob Knight
58. School of Information Studies, Syracuse University, Syracuse, NY, USA
    Samuel L. Peoples
59. School of STEM, University of Washington Bothell, Bothell, WA, USA
    Samuel L. Peoples
60. Department of Biological Sciences, Webster University, St. Louis, MO, USA
    Mary Lai Preuss & Patrick Rosenthal
61. Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA
    Adam Rivers & Kyle C. Weber
62. College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
    Michael S. Robeson II
63. Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
    John R. Spear
64. Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA
    Luke R. Thompson
65. Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
    Luke R. Thompson
66. Department of Biology, San Diego State University, San Diego, CA, USA
    Pedro J. Torres
67. Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
    Pauline Trinh
68. Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
    Anupriya Tripathi & Fernando Vargas
69. Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
    Peter J. Turnbaugh
70. Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
    Sabah Ul-Hasan
71. Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
    Justin J. J. van der Hooft
72. Department of Mathematics, University of Arizona, Tucson, AZ, USA
    Max von Hippel
73. National Laboratory Service, Environment Agency, Starcross, UK
    Jonathan Warren
74. College of Agriculture and Life Sciences, University of Florida, Gainesville, FL, USA
    Kyle C. Weber
75. Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
    Charles H. D. Williamson
76. Department of Biostatistics, University of Washington, Seattle, WA, USA
    Amy D. Willis
77. School of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA
    Jesse R. Zaneveld
78. Merck & Co. Inc., Kenilworth, NJ, USA
    Yilong Zhang
79. Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
    Rob Knight

Authors

1. Evan Bolyen
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2. Jai Ram Rideout
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3. Matthew R. Dillon
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4. Nicholas A. Bokulich
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5. Christian C. Abnet
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6. Gabriel A. Al-Ghalith
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7. Harriet Alexander
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8. Eric J. Alm
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9. Manimozhiyan Arumugam
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10. Francesco Asnicar
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11. Yang Bai
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12. Jordan E. Bisanz
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13. Kyle Bittinger
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14. Asker Brejnrod
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15. Colin J. Brislawn
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16. C. Titus Brown
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18. Andrés Mauricio Caraballo-Rodríguez
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E.B., J.R.R., M.R.D., N.A.B., Y.B., J.E.B., C.J.B., A.M.C.-R., E.K.C., C. Diener, R.D., C.F.E., M. Ernst, M. Estaki, A.G., J.M.G., D.L.G., S.M.G., A.K.J., K.B.K., S.T.K., I.K., T.K., J.L., Y.-X.L., A.V.M., J.L.M., L.F.N., S.B.O., D.P., A.S., S.J.S., A.D.S., L.R.T., P. J. Torres, P. J. Turnbaugh, S.U.-H., F.V., J.W., R.K. and J.G.C. developed documentation, educational materials and/or user/developer support content. E.B., J.R.R., M.R.D., N.A.B., R.K. and J.G.C. wrote the manuscript; all authors assisted with revision of the manuscript. E.B., J.R.R., M.R.D., N.A.B. and J.G.C. designed and developed the QIIME 2 framework. D.M.D., A.G., R.L., E.L., S.C.M., R.S., J.R.S., W.W., C.H.D.W. and R.K. contributed data used in the manuscript and/or testing of QIIME 2. C.C.A., C.T.B., E.K.C., P.C.D., S.H., P.K., E.L., T.P., R.S., E.V., Y.W. and R.K. contributed to the design of analytical methods. E.B., J.R.R., M.R.D., N.A.B., G.A.A.-G., H.A., E.J.A., M.A., F.A., K.B., A.B., B.J.C., J.C., G.M.D., C. Duvallet, M. Ernst, J.F., A.G., K.G., J.G., S.M.G., B.H., H.H., C.H., G.H., S.J., L.J., B.D.K., C.R.K., D.K., J.K., M.G.I.L., C.L., M.M., C.M., B.D.M., D.M., L.J.M., J.T.M., A.T.N., J.A.N.-M., S.L.P., M.L.P., E.P., L.B.R., A.R., M.S.R., P.R., N.S., M.S., P.T., A.T., J.J.J.v.d.H., Y.V.-B., M.V., M.W., K.C.W., A.D.W., Z.Z.X., J.R.Z., Y.Z., Q.Z. and J.G.C. contributed software to QIIME 2 plugins, interfaces, framework and/or build and test systems.

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Correspondence toJ. Gregory Caporaso.

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Editor’s Note: This paper has been peer-reviewed.

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Supplementary Information

Supplementary Figs. 1–3 and Supplementary Methods

Supplementary File 1

Interactive versions of the visualizations presented in Fig. 1. These can be viewed by using QIIME 2, for example at https://view.qiime2.org.

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Bolyen, E., Rideout, J.R., Dillon, M.R. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.Nat Biotechnol 37, 852–857 (2019). https://doi.org/10.1038/s41587-019-0209-9

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• Published: 24 July 2019
• Issue Date: August 2019
• DOI: https://doi.org/10.1038/s41587-019-0209-9