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

Nature Biotechnology volume 37, pages 852–857 (2019)Cite this article

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An Author Correction to this article was published on 09 August 2019

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To the Editor — Rapid advances in DNA-sequencing and bioinformatics technologies in the past two decades have substantially improved understanding of the microbial world. This growing understanding relates to the vast diversity of microorganisms; how microbiota and microbiomes affect disease1 and medical treatment2; how microorganisms affect the health of the planet3; and the nascent exploration of the medical4, forensic5, environmental6 and agricultural7 applications of microbiome biotechnology. Much of this work has been driven by marker-gene surveys (for example, bacterial/archaeal 16S rRNA genes, fungal internal-transcribed-spacer regions and eukaryotic 18S rRNA genes), which profile microbiota with varying degrees of taxonomic specificity and phylogenetic information. The field is now transitioning to integrate other data types, such as metabolite8, metaproteome9 or metatranscriptome9,10 profiles.

The QIIME 1 microbiome bioinformatics platform has supported many microbiome studies and gained a broad user and developer community. Interactions with QIIME 1 users in our online support forum, our workshops and direct collaborations have shown the platform’s potential to serve an increasingly diverse array of microbiome researchers in academia, government and industry. Here, we present QIIME 2, a completely reengineered and rewritten system that is expected to facilitate reproducible and modular analysis of microbiome data to enable the next generation of microbiome science.

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Fig. 1: QIIME 2 provides many interactive visualization tools.
Fig. 2: QIIME 2 iteratively records data provenance, ensuring bioinformatics reproducibility.

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.

References

  1. Smith, M. I. et al. Science 339, 548–554 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Gopalakrishnan, V. et al. Science 359, 97–103 (2018).

    Article  CAS  PubMed  Google Scholar 

  3. Gehring, C. A., Sthultz, C. M., Flores-Rentería, L., Whipple, A. V. & Whitham, T. G. Proc. Natl Acad. Sci. USA 114, 11169–11174 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Lee, K., Pletcher, S. D., Lynch, S. V., Goldberg, A. N. & Cope, E. K. Front. Cell. Infect. Microbiol. 8, 168 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Metcalf, J. L. et al. Science 351, 158–162 (2016).

    Article  CAS  PubMed  Google Scholar 

  6. Rubin, R. L. et al. Ecol. Appl. 28, 1594–1605 (2018).

    Article  PubMed  Google Scholar 

  7. Pineda, A., Kaplan, I. & Bezemer, T. M. Trends Plant Sci. 22, 770–778 (2017).

    Article  CAS  PubMed  Google Scholar 

  8. Kapono, C. A. et al. Sci. Rep. 8, 3669 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  9. Verberkmoes, N. C. et al. ISME J. 3, 179–189 (2009).

    Article  CAS  PubMed  Google Scholar 

  10. Barr, T. et al. Gut Microbes 9, 338–356 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Callahan, B. J. et al. Nat. Methods 13, 581–3 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Amir, A. et al. mSystems 2, e00191–16 (2017).

    PubMed  PubMed Central  Google Scholar 

  13. Bokulich, N. A. et al. Microbiome 6, 90 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  14. Janssen, S. et al. mSystems 3, e00021–18 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  15. Bokulich, N. A. et al. mSystems 3, e00219–18 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Bokulich, N. et al. J. Open Source Softw. 3, 934 (2018).

    Article  Google Scholar 

  17. Sedio, B. E., Rojas Echeverri, J. C., Boya, P. C. A. & Wright, S. J. Ecology 98, 616–623 (2017).

    Article  PubMed  Google Scholar 

  18. Wang, M. et al. Nat. Biotechnol. 34, 828–837 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Hillmann, B. et al. mSystems 3, e00069–18 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  20. Truong, D. T. et al. Nat. Methods 12, 902–903 (2015).

    Article  CAS  PubMed  Google Scholar 

  21. Langille, M. G. I. et al. Nat. Biotechnol. 31, 814–821 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Kluyver, T. et al. Positioning and power in academic publishing: players, agents and agendas. in Proc. 20th International Conference on Electronic Publishing (eds Loizides, F. & Schmidt, B.) 87–90 (IOS Press, 2016).

  23. Amstutz, P. et al. https://doi.org/10.6084/m9.figshare.3115156.v2 (2016).

  24. Gonzalez, A. et al. Nat. Methods 15, 796–798 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Schloss, P. D. et al. Appl. Environ. Microbiol. 75, 7537–7541 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. McMurdie, P. J. & Holmes, S. PLoS One 8, e61217 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Huber, W. et al. Nat. Methods 12, 115–121 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Franzosa, E. A. et al. Nat. Methods 15, 962–968 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. McDonald, D. et al. Gigascience 1, 7 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

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

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Contributions

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.

Corresponding author

Correspondence to J. Gregory Caporaso.

Additional information

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

Supplementary information

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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