Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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

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

This article has been updated

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

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. 1.

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

    CAS  Article  Google Scholar 

  2. 2.

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

    CAS  Article  Google Scholar 

  3. 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).

    CAS  Article  Google Scholar 

  4. 4.

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

    Article  Google Scholar 

  5. 5.

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

    CAS  Article  Google Scholar 

  6. 6.

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

    Article  Google Scholar 

  7. 7.

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

    CAS  Article  Google Scholar 

  8. 8.

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

    Article  Google Scholar 

  9. 9.

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

    CAS  Article  Google Scholar 

  10. 10.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11.

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

    CAS  Article  Google Scholar 

  12. 12.

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

    PubMed  PubMed Central  Google Scholar 

  13. 13.

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

    Article  Google Scholar 

  14. 14.

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

    Article  Google Scholar 

  15. 15.

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

    Article  Google Scholar 

  16. 16.

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

    Article  Google Scholar 

  17. 17.

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

    Article  Google Scholar 

  18. 18.

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

    CAS  Article  Google Scholar 

  19. 19.

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

    Article  Google Scholar 

  20. 20.

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

    CAS  Article  Google Scholar 

  21. 21.

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

    CAS  Article  Google Scholar 

  22. 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. 23.

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

  24. 24.

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

    CAS  Article  Google Scholar 

  25. 25.

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

    CAS  Article  Google Scholar 

  26. 26.

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

    CAS  Article  Google Scholar 

  27. 27.

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

    CAS  Article  Google Scholar 

  28. 28.

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

    CAS  Article  Google Scholar 

  29. 29.

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

    Article  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

Affiliations

Authors

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.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing