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We thank our collaborators for their helpful suggestions on features, documentation and the manuscript, and our funding agencies for their commitment to open-source software. This work was supported in part by Howard Hughes Medical Institute and grants from the Crohn's and Colitis Foundation of America, the German Academic Exchange Service, the Bill and Melinda Gates Foundation, the Colorado Center for Biofuels and Biorefining and the US National Institutes of Health (DK78669, GM65103, GM8759, HG4872 and its ARRA supplement, HG4866, DK83981 and LM9451).

Author information

Author notes

    • J Gregory Caporaso
    • , Justin Kuczynski
    •  & Jesse Stombaugh

    These authors contributed equally to this work.


  1. Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA.

    • J Gregory Caporaso
    • , Jesse Stombaugh
    • , Elizabeth K Costello
    • , Catherine A Lozupone
    • , Daniel McDonald
    • , Meg Pirrung
    • , Jens Reeder
    • , Jeremy Widmann
    •  & Rob Knight
  2. Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA.

    • Justin Kuczynski
    • , William A Walters
    •  & Jesse Zaneveld
  3. Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

    • Kyle Bittinger
    •  & Frederic D Bushman
  4. Cooperative Institute for Research in Environmental Sciences and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.

    • Noah Fierer
  5. Department of Computer Science, University of Colorado, Boulder, Colorado, USA.

    • Antonio Gonzalez Peña
    • , Julia K Goodrich
    •  & Dan Knights
  6. Center for Genome Sciences, Washington University School of Medicine, St. Louis, Missouri, USA.

    • Jeffrey I Gordon
    • , Brian D Muegge
    • , Peter J Turnbaugh
    •  & Tanya Yatsunenko
  7. Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.

    • Gavin A Huttley
  8. Department of Biology, San Diego State University, San Diego, California, USA.

    • Scott T Kelley
  9. Department of Microbiology, Cornell University, Ithaca, New York, USA.

    • Jeremy E Koenig
    •  & Ruth E Ley
  10. Luca Technologies, Golden, Colorado, USA.

    • Joel R Sevinsky
  11. Howard Hughes Medical Institute, Boulder, Colorado, USA.

    • Rob Knight


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Competing interests

J.R.S. is an employee of Luca Technologies.

Corresponding author

Correspondence to Rob Knight.

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