To the Editor: High-throughput sequencing is revolutionizing microbial ecology studies. Efforts like the Human Microbiome Projects1 and the US National Ecological Observatory Network2 are helping us to understand the role of microbial diversity in habitats within our own bodies and throughout the planet.

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Figure 1: QIIME analyses of the distal gut microbiotas of conventionally raised and conventionalized mice, gnotobiotic mice colonized with a human fecal gut microbiota (H-mice), and human adult mono- and dizygotic twins.


1National Institutes of Health Human Microbiome Project Working Group et al. Genome Res. 19, 2317–2323 (2009).

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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).

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Author notes

J Gregory Caporaso, Justin Kuczynski and Jesse Stombaugh: These authors contributed equally to this work.


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

Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA

Justin Kuczynski, William A Walters & Jesse Zaneveld

Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA

Kyle Bittinger & Frederic D Bushman

Cooperative Institute for Research in Environmental Sciences and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA

Noah Fierer

Department of Computer Science, University of Colorado, Boulder, Colorado, USA

Antonio Gonzalez Peña, Julia K Goodrich & Dan Knights

Center for Genome Sciences, Washington University School of Medicine, St. Louis, Missouri, USA

Jeffrey I Gordon, Brian D Muegge, Peter J Turnbaugh & Tanya Yatsunenko

Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.

Gavin A Huttley

Department of Biology, San Diego State University, San Diego, California, USA

Scott T Kelley

Department of Microbiology, Cornell University, Ithaca, New York, USA

Jeremy E Koenig & Ruth E Ley

Luca Technologies, Golden, Colorado, USA

Joel R Sevinsky

Howard Hughes Medical Institute, Boulder, Colorado, USA

Rob Knight


Corresponding author

Correspondence to Rob Knight.

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Competing interests

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