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).
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).
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
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
Correspondence to Rob Knight.
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J.R.S. is an employee of Luca Technologies.