Bioinformatics for the Human Microbiome Project

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Dirk Gevers¹^*, Mihai Pop²^*, Patrick D. Schloss³^*, Curtis Huttenhower¹^,⁴^*

1 The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, 2 Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America, 3 Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, United States of America, 4 Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America

Citation: Gevers D, Pop M, Schloss PD, Huttenhower C (2012) Bioinformatics for the Human Microbiome Project. PLoS Comput Biol 8(11): e1002779. doi:10.1371/journal.pcbi.1002779
Editor: Jonathan A. Eisen, University of California Davis, United States of America
Published: November 29, 2012
Copyright: © 2012 Gevers et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was funded by NIH U54HG004969 (Bruce W. Birren), R01HG004885 to MP, R01HG005975 to PDS, and R01HG005969 to CH. The funders had no role in the preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: dgevers@broadinstitute.org (DG); mpop@umiacs.umd.edu (MP); pschloss@umich.edu (PS); chuttenh@hsph.harvard.edu (CH)

Microbes inhabit virtually all sites of the human body, yet we know very little about the role they play in our health. In recent years, there has been increasing interest in studying human-associated microbial communities, particularly since microbial dysbioses have now been implicated in a number of human diseases [1]–[3]. Dysbiosis, the disruption of the normal microbial community structure, however, is impossible to define without first establishing what “normal microbial community structure” means within the healthy human microbiome. Recent advances in sequencing technologies have made it feasible to perform large-scale studies of microbial communities, providing the tools necessary to begin to address this question [4], [5]. This led to the implementation of the Human Microbiome Project (HMP) in 2007, an initiative funded by the National Institutes of Health Roadmap for Biomedical Research and constructed as a large, genome-scale community research project [6]. Any such project must plan for data analysis, computational methods development, and the public availability of tools and data; here, we provide an overview of the corresponding bioinformatics organization, history, and results from the HMP (Figure 1).