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This article is part of the supplement: Beyond the Genome 2011

Open Access Open Badges Invited speaker presentation

Microbial reference genomes for human metagenomics

Sarah K Highlander

  • Correspondence: Sarah K Highlander

Author affiliations

Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA

Citation and License

Genome Biology 2011, 12(Suppl 1):I7  doi:10.1186/gb-2011-12-s1-i7

The electronic version of this article is the complete one and can be found online at:

Published:19 September 2011

© 2011 Highlander; licensee BioMed Central Ltd.

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 work is properly cited.

Invited speaker presentation

A key resource for metagenomics projects is a representative catalog of annotated microbial genome sequences to serve as a reference for classification and functional annotation [1]. The Human Microbiome Project (HMP) [2], which is funded by the National Institutes of Health, began with the goal of sequencing 600 genomes from culturable prokaryotes that are representative of those inhabiting the major niches within and on the human body. This effort has been expanded to include uncultured organisms, small eukaryotes, and viruses that infect prokaryotes or eukaryotes, and the current sequencing target is 3,000 microbes. An automated pipeline for prokaryotic gene calling and annotation has been established for the project, yet very few of the HMP organisms have been subjected to in-depth analysis. Comparisons of several HMP genomes have revealed substantial intraspecies differences and provide clues about the pathogenic and physiological potential of these organisms.


  1. Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, et al.: A catalog of reference genomes from the human microbiome.

    Science 2010, 328:994-999. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  2. Data Analysis and Coordination Center for the Human Microbiome Project [] webcite