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Science 22 April 2005:
Vol. 308. no. 5721, pp. 554 - 557
DOI: 10.1126/science.1107851
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Reports

Comparative Metagenomics of Microbial Communities

Susannah Green Tringe,1,2* Christian von Mering,3* Arthur Kobayashi,1 Asaf A. Salamov,1 Kevin Chen,4 Hwai W. Chang,5 Mircea Podar,5 Jay M. Short,5 Eric J. Mathur,5 John C. Detter,1 Peer Bork,3 Philip Hugenholtz,1 Edward M. Rubin1,2{dagger}

The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content analysis reveals habitat-specific fingerprints that reflect known characteristics of the sampled environments. The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.

1 Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
2 Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA 94720, USA.
3 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
4 University of California, Berkeley, Department of Electrical Engineering and Computer Science, Berkeley, CA 94720, USA.
5 Diversa Corporation, 4955 Directors Place, San Diego, CA 92121, USA.

* S.G.T. and C.v.M. contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: emrubin{at}lbl.gov

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