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Originally published in Science Express on 1 February 2007
Science 23 February 2007:
Vol. 315. no. 5815, pp. 1126 - 1130
DOI: 10.1126/science.1133420
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Reports

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

C. von Mering,1* P. Hugenholtz,2 J. Raes,1 S. G. Tringe,2 T. Doerks,1 L. J. Jensen,1 N. Ward,3 P. Bork1{dagger}

The taxonomic composition of environmental communities is an important indicator of their ecology and function. We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA–based approaches depending on the polymerase chain reaction. Mapping marker genes from four diverse environmental data sets onto a reference species phylogeny shows that certain communities evolve faster than others. The method also enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time.

1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
2 DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
3 The Institute for Genomic Research, Rockville, MD 20850, USA.

* Present address: University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

{dagger} To whom correspondence should be addressed. E-mail: peer.bork{at}embl.de

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