Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

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
Prev | Table of Contents | Next

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

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Phylogenetic Diversity and Metabolic Potential Revealed in a Glacier Ice Metagenome.
C. Simon, A. Wiezer, A. W. Strittmatter, and R. Daniel (2009)
Appl. Envir. Microbiol. 75, 7519-7526
   Abstract »    Full Text »    PDF »
Windshield splatter analysis with the Galaxy metagenomic pipeline.
S. Kosakovsky Pond, S. Wadhawan, F. Chiaromonte, G. Ananda, W.-Y. Chung, J. Taylor, A. Nekrutenko, and The Galaxy Team (2009)
Genome Res. 19, 2144-2153
   Abstract »    Full Text »    PDF »
Community proteogenomics reveals insights into the physiology of phyllosphere bacteria.
N. Delmotte, C. Knief, S. Chaffron, G. Innerebner, B. Roschitzki, R. Schlapbach, C. von Mering, and J. A. Vorholt (2009)
PNAS 106, 16428-16433
   Abstract »    Full Text »    PDF »
Visual and statistical comparison of metagenomes.
S. Mitra, B. Klar, and D. H. Huson (2009)
Bioinformatics 25, 1849-1855
   Abstract »    Full Text »    PDF »
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix.
M. N. Price, P. S. Dehal, and A. P. Arkin (2009)
Mol. Biol. Evol. 26, 1641-1650
   Abstract »    Full Text »    PDF »
Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level.
M. Keller and R. Hettich (2009)
Microbiol. Mol. Biol. Rev. 73, 62-70
   Abstract »    Full Text »    PDF »
Quantifying environmental adaptation of metabolic pathways in metagenomics.
T. A. Gianoulis, J. Raes, P. V. Patel, R. Bjornson, J. O. Korbel, I. Letunic, T. Yamada, A. Paccanaro, L. J. Jensen, M. Snyder, et al. (2009)
PNAS 106, 1374-1379
   Abstract »    Full Text »    PDF »
Discovering Functional Novelty in Metagenomes: Examples from Light-Mediated Processes.
A. H. Singh, T. Doerks, I. Letunic, J. Raes, and P. Bork (2009)
J. Bacteriol. 191, 32-41
   Abstract »    Full Text »    PDF »
A Bioinformatician's Guide to Metagenomics.
V. Kunin, A. Copeland, A. Lapidus, K. Mavromatis, and P. Hugenholtz (2008)
Microbiol. Mol. Biol. Rev. 72, 557-578
   Abstract »    Full Text »    PDF »
Signature Genes as a Phylogenomic Tool.
B. E. Dutilh, B. Snel, T. J. G. Ettema, and M. A. Huynen (2008)
Mol. Biol. Evol. 25, 1659-1667
   Abstract »    Full Text »    PDF »
Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment.
J. F. Biddle, S. Fitz-Gibbon, S. C. Schuster, J. E. Brenchley, and C. H. House (2008)
PNAS 105, 10583-10588
   Abstract »    Full Text »    PDF »
Signature, a web server for taxonomic characterization of sequence samples using signature genes.
B. E. Dutilh, Y. He, M. L. Hekkelman, and M. A. Huynen (2008)
Nucleic Acids Res. 36, W470-W474
   Abstract »    Full Text »    PDF »
The cbb3 Oxidases Are an Ancient Innovation of the Domain Bacteria.
A.-L. Ducluzeau, S. Ouchane, and W. Nitschke (2008)
Mol. Biol. Evol. 25, 1158-1166
   Abstract »    Full Text »    PDF »
Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton.
D. E. Hunt, L. A. David, D. Gevers, S. P. Preheim, E. J. Alm, and M. F. Polz (2008)
Science 320, 1081-1085
   Abstract »    Full Text »    PDF »
Recent Advances in the Expression, Evolution, and Dynamics of Prokaryotic Genomes.
C. M. Arraiano, J. Bamford, H. Brussow, A. J. Carpousis, V. Pelicic, K. Pfluger, P. Polard, and J. Vogel (2007)
J. Bacteriol. 189, 6093-6100
   Full Text »    PDF »
Quantitative assessment of protein function prediction from metagenomics shotgun sequences.
E. D. Harrington, A. H. Singh, T. Doerks, I. Letunic, C. von Mering, L. J. Jensen, J. Raes, and P. Bork (2007)
PNAS 104, 13913-13918
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)