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Nucleic Acids Research 2006 34(1):e5; doi:10.1093/nar/gnj007
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Published online 10 January 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Methods Online

Rapid quantitative profiling of complex microbial populations

Chana Palmer, Elisabeth M. Bik1,4, Michael B. Eisen5,6, Paul B. Eckburg1,2,4, Theodore R. Sana7, Paul K. Wolber7, David A. Relman1,2,4 and Patrick O. Brown3,8,*

Department of Genetics, Stanford University School of Medicine Stanford, CA, USA 1Department of Microbiology and Immunology, Stanford University School of Medicine Stanford, CA, USA 2Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine Stanford, CA, USA 3Department of Biochemistry, Stanford University School of Medicine Stanford, CA, USA 4Veterans Affairs Palo Alto Health Care System Palo Alto, CA, USA 5Lawrence Berkeley National Laboratory Berkeley, CA, USA 6Department of Molecular and Cell Biology, University of California Berkeley, CA, USA 7Agilent Technologies Santa Clara, CA, USA 8Howard Hughes Medical Institute Chevy Chase, MD, USA

*To whom correspondence should be addressed. Tel: +1 650 723 0005; Fax: +1 650 723 1399; Email: pbrown{at}pmgm.stanford.edu

Received October 14, 2005. Revised December 13, 2005. Accepted December 13, 2005.

Diverse and complex microbial ecosystems are found in virtually every environment on earth, yet we know very little about their composition and ecology. Comprehensive identification and quantification of the constituents of these microbial communities—a ‘census’—is an essential foundation for understanding their biology. To address this problem, we developed, tested and optimized a DNA oligonucleotide microarray composed of 10 462 small subunit (SSU) ribosomal DNA (rDNA) probes (7167 unique sequences) selected to provide quantitative information on the taxonomic composition of diverse microbial populations. Using our optimized experimental approach, this microarray enabled detection and quantification of individual bacterial species present at fractional abundances of <0.1% in complex synthetic mixtures. The estimates of bacterial species abundance obtained using this microarray are similar to those obtained by phylogenetic analysis of SSU rDNA sequences from the same samples—the current ‘gold standard’ method for profiling microbial communities. Furthermore, probes designed to represent higher order taxonomic groups of bacterial species reliably detected microbes for which there were no species-specific probes. This simple, rapid microarray procedure can be used to explore and systematically characterize complex microbial communities, such as those found within the human body.


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