Rapid quantitative profiling of complex microbial populations
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 unders...
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Published in | Nucleic acids research Vol. 34; no. 1; p. e5 |
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Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
Oxford University Press
01.01.2006
Oxford Publishing Limited (England) |
Subjects | |
Online Access | Get full text |
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Summary: | 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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Bibliography: | local:gnj007 ark:/67375/HXZ-6D97ZB34-R To whom correspondence should be addressed. Tel: +1 650 723 0005; Fax: +1 650 723 1399; Email: pbrown@pmgm.stanford.edu istex:B956990DC90E5334F9BF2BD1B1CD6F1FD0AAFD28 ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 |
ISSN: | 0305-1048 1362-4962 |
DOI: | 10.1093/nar/gnj007 |