Metagenomic profiling: microarray analysis of an environmental genomic library

Sebat, J. L., Colwell, F. S., Crawford, R. L. (August 2003) Metagenomic profiling: microarray analysis of an environmental genomic library. Applied and Environmental Microbiology, 69 (8). pp. 4927-34. ISSN 00992240 (ISSN)

DOI: 10.1128/AEM.69.8.4927-4934.2003


Genomic libraries derived from environmental DNA (metagenomic libraries) are useful for characterizing uncultured microorganisms. However, conventional library-screening techniques permit characterization of relatively few environmental clones. Here we describe a novel approach for characterization of a metagenomic library by hybridizing the library with DNA from a set of groundwater isolates, reference strains, and communities. A cosmid library derived from a microcosm of groundwater microorganisms was used to construct a microarray (COSMO) containing approximately 1-kb PCR products amplified from the inserts of 672 cosmids plus a set of 16S ribosomal DNA controls. COSMO was hybridized with Cy5-labeled genomic DNA from each bacterial strain, and the results were compared with the results for a common Cy3-labeled reference DNA sample consisting of a composite of genomic DNA from multiple species. The accuracy of the results was confirmed by the preferential hybridization of each strain to its corresponding rDNA probe. Cosmid clones were identified that hybridized specifically to each of 10 microcosm isolates, and other clones produced positive results with multiple related species, which is indicative of conserved genes. Many clones did not hybridize to any microcosm isolate; however, some of these clones hybridized to community genomic DNA, suggesting that they were derived from microbes that we failed to isolate in pure culture. Based on identification of genes by end sequencing of 17 such clones, DNA could be assigned to functions that have potential ecological importance, including hydrogen oxidation, nitrate reduction, and transposition. Metagenomic profiling offers an effective approach for rapidly characterizing many clones and identifying the clones corresponding to unidentified species of microorganisms.

Item Type: Paper
Uncontrolled Keywords: Base Sequence DNA, Bacterial/*analysis/chemistry *Gene Expression Profiling *Genomic Library Nucleic Acid Hybridization *Oligonucleotide Array Sequence Analysis
Subjects: bioinformatics > genomics and proteomics > analysis and processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
organism description > bacteria
CSHL Authors:
Communities: CSHL labs > Sebat lab
Depositing User: Matt Covey
Date: August 2003
Date Deposited: 02 Apr 2013 16:32
Last Modified: 02 Apr 2013 16:32
PMCID: PMC169101

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