Development and Evaluation of Microarray-Based Whole-Genome Hybridization for Detection of Microorganisms within the Context of Environmental Applications

The detection and identification of microorganisms in natural communities is a great challenge to biologists. Microarray-based genomic technology provides a promising high-throughput alternative to traditional microbial characterization. A novel prototype microarray containing whole genomic DNA, ter...

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Bibliographic Details
Published in:Environmental science & technology 2004-12, Vol.38 (24), p.6775-6782
Main Authors: Wu, Liyou, Thompson, Dorothea K, Liu, Xueduan, Fields, Matthew W, Bagwell, Christopher E, Tiedje, James M, Zhou, Jizhong
Format: Article
Language:English
Subjects:
Bacteria - genetics
Bacteriological methods and techniques used in bacteriology
Bacteriology
Biological and medical sciences
Biologists
DNA Probes
DNA, Bacterial - analysis
Environmental Monitoring - methods
Environmental science
Fundamental and applied biological sciences. Psychology
Genome
Genomes
Genomics
Hybridization
Microbiology
Microorganisms
Nucleic Acid Hybridization
Oligonucleotide Array Sequence Analysis
Soil Microbiology
Water Microbiology
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Summary:The detection and identification of microorganisms in natural communities is a great challenge to biologists. Microarray-based genomic technology provides a promising high-throughput alternative to traditional microbial characterization. A novel prototype microarray containing whole genomic DNA, termed community genome array (CGA), was constructed and evaluated. Microarray hybridizations at 55 °C using 50% formamide permitted the examined bacteria to be distinguished at the species level, while strain-level differentiation was obtained at hybridization temperatures of 65 or 75 °C. The detection limit was estimated to be approximately 0.2 ng with genomic DNA from a single pure culture using a reduced hybridization volume (3 μL). Using mixtures of known amounts of DNA or a known number of cells from 14 or 16 different species, respectively, about 5 ng of genomic DNA or 2.5 × 105 cells were detected under the hybridization conditions used. In addition, strong linear relationships were observed between hybridization signal intensity and target DNA concentrations for pure cultures, a mixture of DNA templates, and a population of mixed cells (r 2 = 0.95−0.98, P < 0.01). Finally, the prototype CGA revealed differences in microbial community composition in soil, river, and marine sediments. The results suggest that CGA hybridization has potential as a specific, sensitive, and quantitative tool for detection and identification of microorganisms in environmental samples.
ISSN:0013-936X
1520-5851
DOI:10.1021/es049508i