The DNA chip microarray technology is a direct result of the availability of genome sequence information. The technique involves very large (approximately 100,000) cDNA sequences or synthetic DNA oligomers being attached onto a glass slide (the chip) in known locations on a grid. An RNA sample is then labeled and hybridized to the grid and relative amounts of RNA bound to each square in the grid are measured. Such DNA chips can be used for simultaneous monitoring of levels of expression of all of the genes in a cell, in order to study whole genome expression patterns in various matrices during development. Moreover, since parallel hybridizations to hundreds or thousands of genes in a single experiment can be performed by high throughput DNA microarrays, direct profiling of microbial populations are achievable. Rudi, et al. (2002) combined the specificity obtained by enzymatic labeling of species-specific oligonucleotide probes with the possibility of detecting several targets simultaneously by DNA array hybridization with 16S rRNA gene from pure cultures. The hybridization of bulk DNA extracted from food to chip-bound probes is a promising tool for microbial community analyses in foods. In one recent development of this basic technique, Bae, et al. (2005) described genome-probing microarrays (GPM), which deposits hundreds of microbial genomes as labeled probes on a glass slide and hybridizes them with bulk community DNAs. GPM enabled quantitative, high-throughput monitoring of LAB community dynamics during fermentation of Kimchi, a traditional Korean food. Compared to currently used oligonucleotide microarrays, the specificity and sensitivity of GPM was remarkably increased (Bae, et al. 2005).
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