DNA Microarray Technology in Environmental Microbiology

The microarray-based genomic technologies for bacterial detection and microbial community analysis have received a great deal of attention. The high density and high-throughput capacity of microarray-based genomic technologies have considerably changed the analysis of microbial community structure, function, and dynamics. The initial targets for sequencing projects have been microorganisms of medical of biotechnological interest. However, ecologically relevant organisms have recently become the focus of many whole genome sequencing projects. Large-scale metagenomic approaches, which comprise culture-independent geno-mic analyses of an assemblage of microorganisms, have been performed to accumulate an increasing number of DNA sequences. The tremendous input of sequence information in the past decades improves our ability to engineer more and better probes to target specifically phylogenetic and functional markers, and microarrays provide the platforms for detailed phylogenetic and functional analyses of environmental samples [74]. These projects reveal a plethora of new genes and a high prokaryotic diversity. From this, several different microarray formats have been developed and evaluated for bacterial detection and microbial community analyses of environmental samples. Going beyond the genomes of cultured organisms, meta-genomics analyses attempt to gain insight into the genomic potential of microbial communities as a whole. However, more rigorous and systematic assessment and development are needed to realize the full potential of microarrays for microbial ecology studies.

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