from Luo et al (2011) in Microbial Population Genetics

The advent of DNA microarray technology has greatly expanded our ability to monitor changes in the abundance of transcripts. Such a development has been a milestone in several areas of microbiology. In clinical microbiology, microarrays are used for microorganism detection and identification and gene-expression analysis. DNA microarrays have allowed us to monitor the effects of pathogens on host-cell gene expression in a much greater depth and on a significantly broader scale than previous single gene studies. The results generated by these studies are complex, and few systematic studies have been carried out to compare results among studies. Comparative transcriptomics - whole genome mRNA transcript profiling using microarrays.

Whole-genome microarrays from fully sequenced genomes are a powerful platform for identifying differences in gene content between organisms and for studying gene expression dynamics. The generation of messenger RNA expression profiles is referred to as transcriptomics, as these are based on the process of transcription. Given the inhospitable in vivo and the varied ex vivo environments encountered by most microbial pathogens, transcriptome analysis holds particular promise for identifying and determining the functions of differentially regulated, virulence associated genes. The basic principle of this technique involves extracting the mRNA expressed under a range of environmental conditions and hybridizing these sequences to a high-density gridded microarray of the DNA content of an organism. Such high-throughput analysis allows massive parallel gene expression and gene discovery studies to be undertaken. DNA microarray analysis will complement other technologies such as in vivo expression technology and differential fluorescence analysis to identify and investigate which bacterial genes are differentially expressed in the host.

The application of DNA microarrays to microbial pathogens
The study of the complete set of genes expressed and modified in a cell is an important and rapidly evolving discipline that is readily applicable to microbial pathogens. For example, strains of Staphylococcus aureus resistant to the antibiotic vancomycin present a potentially serious public-health problem. In the case, the Gaasterland group described the development of a multi strain S. aureus microarray. Pairwise comparisons of the available genomes of strains of S. aureus have revealed considerable variation in gene content across the epidemiological landscape. They identified changes in protein-coding potentials that correlate with antibiotic resistance by measuring differences in gene expression in vancomycin-sensitive and vancomycin-resistant pairs of S. aureus isolates. Philip Butcher's group used microarrays to help understand the complex pathophysiology of Mycobacterium tuberculosis infection. Besides discussing some methodological aspects of microarray work, They focused on the use of M. tuberculosis microarrays to investigate the intracellular lifestyle of this organism and its interaction with host macrophages. In the future, it would be exciting to integrate results from in vitro work like this with results from in vivo microarray work on mammalian hosts to provide a whole-genomic view of host-pathogen interactions.

Tags: Microbial Population Genetics | Population Genetics | Analytic Tools in Comparative Genomics | Comparative Genomics | Comparative Genomics Tools | Comparative Microbial Genomics | Population Genetic Patterns and Evolutionary Implications | Microbial genomics