Expression profiling

An emerging alternative approach is to use oligonucleotide or cDNA microarrays designed to detect specific rDNA or gene sequences known to be present in important lineages of microorganisms that are thought to be in a specific microbial community (104-106). Loy and coworkers successfully developed and used a microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes covering all recognized lineages of sulfate reducing prokaryotes (SRP) for high-resolution screening of clinical and environmental samples (107, 108). The microarray, named SRP — PhyloChip, has great potential for rapid screening of SRP diversity in complex samples and microarray SRP diversity fingerprints allow identification of relevant probes for further characterization of a sample by PCR or quantitative hybridiza­tion. This is a valuable option if large numbers of samples are to be analyzed for temporal or spatial variations in SRP diversity. While this approach can provide a comprehensive survey for the presence or absence of a particular sequence, the technique has a closed architecture and cannot identify novel sequences nor can microarrays easily distinguish between two or more closely related sequences in mixed samples.