Arrays with potential application to diagnostic clinical research can be divided into at least four major categories based on what genes are represented on the array: (1) phylogenetic oligonucleotide arrays (POAs), which are designed based on a conserved marker such as the 16S rRNA gene and are used to detect specific organisms and compare the relatedness of microbial communities; (2) functional gene arrays (FGAs), which are designed for key functional genes involved in various physiological processes, such as antibiotic resistance, and provide information
on the genes and microbial populations involved with these processes; (3) community genome arrays (CGAs), which contain the whole genomic DNA of cultured microorganisms and can describe an isolate or community based on its relationship to these cultivated organisms; and (4) metagenomic arrays (MGA), which contain probes produced directly from environmental DNA itself and can be a potentially powerful technique because, unlike the other arrays, they can applied with no prior sequence knowledge of the community.
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