There were 638 species-level targets recognizing 538 species. In addition, there are 129 genus-level targets.


For some taxa such as Streptococcus, identification was limited to a group of several closely related species rather than an individual species. 16S rDNA sequences for the genus Streptococcus are highly conserved and many species cannot be differentiated in the targeted region (E. coli positions ~341 to 806). Thus, genus or higher taxa probes were developed to account for those taxa that could not be differentiated at the species level.


Each species had a Human Oral Taxon (HOT) designation as defined at the time in the Human Oral Microbiome Database (HOMD), which provided the scientific community with comprehensive information on the approximate 700 predominant prokaryote species that are present in the human oral cavity. More recently, HOMD has been updated to eHOMD (expanded HOMD), that now includes bacterial species present in the upper digestive and upper respiratory tracts, including the oral cavity, pharynx, nasal passages, sinuses and esophagus. HOT numbers are now referred to as HMT (Human Microbial Taxon) numbers.