Molecular microbial diagnosis

Based on culture-independent molecular methods using sequence analysis of 16S rRNA genes, most of the predominant bacterial species in the oral cavity have been identified (1,2,3,6, 14 , 17 , 20 , 26 , 28 , 30 , 36 ,39,40,46,48). Collectively speaking, there are about 620 predominant oral bacterial species, of which about 35% have not yet been cultivated in vitro. Whereas there is considerable debate as to what defines a bacterial species (53,54), the 16S rRNA approach defines, in general, a species (or more precisely a phylotype) as 16S rRNA gene sequences of strains or cloned 16S rRNA inserts with >98.5% similarity. Consequently, strain or clone sequences with <98.5% similarity to previously defined phylotypes are considered representatives of new phylotypes (for details, see the Human Oral Microbiome Database [HOMD, http://www.homd.org/]). More recently, based on evaluations of 35,000 16S rRNA gene sequences from about 400 patients, it is estimated that there are approximately 1,200 predominant species (unpublished data, HOMD). In contrast, investigators in a recent study utilizing pyrosequencing analysis of 197,600 sequences derived from the oral cavity have suggested that the microbial diversity of the human oral microbiome is much greater with approximately 19,000 phylotypes (27). However, most of these phylotypes are those found at very low densities.