The number of different microorganisms recognized in the oral cavity using molecular methods has more than doubled compared with the number isolated using cultural techniques. This finding necessitates a reevaluation of which species may be pathogens in dental infections. Molecular methods used to determine microbial diversity include broad range target Polymerase Chain Reaction with ‘universal primers’, and cloning amplicons or denaturing gradient gel electrophoresis to separate DNA fragments before sequencing. These molecular methods have clarified and expanded the taxonomy of oral microbial species. Discrepancies between comprehensive molecular and cultural methods suggest that neither method alone can adequately evaluate associations of specific microorganisms with disease. Oligonucleotide DNA probes, direct PCR, and DNA arrays of the future, can detect cultured and uncultivated phylotypes, so these methods have the potential for use in reevaluating microbial associations with oral diseases. Assigning pathogenicity to newly described and uncultivated species will require new approaches. These include linking the presence of species in biofilms or intracellularly as well as assessing host reactions to stimulation of pathogens within the microbiome.
Conclusions: A wide range of microorganisms has been identified in the oral cavity, and rapid methods have been developed to evaluate their associations with oral infections. New methods are needed to asses the role of phylotypes and fasitidious new species, or specific groups of microorganisms, as etiologic pathogens for oral infections.
Keywords: oral bacteria, caries, periodontal disease