Characterisation of the human oral microbiome and metagenome

Abstract

Members of the oral microbiota are responsible for the commonest bacterial diseases of man: dental caries and the periodontal diseases. Although some specific organisms have been implicated in the pathogenesis of these conditions, it is now recognised that they are not classical infectious diseases but, rather, complex diseases resulting from a breakdown in the normal homeostasis between the human host and its commensal microbiota. The first goal in understanding the mechanisms involved must be the comprehensive characterisation of the oral bacterial community. Since around half of oral species cannot be cultured on artificial media, molecular techniques have been developed based on PCR, cloning and sequencing of housekeeping genes such as that encoding 16S rRNA. These methods have revealed numerous novel bacterial lineages, including deep branches of the phyla Bacteroidetes and Firmicutes and novel phyla such as Synergistes. Taxa belonging to these newly described lineages are associated with oral diseases. In addition, novel genetic typing methods, such as multi locus sequence typing, are showing that intra-specific diversity is far greater than previously thought. Given this level of complexity, investigation of the oral bacterial metagenome is under way, which treats the oral bacterial community and its constituent genes as a whole. Functional screening of metagenomic libraries is a powerful tool for the identification of novel genes of interest in oral bacteria. These new molecular tools are revolutionising concepts of oral infectious disease pathogenesis and will enable new treatments to be developed based on modification of the composition and function of the oral microbiota.