The human oral microbiome currently comprises 600–700 taxa, but estimates suggest that overall species numbers may turn out to be higher (˜1200). Within the oral cavity, groups of microbial species become arranged into surface-localized communities that vary considerably in composition according to sites of establishment. Factors such as nutrient availability, pH, toxic metabolites, shear forces and host conditions contribute to modelling the structure and activities of these oral microbial communities. With development of more rapid and accurate molecular techniques it has become possible to begin to characterize the genome contents of individual communities. However, understanding the phenotypic interactions between cultivable microorganisms within communities is essential in order to complement the genomic data. This will then enable construction of microbial community interactomes, incorporating genomic and spatial information with functional knowledge of physical and metabolic interplays between the microorganisms. Enlightenment of the changes in genome composition and phenotypic interactions as functions of niche, time and intrusions will help towards developing better means of manipulating communities for host benefit.