This review discusses polymicrobial interactions with the host in both health and disease. As our ability improves to identify specific bacterial clonal types both with respect to abundance and location in the oral biofilm we will learn more concerning their contribution to both oral health and disease. Recent studies examining host-bacterial interactions have revealed that commensal bacteria not only protect the host simply by niche occupation, but that bacterial interactions with host tissue can promote the development of proper tissue structure and function. These data indicate that our host-associated polymicrobial communities, such as those found in the oral cavity, co-evolved with us and have become an integral part of who we are. Understanding the microbial community factors that underpin associations with host tissue that contribute to periodontal health may also reveal how dysbiotic periodontopathic oral communities disrupt normal periodontal tissue functions in disease. A disruption of the oral microbial community creates dysbiosis, either by overgrowth of specific or nonspecific microorganisms or changes in the local host response where the community can now support a disease state. Dysbiosis provides the link between systemic changes (e.g., diabetes), exogenous risk factors (e.g., smoking), and the dysbiotic community and can drive the periodontal tissue destruction. Many other risk factors associated with periodontal disease such as stress, aging, and genetics also likely affect the microbial community, and more research is needed utilizing sophisticated bacterial taxonomic techniques to better elucidate these effects on the microbiome and to develop strategies to target the dysbiotic mechanisms and improve periodontal health.