Oral diseases are associated with systemic diseases; such as type II diabetes, cardiovascular disease, rheumatoid arthritis (RA), and neurological diseases. Coincidentally, the oral microbiome (fluids or extracts) is readily accessible and easily sampled; therefore, serving as a diagnostic or prognostic tool for health status. The oral microbiome is a useful research model for studying fundamental questions of the human microbiome. In this narrative literature review, we examine the characteristics of oral microorganisms, the relationship between oral microorganisms and human diseases, and the important role of oral microorganisms in disease prevention. Also, we illustrate the usefulness of sampling the oral microbiome in developing the diagnosis and prognostic treatment strategies for oral and systemic diseases to accelerate their clinical application. Selective saliva biomarkers and microbiome can serve for useful indices to oral diseases and systemic diseases, and as a model research tool, the oral cavity has many uses in the clinical and research environment. The relationships between oral health and systemic diseases are quite profound, and future research will illuminate opportunities for fruitful preventative measures and therapeutics.