Caries is still a relevant problem in clinical medicine. Scientists propose a critically important role of the members of genus Streptococcus in the transition from the state of dental health to a diseased state. Metagenomics of the oral microorganisms gives us a chance to study the roles of pathogenic microbes and functions of the specific genes in the case of periodontal diseases or caries. This field of science at the intersection of disciplines is one of the most promising methods of studying the fundamentals of the pathogenesis of dental pathology. In this article are summarized and presented data from the scientific literature sources on the investigation of the microbiological aspects of caries process in the period 2001-2016 years. Data from scientific databases Web of Science, PubMed, Cochrane Library have been collected. Refs 19. Fig. 1.