The alteration of microbiota in different host niches has been associated with numerous adverse health outcomes that affect millions of human patients annually. In last few years the interest has been increased to study the microbiota that is present in the female genital tract and may associate with various disease symptoms. Vaginal microbiota contributes to the maintenance of a healthy vaginal environment and simultaneously reduces the deleterious effect of various infectious agents. The change of vaginal microbiota has been observed using culture-independent methods such as next generation sequencing (NGS) technology, and its fluctuation was found to link with various endogenous and exogenous factors. Among them, a dynamic interplay between the vaginal microbiota and human papillomavirus (HPV) was found to be important in the acquisition and persistence of HPV and contributed to the development of cervical intraepithelial neoplasia (CIN) and cervical cancer (CC). Accumulating evidence has shown that persistent HPV infection depends upon regulation of the immune response and its associated factors such as hormones, human genetics and vaginal microbial interactions. Here, we reviewed the association of the microbiota with HPV persistence, factors in shaping the vaginal microbiota and their interplay with the regulation of immuno-regulatory molecules. The understanding of these associations could help identify important targets having impact on HPV persistence. Further, we discussed the predictive diagnostic and clinical therapeutic applications of vaginal microbiota in prevention and treatment of HPV persistence and subsequent progression of CIN and CC.
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