The human vagina and the bacterial communities that reside therein exist in a finely balanced mutualistic association. Dysbiotic states of the vaginal microbiota, including bacterial vaginosis (BV), are characterized by a paucity of Lactobacillus spp., the presence of a wide array of strict and facultative anaerobes, and a pH >4.5. Symptoms such as odor and discharge can accompany these microbial dysbiotic states, however, epidemiologically, vaginal dysbioses have been associated with increased susceptibility to STIs, including chlamydia. The mechanisms by which vaginal microbiota protect or increase the risk to infections remain unknown. This thesis aimed to identify the molecular factors that control host cellular responses to Lactobacillus spp.-dominated and dysbiotic microbiota. Chapter 2 characterized the in vivo host microRNA (miRNA) response to different types of vaginal microbiota to gain insight into host functions that play a role in vaginal homeostasis. Leveraging daily collected vaginal samples in conjunction with a machine learning approach, eight miRNAs were discovered to be differently controlled by vaginal microbiota. Of these, expression of miR-193b, known to regulate host cell proliferation, was increased by Lactobacillus spp.-dominated microbiota. In vitro, vaginal epithelial cells exposed to Lactobacillus spp. culture supernatants exhibited reduced epithelial cell proliferation, high miRNA-193b expression and decreased abundance of cyclin D1. More importantly, epithelial cell proliferation was identified as a requirement for efficient Chlamydia trachomatis infection. Chapter 3 characterized the in vitro transcriptome of epithelial cells exposed to Lactobacillus spp. relative to Gardnerella vaginalis, a surrogate for dysbiotic vaginal microbiota. Immune response and cell cycle pathways were found to be among the most modulated by Lactobacillus spp. Longitudinal gene expression suggested a role of histone deacetylases (HDAC) as an intermediary between immune stimulation and cell proliferation. Additionally, the epidermal growth factor receptor (EGFR), required for C. trachomatis infection, was decreased when epithelial cells were exposed to Lactobacillus spp. These findings contribute to the fundamental understanding of the vaginal microbiota’s role in cellular homeostasis as a requirement for resistance to STI agents such as C. trachomatis, and ultimately will lead to improved preventive strategies against STIs through the modulation of vaginal microbiota composition and function.