The vaginal microbiome is emerging as central to genital tract health, impacting the risk of infection, preterm birth, and HIV acquisition. Despite this importance, we know relatively little about the ecological drivers that shape the vaginal microbiome. One of the major barriers to further progress in this area is the lack of in depth phenotypic knowledge of the diverse bacterial species that occupy the vaginal niche, much less their potential for specific interactions. My work aims to address this gap by 1) phenotypic, genetic and molecular characterization of a broad collection of genital tract isolates representing the major constituents of the vaginal microbiome; 2) developing a robust in vitro culture system to study ecological interactions and evolution of multispecies communities, and 3) applying “multiomics” approaches to measure both in vitro and in vivo interactions in the genital tract ecosystem. By better understanding the functions and interactions of these microbes, and how they behave within a community, we can design strategies to target the microbiome for the treatment or prevention of disease.