Microdroplet co-cultivation and interaction characterization of human vaginal bacteria

The human vaginal microbiome (HVM) plays a fundamental role in women's reproductive health. For instance, bacterial vaginosis (BV) is characterized by a depletion of lactobacilli and an overgrowth of strict anaerobes. Women with BV may have an increased risk of acquiring sexually transmitted diseases and adverse pregnancy outcomes. Although the HVM is important, the ecological roles of many vaginal species remain unclear and current approaches for investigating them have severe limitations. We previously developed a new high-throughput technology based on the co-cultivation of bacteria in microdroplets to dissect inter-species interactions in microbial communities. Here, we adapted and extended this technology to investigate the HVM and tested it using pairwise model systems. In one case, Lactobacillus jensenii JV-V16, a lactic acid bacterium, and Gardnerella vaginalis ATCC 49145, a bacterium associated with BV, were cultured in microdroplets as pure cultures and co-cultures. Two assays were developed to analyze their growth in microdroplets. First, qPCR was used to quantify the bacteria in pooled microdroplets. Second, cells in individual microdroplets were plated and enumerated on agar media. The results showed that growth of G. vaginalis was severely inhibited by L. jensenii, which recapitulated previous findings of studies conducted in flask batch cultures. Additionally, we validated the general applicability of our technology pipeline with a second co-culture model system by observing that Enterococcus faecalis, another bacterium from the urogenital tract, was also inhibited by L. jensenii. Our results show that co-cultivation and characterization of bacteria in microdroplets provides an effective way to study inter-species interactions in microbial ecosystems.