Microdroplet-enabled high-throughput cultivation of vaginal bacteria using cervicovaginal fluids

Abstract

The human vaginal microbiome (HVM) is closely associated with the health of the host. In particular, bacterial vaginosis, a condition where vaginal lactobacilli are reduced dramatically by an overgrowth of various other bacteria, has been linked to increased risk of sexually transmitted infectious diseases, including HIV, and preterm birth. Recent culture-independent studies leveraging next-generation sequencing technology have revealed that the HVM composition differs between women and changes over time. However, questions remain as to the underlying mechanisms and culture-dependent studies are needed for further elucidation of the HVM’s genotype-phenotype relationships and system-level properties in vivo. In this work, we have adapted a previously developed microdroplet-based high-throughput cultivation platform for the investigation of vaginal bacteria using the cervicovaginal fluid (CVF) as cultivation medium. Using undiluted CVF collected with Softdiscs discs, we observed the growth of L. iners in microdroplets containing CVF pooled from samples with a high prevalence of L. crispatus. Although demonstrated with L. iners, this work establishes a new framework for culturing microorganisms under clinically-relevant conditions ex vivo using minute volumes of host fluids; it can be further extended and adapted for addressing numerous questions about the HVM and other complex microbiomes.