Host-associated microbiomes like the human vaginal microbiome (HVM) play crucial roles in the regulation of host health. However, investigation of mechanisms driving this microbiome-host interface is difficult due to the inability to replicate relevant biotic and abiotic culture conditions. Additionally, host environments such as the HVM are highly variable spatiotemporally and across individuals. While metagenomic surveys have provided insight into microbiome composition and dynamics, questions remain as to their underlying mechanisms, and phenotypic data from culture-dependent studies are needed to further elucidate the HVM’s genotype-phenotype relationships. In this work, we have adapted a previously developed microdroplet-based high-throughput cultivation platform for the study of hundreds of replicate cultures in host-derived fluid. We applied this pipeline to formulate and implement host-mimetic media for vaginal species using cervicovaginal fluid. 16S sequencing revealed a high prevalence of Lactobacillus crispatus in the vaginal microbiome of donors in this study. Volume of CVF from donors exhibited variability while the pH remained consistent around 4 in samples. Host-mimetic media was used to culture Lactobacillus iners as a biofilm in pooled CVF at neutral pH, which suggests cultivation in CVF confers a meaningful physiological response. As demonstrated with L. iners, a fastidious bacterium in the HVM, this work provides a new framework for culturing microorganisms under clinically-relevant conditions ex vivo, using as low as 20 µL fluid volume per experimental condition. This work can be further extended and adapted for addressing numerous questions about the HVM and other host-associated microbiomes.
