Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar case

Using this unified framework, we reveal marked heterogeneity and high inter-individual variability in the vulvar microbiota of healthy individuals, identifying community state types that mirror those described in the vaginal ecosystem. Importantly, we show that distinct microbial configurations are associated with specific host transcriptional programs: Lactobacillus crispatus dominated communities correlate with epithelial differentiation and barrier integrity, whereas communities enriched in taxa associated with dysbiosis exhibit transcriptional signatures linked to inflammation.

Beyond providing new biological insights into an understudied anatomical niche, our study introduces a broadly applicable strategy with substantial impact for the field. With tens of thousands of human RNA-seq datasets already available in public repositories, our approach enables retrospective extraction of microbiome information and host-microbe interaction signals from existing transcriptomic data, without the need for additional sequencing or specialized microbiome protocols.

This unlocks a powerful and cost-effective opportunity to revisit archived RNA-seq studies across tissues, diseases, and low-biomass environments, revealing previously inaccessible layers of host-microbiome crosstalk and maximizing the scientific value of data that already exist.