# The cervicovaginal microbiome associates with spatially restricted host transcriptional signatures throughout the human ectocervical epithelium and submucosa

## TL;DR

This study shows that different vaginal bacteria are linked to gene activity changes in cervical tissue, which could affect HIV susceptibility.

## Contribution

The study reveals that cervicovaginal microbiome influences gene expression throughout the ectocervical tissue, not just on the surface.

## Key findings

- Highly diverse microbiome groups are linked to significant gene expression changes near the epithelial basal membrane.
- Lactobacillus crispatus/acidophilus-dominated microbiomes are associated with genes supporting mucosal barrier integrity.
- Microbiome effects on gene expression are observed throughout the mucosa, not just at the surface.

## Abstract

The cervicovaginal microbiome is a key biological determinant of human immunodeficiency virus (HIV) susceptibility, but its underlying impact on the ectocervical transcriptional landscape is unclear. Ectocervical tissue samples from Kenyan female sex workers were categorized into pre-defined cervicovaginal microbiome groups based on dominant compositions: Lactobacillus crispatus/acidophilus, Lactobacillus iners, Gardnerella, and ‘highly diverse’. The tissue samples (n = 21) were assessed using spatial transcriptomics, revealing three epithelial, one mixed border, and nine submucosal gene clusters. Differential gene expression analysis across the microbiome groups and gene clusters identified 3,771 unique genes. The highly diverse microbiome group associated with the largest differences, mostly located near the epithelial basal membrane, encompassing genes involved in epithelial maintenance, submucosal extracellular matrix structures, and immune function. The L. crispatus/acidophilus-dominated group was identified by genes involved in active immune engagement, supporting mucosal barrier integrity. Weighted gene co-expression analysis confirmed tissue-wide altered gene expression associated with all microbiome groups and with individual bacterial taxa. Despite the assumption that microbiome colonization is restricted to the luminal surface, the transcriptional landscape was affected throughout the mucosa, with the most pronounced effect near both sides of the basal membrane. This broad association with the mucosal barrier integrity could affect susceptibility to HIV acquisition.

The microorganisms that live in and on our bodies—collectively known as the microbiome—can influence our health in many ways, including how our immune system behaves and how susceptible we may be to infections. In this study, we focused on the human cervix, a key part of the reproductive tract, and investigated how different types of vaginal bacteria might influence the activity of genes in this tissue. By combining microbiome profiling with a powerful technique called spatial transcriptomics, we were able to see how gene activity varies across different regions of the cervix and how it associated with the surrounding microbes. We found that certain bacterial communities are linked to changes in gene expression deep within the tissue, not just on the surface. These findings help us understand how microbial communities might contribute to health risks like infection or inflammation and may one day inform strategies to prevent conditions such as HIV or adverse pregnancy outcomes. Our work shows the importance of looking beyond surface-level changes and considering how microbes influence whole tissues in complex ways.