Distinct cervical tissue-adherent and luminal microbiome communities correlate with mucosal host gene expression and protein levels in Kenyan sex workers

Abstract

Background The majority of studies characterizing female genital tract microbiota have focused on luminal organisms, while the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that these communities may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a cohort of Kenyan female sex workers. Results We identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners-dominated luminal samples had a corresponding Gardnerella-dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbial community was associated with epithelial remodeling and pro-inflammatory pathways. Tissue-adherent communities dominated by L. iners and Gardnerella were associated with lower host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, although with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity. Conclusion We identified ectocervical tissue-adherent bacterial communities in all study participants of a female sex worker cohort. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. We further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community could possibly act as a reservoir that seed the lumen with less optimal, non-Lactobacillus, bacteria.

Vaginal candida infection is associated with host molecular signatures of neutrophil activation in the adjacent ectocervical mucosa in Kenyan sex workers

“…For example, these findings contrast with those in the same cohort when participants were stratified into groups based on their cervicovaginal microbiome composition. 10 That is, the transcriptional signatures of women with non-Lactobacillus dominance were characterized by both inflammation and disrupted epithelial barriers in contrast with the non-inflammatory and intact epithelium observed in women with Lactobacillus crispatus dominance. In the present study, cases ranged from relatively mild candidiasis with a few visible fungal cells in wet smear samples to presentations of characteristic candidaassociated vaginal discharge.…”

“…52 Characterizing gene expression in the mucosal epithelium has proven relevant for understanding molecular mechanisms underlying susceptibility to HIV. Such risk factors include cervicovaginal microbiome composition 4,10 and use of the injectable hormonal contraceptive DMPA. 16,53 HIV susceptibility is characterized by loss of epithelial barrier function, accumulation of CD4 + HIV target cells, elevated pH, enhanced inflammation, and the production of metabolites such as indole and biogenic amines.…”

“…The host transcriptomic profile of the ectocervical tissue samples from this cohort of women were previously defined. 10 In the present study, we re-calculated these profiles based on the stratification of candida (n = 7) versus control (n = 101) groups. The analysis identified 162 DEGs out of the 15 435 genes detected in the data set, with a p-value set at .01 and absolute fold changes above 1.5 (Table S2).…”

“…Bulk RNA-sequencing (RNA-seq) data from the samples were previously published 10,15,16 and are available in the Gene Expression Omnibus (GEO) public repository (accession ID GSE217237). Here, we utilized the gene expression counts for comparison between the candida and control groups.…”

“…Host transcriptional profiles of the cervicovaginal mucosa dominated by polymicrobial, non-Lactobacilli-dominated bacterial communities reveal signatures of mucosal inflammation, altered immune function, and epithelial disruption. 4,9,10 Host immune functions can also be altered in women with vulvovaginal candidiasis. 11,12 Vaginal epithelial cells are rapidly shed as a first line of defense against the overgrowth of candida species.…”