Fig. 1

Characterization of a highly diverse microbiome in cervicovaginal (luminal) samples from Kenyan sex workers. Cervicovaginal lavage (luminal) and ectocervical tissue study samples were assessed by 16S rRNA sequencing, gene expression, and protein profiling. a Schematic drawing depicting the sampling scheme and the resulting omics datasets. b Bar plots of alpha diversity indices and taxonomy profiles for each individual luminal sample. Color-coded squares above the stacked bar plots indicate bacterial vaginosis (BV, binned Nugent’s scores): Gray: negative, orange: intermediate, red: positive; and HIV diagnosis: Gray: HIV seronegative, red: HIV seropositive. Two12-SNN graphs were constructed using: c Louvain community detection algorithm, and d Uniform Manifold Approximation (UMAP). The two graphs were overlayed in color with the predefined luminal study groups. The undirected edges are included in gray connecting the nodes