Fig. 6

Longitudinal changes in FGT metaproteomic profiles. Liquid chromatography-tandem mass spectrometry was used to evaluate the metaproteome in lateral vaginal wall swabs from 74 women from Cape Town, South Africa, at two visits 9 weeks (interquartile range 9–11 weeks) apart. a Sankey diagram was used to visualize changes in inflammatory cytokine profiles between visits. b Principal component analysis (mixOmics R package) was used to group women based on the log₂-transformed intensity-based absolute quantification (iBAQ) values of all proteins identified at both visits. Grouping is based on vaginal pro-inflammatory cytokine concentrations, and each point represents an individual woman. c Top 20 proteins (UniProt IDs) distinguishing women with and without inflammation at both visits determined by moderated t test (limma R package) and random forest analysis (randomForest R package). d Top 10 taxa distinguishing women with and without inflammation at both visits determined by moderated t test (limma R package) and random forest algorithm (randomForest R package). e Top 14 biological process and cellular component gene ontology terms distinguishing women with and without inflammation at both visits determined by moderated t test (limma R package) and random forest algorithm (randomForest R package). Positions of participants in each heatmap are fixed, and the inflammation status of each participant across the visits can be tracked using the row sidebars. Inflammation groups were defined based on hierarchical followed by K-means clustering of nine pro-inflammatory cytokines [interleukin (IL)-1α, IL-1β, IL-6, IL-12p40, IL-12p70, tumor necrosis factor (TNF)-α, TNF-β, TNF-related apoptosis-inducing ligand (TRAIL), interferon (IFN)-γ]. ABC ATP-binding cassette, Agg aggregated, BP biological process, CC cellular component, Infla inflammation, PC principal component, PEP-PTS phosphoenolpyruvate-dependent phosphotransferase system, RNDP complex ribonucleoside-diphosphate reductase complex