Fig. 1

Bacterial relative abundance determined using metaproteomics versus 16S rRNA gene sequencing by inflammation cytokine profile. Liquid chromatography-tandem mass spectrometry was used to evaluate the metaproteome in lateral vaginal wall swabs from 113 women from Cape Town, South Africa. Proteins were identified using MaxQuant and a custom database generated using de novo sequencing to filter the UniProt database. Taxonomy was assigned using UniProt, and relative abundance of each taxon was determined by aggregating the intensity-based absolute quantification (iBAQ) values of all proteins identified for each taxon. a Proteins identified were assigned to the Eukaryota and Bacteria domains. Eukaryota proteins included those assigned to the fungi kingdom and metazoan subkingdom, while the bacteria domain included actinobacteria, firmicutes, fusobacteria, bacteriodetes, and gammaproteobacter phyla. b Distribution of taxa identified is shown as a pie chart. c Number of proteins detected for taxa for which the greatest number of proteins were identified. d Protein relative abundance per taxon for taxa with the highest relative abundance. The relative abundance of the top 20 most abundant bacterial taxa identified using e 16S rRNA gene sequencing and f metaproteomics is shown for all participants for whom both 16S rRNA gene sequence data and metaproteomics data were generated (n = 74). For 16S rRNA gene sequence analysis, the V4 region was amplified and libraries sequenced on an Illumina MiSeq platform. Inflammation groups were defined based on hierarchical followed by K-means clustering of all women according to the concentrations 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]. OTU operational taxonomic unit