Fig. 3: Comparison of different saliva sample processing workflows in enriching the microbial metaproteome.

a Proportions of bacterial-originated peptide intensity and count among all identified peptides. b Numbers of identified bacterial and human peptides. Panels a and b show comparisons across BL, CT_Sup, GX_Sup and GT_Sup groups. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001 indicate statistical significance levels determined by one-way ANOVA followed by Tukey’s post hoc test. Error bars represent mean ± SD, and individual values are shown as black dots. c UpSet plot illustrating the intersections of microbial protein sets among of the BL, CT_Sup, GX_Sup groups, the results are based on merged data from technical replicates of each group. d Volcano plot showing significantly differentially quantified proteins between GX_Sup and CT_Sup groups, with a fold change threshold of > 1.5 and p value < 0.05). e Stacked bar chart representing the originations of differentially quantified proteins in panel d).