fig3

Figure 3. Taxonomic composition and functional co-occurrence network structure are altered in vaginal samples over time. (A) PCA biplot based on sample-wise CLR-transformed Aitchison distance. Each point represents a vaginal sample. Strength and association for genera (SVs) are depicted by the length and direction of the gray arrows, respectively. Samples are colored by perinatal period and ellipses represent 95% confidence intervals. Plots of networks indicate (B) copresence and (C) mutual exclusion patterns of enzymes, and (D) copresence and (E) mutual exclusion patterns of functional pathways in prenatal vaginal samples. Only significant edges are plotted. Edges are colored based on the enzyme or pathway group with more total edges (of the two involved in the interaction). Relative network positivity at both the enzymatic (F) and pathway (G) levels was calculated as the number of copresence edges divided by the number of mutual exclusion edges for the network from vaginal samples at each perinatal period. (H) Total number of nodes and significant edges are plotted for vaginal samples at each perinatal period.