Figure 3.

Principal component analysis (PCA) plots displaying the microbial profiles of (A) saliva of children (n = 356 samples), (B) plaque of children (n = 323), and (C) saliva of children and caregivers (n = 471) by time points. Blue dots indicate samples collected at T1 (~1 y of age); red dots, at T2 (~2.5 y of age); and green dots, at T3 (~4 y of age). Orange dots (C) indicate saliva samples of caregivers (n = 115) at T1. Panel C shows a comparison of salivary microbial profiles of children at all time points (T1, T2, T3) and saliva of their caregivers collected at T1. PCA was performed on subsampled and log-2 transformed zero-radius operational taxonomic unit data. Axis shows the first 2 greatest principal components (PCs) explaining the highest intersample variation (percentage of variance). The P and F values indicate the output of PERMANOVA analyses, using the Bray-Curtis similarity measure, in comparing the respective samples. Similarity (D) of salivary (black boxes) and plaque (gray boxes) samples collected at different time points from the same child (pairwise comparison). Saliva (black) and plaque (gray) samples were tested separately and plotted together as they showed the same pattern of changes. Different letters indicate statistically significant differences between the sample pairs (P < 0.05, paired samples Friedman test followed by Wilcoxon rank-sum test). The pairwise comparisons of the 2 types of samples (saliva vs. plaque) were significantly different (P < 0.05) in all but the time point indicated with $.