Fig. 2: Beta-diversity and redundancy analysis in subgingival plaque.

A RPCA colored by periodontal pocket depth. Permanova pseudo-F statistic = 397.062, p-value < 0.001. B RPCA distance among pairwise samples; Subgingival plaque samples from shallow periodontal pockets of different people (n = 308,505 pairs), subgingival plaque samples from deep periodontal pockets samples of different people (n = 54,285 pairs), subgingival plaque samples from shallow versus deep periodontal pockets from the same person (n = 322 pairs), subgingival plaque samples from shallow versus deep periodontal pockets from different people (n = 259,058 pairs). Each group is significantly different from all other groups (one-way ANOVA with Tukey’s multiple corrections, p < 0.05). The box shows the quartiles of the dataset while the whiskers extend to show the rest of the distribution, except for points that are determined to be “outliers” using a method that is a function of the inter-quartile range. C Redundancy analysis (RDA) estimates the percent microbial diversity explained by each variable. Inset donut chart sums effect sizes by category; periodontal variables explained the majority of microbial variation (20.0%), followed by demographic variables (1.7%) and metabolic variables (0.6%). D Empress plot displaying ASV-level phylogeny with branches colored by phylum. Outer bar plot represents songbird differentials on a color scale where high values (blue color) are taxa associated with health, and low values (red color) are associated with disease. Inner bar plot highlights features from the genera Corynebacterium (blue) and Treponema (red), which have high and low Songbird differentials, respectively.