Fig. 2

Factors that explain variance in the subgingival microbiome. k-means clustering of Bray-Curtis distances revealed three clusters (LAP blue, CP red, GAP green) based on function (a, p-value < 0.001) and taxa (b, p-value < 0.001). The ellipses represent the centroids of each cluster. Linear discriminant analysis of relative abundances of function (top panels) and phylogeny (bottom panels) revealed that disease phenotype (c, d), but not disease grade (e, f), was able to discriminate between subjects with disease. The differences based on age-decade (g, h) and ethnicity (i, j) were explained by the disease phenotype. In each cluster, the larger ellipse indicates the 95% confidence region to contain the true mean for the group, and the smaller (inner) ellipse represents the region estimated to contain 50% of the population for the group. The misclassification rates of each variable are shown within each panel