Fig. 3

For unweighted distance measures, rarefying diminishes the effect of original library size. Nonparametric multivariate ANOVA (PERMANOVA) was calculated on the Inflammatory Bowel Disease (IBD) dataset of Gevers et al., using type I sequential sums of squares in the linear model (y~Library_Size + Microbial_Dysbiosis_Index). Unweighted UniFrac was used for clustering, except for letters (e–f) corresponding to weighted UniFrac DESeq and edgeR. The unweighted UniFrac distance matrix for DESeq and edgeR was zero, so a PCoA plot could not be made. For each letter (a–f), the left PCoA plot is colored according to microbial dysbiosis (left legend), and the right PCoA plot is colored according to library size (right legend)