Fig. 2

Dominant microbes in the coral microbiome. (A) Dominant bacterial or archaeal genera in coral mucus (cyan), tissue (orange), or skeleton (purple) microbiomes. Pie wedges represent the fraction of coral host genera in which the labeled bacterium is more abundant than all other bacterial or archaeal taxa. Cyan shades represent microbes dominant in mucus, oranges represent microbes dominant in tissue (but not mucus), purple shades represent microbes dominant in skeleton (but not mucus or tissue). Endozoicomonas, which is of special significance later in the paper, is highlighted in aqua. (B) Bar charts showing correlations between microbiome alpha and beta diversity metrics and disease, represented by the R² for PGLS correlations. Alpha diversity metrics include richness, evenness (Gini index), and dominance (Simpson’s index), and weighted UniFrac beta diversity metrics including the three principal component axes (PC1, PC2, PC3) that represent measures of community structure. Significant relationships (p < 0.05, Supplementary Data Table S4) are marked by an asterisk (*). (C) Bubble plot showing correlations between dominant microbial taxa and coral disease prevalence. The size of each triangle represents the R² for PGLS correlations between disease susceptibility and microbial relative abundance for each listed taxon in either all samples (top row), mucus samples (cyan row), tissue samples (orange row), or skeleton samples (purple row). Colored points were significant (p < 0.05, FDR q < 0.05) and hashed points were nominally significant (p < 0.05, FDR q > 0.05; Supplementary Data Table S7a). Points that were not significant or had too little data (n < 5) for reliable testing are marked in white. Taxa whose relative abundance is significantly correlated with disease are marked in bold on the x-axis