Microbiome Composition Analysis with ANCOM-BC

The program Analysis of Compositions of Microbiomes with Bias Correction (ANCOM_BC) was used to identify differentially abundant microbial taxa [75 ]. ANCOM_BC was used with the global test option and the results were considered significant if the false discovery rate adjusted p-value (Padj) was <0.001 and if the W statistic was >90. Field-sourced AH samples were tested for differential abundance among zones (vulnerable, endemic, and epidemic), and SCTLD-susceptible coral samples (without Acropora spp.) were evaluated for differences in disease state (AH, DU, and DL). For SCTLD-susceptible corals, the data were parsed by the three coral compartments (mucus, tissue slurry, and tissue slurry skeleton). ANCOM_BC analyses were run for each compartment due to the relatively low sample size of tissue slurry skeleton samples compared to the two other compartment types. The taxa were further evaluated if they had a log-fold change between −1.5< and >1.5. The ASVs that were significantly enriched were used to identify the relative abundance of the ASVs across sample types and zones. In addition, those enriched only in either DU or DL were used to identify the presence or absence of each ASV in coral species and study per biome. The same ANCOM_BC analysis was repeated without MCAV and OFAV to evaluate if the two dominant coral species in our meta-analysis were driving the enriched bacteria.