Fig. 5

Exposure to Mycobacterium chelonae inhibits diversification of gut microbiome. (A) Shannon Index for diversity of pre-exposed 129 days post fertilization (dpf), 214 dpf exposed and unexposed fish, and (B) for exposure groups within each diet. Capscale ordination based on the Bray-Curtis dissimilarity of gut microbiome composition of fish by (C) diet. (D) Log fold change of Mycobacterium of pre-exposed, exposed and unexposed fish within each diet as calculated by ANCOM-BC. Values are in reference to exposed fish within each diet. The analysis shows gut microbiome’s sensitivity to pathogen exposure is linked to diet, but Mycobacterium’s abundance is diet-dependent. A “ns” indicates not significantly different, and * indicates significant differences below the 0.05. An “X” indicates a group is significantly differentially abundant compared to the exposed treatment reference group