Fig. 2

Alpha and beta diversities of the ileal mycobiota in healthy and NE chickens. Chickens were sequentially infected with E. maxima and C. perfringens to induce NE and separated into five groups based on their intestinal lesion scores. The number of amplicon sequence variants (ASVs) A, Peilou’s evenness index B, and Shannon index C were shown in box and whisker plots. Each box indicated median, 25th and 75th percentiles, while whiskers extended to 1.5 interquartile range. Significance was evaluated using Kruskal-Wallis test, while pairwise comparisons were implemented using Mann–Whitney U test. Different superscripts denoted significance (P < 0.05) in pairwise comparisons. Principal coordinates analysis (PCoA) plots were based on unweighted D and weighted UniFrac distances E. Each dot represented an individual ileal digesta sample. The x and y axes indicated the percentage of variation explained by two principal coordinates. Significance was determined using PERMANOVA