Fig. 2

Alterations in α- and β-diversities of the ileal microbiome among three chicken breeds in response to coccidiosis. Cobb, Leghorn Ghs6, and Fayoumi M5.1 chickens were challenged with sporulated E. maxima (EM) or mock-infected on d 10. Ileal digesta samples (n = 10–15) were collected on d 17 and subjected to DNA isolation and 16S rRNA gene sequencing. Box plots of observed amplicon sequence variants (ASVs) (A), Pielou’s Evenness index (B), and Shannon Index (C) were calculated for each group. Statistical analysis was performed using the nonparametric Mann-Whitney U test for each breed. ^*P < 0.05, ^***P < 0.001. Principal coordinate analysis (PCoA) plots of weighted UniFrac (D) and unweighted UniFrac distances (E) are shown for each breed with or without EM challenge. Statistical significance was determined using PERMANOVA with 999 permutations and is indicated in each panel