Fig. 4

Differential abundance 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 16S rRNA gene sequencing. Differential abundance analysis of the ileal microbiome at the genus (A) and amplicon sequencing variant (ASV) (B) levels was performed using ANCOM–BC [30]. The left two panels in each heatmap depict log₂ transformations of the fold changes of differentially enriched bacteria in the ileum of mock and EM-infected chickens, relative to mock-infected Cobb chickens. The right panel in each heatmap illustrates log₂ transformations of fold differences of individual bacteria between EM- and mock-infected chickens in each breed. ASVs are further color-coded by family. ^*P < 0.05, ^**P < 0.01, and ^***P < 0.001