Fig. 3

Alterations in relative abundances (%) 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. The compositional changes in the ileal microbiome are shown for different groups of chickens at the phylum (A), family (B), genus (C), and amplicon sequence variant (ASV) (D) levels