Dynamic response of the intestinal microbiome to <i>Eimeria maxima-</i> induced coccidiosis in chickens

We have observed for the first time the dynamic response of the intestinal microbiota to <i>Eimeria maxima</i> infection, synchronized with its life cycle. Minimal changes occur in both the ileal and cecal microbiota during early infection, while significant alterations coincide with acute infection and disruption of the intestinal mucosal lining. As animals recover from coccidiosis, the intestinal microbiota largely returns to normal. <i>E. maxima</i>-induced intestinal inflammation likely creates an environment conducive to the growth of aerotolerant anaerobes such as <i>Lactobacillus</i>, as well as facultative anaerobes such as <i>Escherichia</i>, <i>Enterococcus</i>, and <i>Staphylococcus</i>, while suppressing the growth of obligate anaerobes such as short-chain fatty acid-producing bacteria. These findings expand our understanding of the temporal dynamics of the microbiota structure during <i>Eimeria</i> infection and offer insights into the pathogenesis of coccidiosis, supporting the rationale for microbiome-based strategies in the control and prevention of this condition.