Dynamic response of the intestinal microbiome to induced coccidiosis in chickens.

Unlabelled: is a major cause of coccidiosis in chickens and a key predisposing factor for other economically significant diseases such as necrotic enteritis. However, a detailed understanding of the intestinal microbiome response to infection is still lacking. This study aimed to comprehensively investigate the dynamic changes of the intestinal microbiome for 14 days post-infection (dpi) with . Bacterial 16S rRNA gene sequencing was performed with the ileal and cecal digesta collected from mock and infected chickens at the prepatent (3 dpi), acute (5 and 7 dpi), and recovery phases (10 and 14 dpi) of infection. Although no notable changes were observed at 3 dpi, significant alterations of the microbiota occurred in both the ileum and cecum at 5 and 7 dpi. By 14 dpi, the intestinal microbiota tended to return to a healthy state. Notably, was enriched in response to infection in both the ileum and cecum, although individual , , and species varied in the temporal pattern of response. Concurrently, major short-chain fatty acid-producing bacteria, such as , were progressively suppressed by in the cecum. On the other hand, opportunistic pathogens such as , , and were significantly enriched in the ileum during acute infection.

Importance: We have observed for the first time the dynamic response of the intestinal microbiota to 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. -induced intestinal inflammation likely creates an environment conducive to the growth of aerotolerant anaerobes such as , as well as facultative anaerobes such as , , and , 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 infection and offer insights into the pathogenesis of coccidiosis, supporting the rationale for microbiome-based strategies in the control and prevention of this condition.