Breed-specific responses to coccidiosis in chickens: Identification of intestinal bacteria correlated with disease resistance

Coccidiosis, caused by obligate intestinal parasites of the genus Eimeria, is a significant enteric disease in poultry. Beyond its direct impact on animal health, production performance, and welfare, coccidiosis imposes a substantial economic burden, costing the global poultry industry up to $13 billion annually. Effective mitigation strategies for coccidiosis are still lacking, further complicated by restrictions on antimicrobial use and consumer demands for antibiotic-free production. Although different chicken breeds exhibit varying resistance to coccidiosis, no commensal bacteria have been directly linked to coccidiosis resistance. We hypothesize that coccidiosis-resistant chickens harbor unique commensal bacteria that confer colonization resistance against coccidiosis. To determine the relative resistance of different chicken breeds to coccidiosis, three chicken lines, including Fayoumi M5.1, Leghorn Ghs6, and Cobb broilers, were challenged with 50,000 sporulated Eimeria maxima (EM) oocysts or mock-infected on day 10. Evaluations of body weight changes, small intestinal lesions, and fecal shedding of oocysts were conducted on day 17. Ileal and cecal digesta were further collected from each chicken on day 17 and subjected to 16S rRNA sequencing for microbiome analysis. Our results indicated that Fayoumi M5.1 chickens are the most resistant to coccidiosis and intestinal dysbiosis compared to Cobb and Ghs6 chickens. Both the ileal and cecal microbiota were markedly different among the three chicken breeds under both healthy and coccidiosis conditions. Notably, various Lactobacillus, Ligilactobacillus, and Limosilactobacillus species were highly enriched in both the ileum and cecum of M5.1 chickens in response to coccidiosis, suggesting the potential of these lactic acid bacteria as probiotics for the mitigation of coccidiosis.