Intestinal Microbiome Confers Strong Colonization Resistance Against Necrotic Enteritis

Necrotic enteritis (NE), caused by Clostridium perfringens , is a major enteric disease in poultry that leads to severe dysbiosis, morbidity, and mortality. Modulating the intestinal microbiota holds promise for enhancing animal health and disease resistance; however, specific commensal bacteria associated with NE protection remain elusive. Chicken breeds differ markedly in disease susceptibility, with Fayoumi chickens exhibiting greater resistance than Leghorn and Cobb chickens. We hypothesized that Fayoumi chickens harbor unique commensal bacteria that confer robust colonization resistance against NE. To test this, we challenged two inbred lines, Fayoumi M5.1 and Leghorn Ghs6, alongside commercial Cobb broilers with NE. Among these, M5.1 chickens demonstrated the highest resistance to NE. Cecal microbiota transplantation from the three breeds into newly hatched Cobb chicks revealed that M5.1-derived microbiota provided completion protection against NE. Comparative microbiome analysis demonstrated significant differences among breeds under both healthy and NE-challenged conditions. Notably, Bifidobacterium , largely absent in healthy chickens of all three breeds, was highly enriched in both the ileum and cecum of M5.1 chickens following NE challenge. Furthermore, oral administration of Bifidobacterium pseudolongum significantly reduced NE mortality in Cobb chickens. Collectively, these findings highlight the protective role of commensal bacteria from NE-resistant Fayoumi chickens and suggest their potential for microbiota-based strategies to mitigate NE in poultry.