Intestinal dysbiosis in necrotic enteritis: dissecting the roles of Eimeria and Clostridium perfringens

ABSTRACT Necrotic enteritis (NE), caused by Clostridium perfringens , is a major enteric disease in poultry with substantial economic impact. NE is frequently triggered by co-infection with Eimeria spp., yet the relative contributions of Eimeria and C. perfringens to NE-induced dysbiosis and disease progression remain poorly defined. To address this, Cobb broiler chickens were challenged with Eimeria maxima , C. perfringens , or both, and ileal and cecal microbiota were analyzed using 16S rRNA gene sequencing and shotgun metagenomics. Temporal dynamics of intestinal microbiota shifts were further assessed at multiple time points post-infection. Our findings demonstrate that NE-associated dysbiosis is characterized by enrichment of pathobionts including C. perfringens , Escherichia , and Enterococcus cecorum , along with differential abundance of certain lactic acid- and short chain fatty acid-producing bacteria. Dysbiosis and disease progression were driven by synergistic interactions between E. maxima and C. perfringens , with E. maxima exerting a dominant influence. Notably, E. maxima alone promoted expansion of commensal C. perfringens or closely related bacteria, even without prior exposure. Metagenomic analysis of the cecal microbiota further revealed a functional shift favoring utilization of host-derived glycans and simple carbohydrates over dietary fibers, in response to E. maxima and NE challenges. This transition coincided with E. maxima -induced epithelial damage, increased mucogenesis, and nutrient malabsorption. NE-associated dysbiosis emerged four days post- E. maxima infection and peaked 2–3 days following C. perfringens challenge. These findings suggest that Eimeria infection creates a permissive intestinal environment for C. perfringens colonization and proliferation, underscoring its pivotal role in NE pathogenesis. IMPORTANCE NE is a major health and economic burden in poultry production, primarily driven by C. perfringens and potentiated by Eimeria infection. This study provides critical mechanistic insights into the distinct and synergistic roles of E. maxima and C. perfringens in NE disease progression. We show that Eimeria plays a dominant role in driving NE-associated dysbiosis and disease progression by inducing epithelial damage, inflammation, and nutrient malabsorption, which facilitate C. perfringens colonization, proliferation, and toxin production. Comprehensive characterizations of both structural and functional microbiome shifts revealed that NE-associated dysbiosis is marked by enrichment of facultative pathobionts that favor utilization of host-derived mucins and simple dietary carbohydrates, alongside depletion of strictly anaerobic, fiber-fermenting, SCFA-producing bacteria. These microbial shifts reflect disease progression and offer potential biomarkers for early diagnosis and therapeutic intervention. Our findings lay a foundation for microbiota-based diagnostics and interventions to mitigate NE and potentially other enteric diseases.