Abstract
Tan sheep, a valuable indigenous breed in China, are vulnerable to coccidiosis caused by Eimeria ovinoidalis. In this case-control study, four 8-month-old Tan sheep raised under identical conditions were enrolled, including two with confirmed E. ovinoidalis infection (the Eo group) and two healthy controls (the HC group). Integrated metagenomic and untargeted metabolomic analyses were performed to assess gut microbiota and metabolic alterations. Results showed reduced alpha diversity and a distinct microbial composition in the Eo group. LEfSe identified 38 differentially abundant bacterial species, with Prevotella sp. and Fusobacterium necrophorum enriched in the Eo group and Faecalibacterium sp. and Lachnospira sp. enriched in the HC group. KEGG and VFDB analyses revealed significant differences in microbial functional pathways and virulence factor profiles. A total of 543 metabolites were differentially expressed, involving pathways related to inflammation, stress response, and amino acid metabolism. Microbiome-metabolome correlation analysis showed that Eo-associated bacteria were positively linked to pro-inflammatory metabolites, while HC-associated taxa correlated with markers of metabolic homeostasis. These findings provide new insights into the pathogenesis of ovine coccidiosis and may inform targeted interventions.