Comparison of Gut Microbiota and Metabolic Characteristics Between Miechongshu-Treated and Untreated Yili Horses

Anthelmintic treatment is widely used in equine health management to control parasitic infections; however, its potential effects on the gut microbiota and metabolic characteristics remain poorly understood. In this study, twelve Yili horses were randomly assigned to two groups: a control group (C), which received no anthelmintic treatment, and a Miechongshu-treated group (T), which was orally administered Miechongshu at a dose of 0.36 g/kg body weight on day 0. Fecal samples were collected from the rectums of Yili horses on day 14 after administration, and differences in gut microbial composition and metabolic characteristics between the two groups were further examined using 16S rRNA gene sequencing in combination with LC–MS/MS-based metabolomic analysis. The results showed that there was no significant difference in α diversity (p > 0.05). At the phylum level, compared with Group C, the relative abundance of Halobacterota significantly increased (p < 0.05). At the family level, the relative abundance of Prevotellaceae in Group T was significantly higher than that in Group C, while the relative abundance of Christensenellaceae decreased (p < 0.05). At the genus level, the relative abundance of Christensenellaceae_R-7_group was significantly decreased (p < 0.05). A total of 98 differentially expressed metabolites were identified in the total ion mode. Among them, 64 were upregulated compared with Group C, and 34 were downregulated. KEGG analysis revealed that four enriched metabolic pathways showed significant differences. Metabolic pathways, tryptophan metabolism, purine metabolism, fatty acid biosynthesis and carotenoid biosynthesis differed between the two groups. Compared with Group C, the contents of the metabolites tetradecanoic acid and adenosine were significantly decreased, while tryptophol was significantly increased. These results indicate that anthelmintic treatment is associated with alterations in the intestinal microecological balance and metabolic homeostasis of the host, providing new insights for evaluating the use of anthelmintics and the management of intestinal health in horses.