Pathogen-guided herbal formulas modulate lamb gut microbiota and metabolites

Gut microbiota and microbial metabolites are closely associated with enteric infection outcomes in livestock. In this study, 258 fecal samples were collected from lambs across four regions of China to characterize major diarrhea-associated pathogen patterns. Eimeria spp. were frequently detected, and Eimeria – Escherichia coli co-detection represented a prominent mixed-detection pattern. Based on these field observations and traditional Chinese medicine compatibility principles, an anti-parasitic formula (PAR) and an anti-mixed infection formula (MIX) were developed. Their effects were evaluated in a 21-day trial involving 24 naturally coccidia-positive lambs. Fecal microbiota and metabolomic profiles were further characterized in four lambs per group using 16S rRNA gene sequencing and untargeted metabolomics. PAR was associated with the clearest reduction in fecal oocyst shedding during the treatment period, whereas growth-related outcomes did not differ significantly among groups. PAR also showed distinct microbial and metabolic features involving the NK4A214 group and steroid-, amino acid-, and bile acid-related metabolites associated with Eimeria oocysts per gram of feces (OPG) variation. MIX showed broader associations with inflammatory and antioxidant indicators. Exploratory mediation models identified inosine-associated relationships linking selected bacterial taxa with IL-6 and MDA variation. Berberine was more appropriately interpreted as a treatment-associated metabolic signal than as a microbiota-mediated metabolite. These findings indicate that PAR and MIX were associated with distinct phenotypic, microbial, and metabolic response profiles in naturally coccidia-positive lambs. The microbiota-metabolite patterns and exploratory mediation signals should be regarded as hypothesis-generating and require validation in larger cohorts. This pathogen-guided framework may support the development of microbiota-oriented botanical strategies for sustainable sheep production.