Integrated 16S rRNA gene sequencing and LC-MS/MS-based metabolomics to explore potential mechanisms of Coptidis Rhizoma-Aucklandiae Radix herb pair against antibiotic-associated diarrhea.

Antibiotic-associated diarrhea (AAD) incidence has been continuously increasing in recent years; however, effective treatments remain limited. Coptidis Rhizoma-Aucklandiae Radix (CR-AR) is a classic herbal combination widely used clinically for managing gastrointestinal diseases. Studies have demonstrated that it exerts significant therapeutic effects against AAD, although its underlying mechanisms of action remain unclear. This study integrated metabolomics based on UPLC-Q-Exactive-Orbitrap-HRMS and 16S rRNA gene sequencing to investigate the potential mechanism of CR-AR against AAD. The results showed that CR-AR effectively ameliorated diarrhea symptoms and alleviated intestinal pathological changes. Metabolomics analysis revealed that CR-AR significantly reversed the expression changes of 34 metabolites in the cecal contents, including amino acids and bile acids, whereas its regulatory effects on serum and colon were relatively limited, modulating only 16 and 17 metabolites, respectively. The systemic regulatory effects mediated by CR-AR through gut-host interactions were supported by the co-regulation of metabolic pathways, specifically tryptophan metabolism and primary bile acid biosynthesis, in the serum, colon, and cecal contents. CR-AR also effectively enriched Blautia and Lachnoclostridium, while inhibiting the proliferation of Escherichia-Shigella and Enterococcus. Furthermore, significant correlations were observed between key bacterial genera and differential metabolites. This study demonstrated that CR-AR exerted therapeutic effects on AAD by regulating gut microbiota and metabolic homeostasis, and provided an experimental basis for further in-depth investigations into its underlying mechanism.