Deciphering the microbiological mechanism of Tongxie Yaofang in treating IBS-D: a multimodal mechanistic study in mice integrating network pharmacology, computational simulation, and 16S rRNA sequencing

Irritable bowel syndrome with diarrhea (IBS-D), associated with the traditional Chinese medicine (TCM) pattern of liver hyperactivity with spleen deficiency pattern, lacks effective Western treatments. The modern biological relevance of the “intestine–liver–bile acid” axis aligns with this TCM concept, and interactions between intestinal microbiota and diarrhea remain unclear. Network pharmacology, molecular docking, and molecular dynamics were applied to elucidate the mechanisms and compound–target stability of Tongxie Yaofang. An IBS-D mouse model was established using Senna alexandrina Mill. combined with confinement stress. Histopathological changes in the liver and spleen were assessed by hematoxylin–eosin (HE) staining, and enzyme-linked immunosorbent assay (ELISA) was performed to quantify total bile acid levels in serum and liver. Ultimately, 16S rRNA high-throughput sequencing was employed to identify predominant and distinctive bacterial species. Network pharmacology and molecular docking revealed that Tongxie Yaofang acts primarily through the TNF-α and IL-17 pathways. Molecular dynamics confirmed strong binding affinities between active compounds (naringenin, divaricatol, and kaempferol) and target proteins. In vivo , Tongxie Yaofang alleviated colonic inflammation, increased serum bile acid levels, reduced hepatic bile acid concentrations, and increased intestinal microbial diversity and abundance. The therapeutic effects of Tongxie Yaofang on IBS-D are mechanistically linked to its multi-target actions, including suppression of inflammatory responses, inhibition of pathogenic bacterial overgrowth, restoration of immune homeostasis, and modulation of intestinal microbiota composition toward a probiotic-enriched community.