Integrative Proteomics Reveals Distinct Lipid Metabolic and Gut Microbiota-Associated Antidepressant Mechanisms of Two Herbal Medicines in a Chronic Stress Model

L. (St. John's Wort [SJW]) and Chaihu Shugan San (CSGS) have been widely used to treat depressive symptoms, yet their system-level molecular mechanisms remain incompletely understood. In this study, we applied a multi-omics strategy centered on quantitative proteomics, combined with metabolomics and microbiota profiling, to investigate the antidepressant mechanisms of CSGS and SJW in a chronic unpredictable mild stress rat model. Behavioral assessments confirmed that both treatments significantly alleviated depressive-like behaviors. Proteomic analysis identified 204 differentially expressed proteins (DEPs) in the CSGS group and 473 DEPs in the SJW group. Functional enrichment analyses suggested that CSGS was more closely associated with lipid metabolism, whereas SJW was linked to broader metabolic processes. Integrative metabolomic and microbiota analyses further supported these proteomics-driven pathway distinctions, with SJW showing stronger associations with gut microbiota alterations. CSGS and SJW alleviated depressive-like behaviors through divergent yet partially overlapping molecular mechanisms. These findings highlight the utility of multi-omics approaches for elucidating system-level mechanisms of complex herbal medicines.