Tanshinones from Salvia miltiorrhiza alleviate ulcerative colitis via reprogramming the gut microbiota-metabolite axis

• Tanshinones from Salvia miltiorrhiza significantly alleviate DSS-induced ulcerative colitis by reducing inflammation and restoring intestinal barrier integrity. • Integrated multi-omics reveals that tanshinones reprogram the gut microbiota-metabolite axis, reversing dysbiosis and correcting metabolic disturbances in linoleic acid, bile acids, and amino acids. • Key microbial-metabolite modules link beneficial bacteria like Akkermansia to anti-inflammatory lipids, while pathobionts like Desulfovibrio are associated with disrupted bile acid metabolism. • Supplementation with Akkermansia muciniphila synergizes with tanshinone IIA, enhancing barrier restoration and metabolic normalization, highlighting a microbiome-targeting therapeutic strategy for IBD.