Silibinin-derived microbiota enrich (R)-2,3-dihydroxy-isovalerate and ameliorate colitis via the GAT-3/RARβ/RORγt axis

Microbiota-associated factors are increasingly recognized as significant contributors to the progression of ulcerative colitis, and microbial modulation has emerged as an effective therapy for this condition. The herbal compound silibinin has demonstrated properties that modulate gut microbiota. Herein, we investigated the response of gut microbiota to silibinin in ameliorating colitis, using a mouse model of colitis coupled with antibiotic exposure. Results indicated that antibiotic pretreatment negated the benefits of silibinin in mice with colitis. Furthermore, fecal microbiota transplantation involving silibinin-modulated gut microbiota further substantiated the gut microbiota-dependent effects of silibinin. Within the metabolic profiles of silibinin-regulated microbiota, we identified that Alistipes-associated (R)-2,3-dihydroxy-isovalerate exhibited the most pronounced anti-inflammatory effects in vitro and demonstrated protective effects against colitis. Moreover, (R)-2,3-dihydroxy-isovalerate reinstated the protective effects of silibinin in mice with colitis under antibiotic exposure. These effects were primarily mediated via the targeting of the colonic GABA transporter 3 (GAT-3) by (R)-2,3-dihydroxy-isovalerate. We further revealed that the retinoic acid receptor β and the retinoid-related orphan nuclear receptor γt may mediate the impact of silibinin-derived microbiota and (R)-2,3-dihydroxy-isovalerate on colitis. Additionally, the knockdown of colonic GAT-3 diminished the impact of silibinin on the GAT-3/retinoic acid receptor β/retinoid-related orphan nuclear receptor γt axis and colitis. Our findings highlight that (R)-2,3-dihydroxy-isovalerate, enriched from microbiota derived from silibinin, can target the GAT-3/retinoic acid receptor β/retinoid-related orphan nuclear receptor γt axis, which is essential for anti-colitis properties of silibinin-regulated microbiota.