Single-cell encapsulation of Agathobacter rectalis in Aloe vera gel alleviates DSS-induced colitis by remodeling the gut microbiota-metabolite axis

Gut microbiota dysbiosis and metabolic disturbances are implicated in inflammatory bowel disease (IBD). Current probiotic therapies are limited by poor bioavailability and inadequate colonic colonization. Here, we identified Agathobacter rectalis from IBD patient feces and demonstrated that it alleviated dextran sulfate sodium-induced colitis in mice by reshaping the gut microbiota and bile acid pool. To overcome these delivery barriers, we developed a single-cell encapsulation system using Aloe vera gel, a natural acid-resistant and anti-inflammatory hydrogel, and designated it as A. rectalis @Aloe to enhance probiotic bioavailability and targeted colonic retention. Comprehensive characterization confirmed that encapsulation significantly improved bacterial viability in simulated gastric fluid and enhanced colonic colonization. In murine colitis models, A. rectalis @Aloe synergistically suppressed inflammation, reinforced barrier function, modulated gut microbiota, and increased short-chain fatty acid production. Mechanistically, it inhibited cytokine–cytokine receptor interactions and the PI3K-Akt pathway. By synergistically enhancing gastric acid survival, mucosal colonization, and multi-pathway anti-inflammatory effects, this single-cell aloe gel encapsulation strategy offers a clinically promising and readily translatable platform for live biotherapeutics targeting the gut microbiota–metabolite axis in IBD.