Berberine protects against hypoxia-induced intestinal injury through modulation of gut microbiota and bile acid metabolism

Background High-altitude hypoxia disrupts intestinal homeostasis by impairing the epithelial barrier, triggering inflammation, and promoting microbial translocation. Berberine (BER), a natural isoquinoline alkaloid with antimicrobial and anti-inflammatory properties, has shown potential in protecting intestinal integrity; however, its efficacy under hypoxic conditions and its interaction with the gut microbiota remain unclear. Methods A chronic hypoxia mouse model was used to investigate the protective effects of BER against intestinal injury. Microbiota dependency was assessed through antibiotic-mediated depletion and fecal microbiota transplantation (FMT), combined with 16S rRNA gene sequencing, metabolomics, and immune profiling. The functional role of a BER-responsive bacterium was validated by oral administration in antibiotic-treated mice. Results BER supplementation restored epithelial barrier integrity, including tight junctions, antimicrobial peptide expression, and goblet cell function, while reducing inflammation and epithelial apoptosis under hypoxic conditions. BER also reshaped gut microbial composition and network structure, accompanied by coordinated alterations in cecal metabolites, particularly purine metabolites and bile acids. Microbiota depletion abolished the protective effects of BER, whereas FMT from BER-treated donors recapitulated these effects, confirming a microbiota-dependent mechanism. Among BER-responsive taxa, Bacteroides thetaiotaomicron (B. thetaiotaomicron) emerged as a key effector, correlating with metabolite profiles and barrier integrity. Oral administration of B. thetaiotaomicron alone protected against hypoxia-induced intestinal injury, restoring mucin production and antimicrobial peptide expression, and attenuating inflammation and apoptosis. Mechanistically, both BER and B. thetaiotaomicron reactivated bile acid–FXR signaling and normalized intestinal immune homeostasis, including T-cell subset distribution. Conclusion These findings demonstrate that BER protects against hypoxia-induced intestinal injury through microbiota-dependent metabolic and immune regulation. B. thetaiotaomicron acts as a central mediator of this protective effect, highlighting microbiota-targeted strategies as potential interventions for maintaining intestinal homeostasis under hypoxic stress.