Multi-omics analysis reveals gut microbiota-metabolite interactions and their association with liver function in autoimmune overlap syndrome

BACKGROUND Autoimmune liver diseases, including primary biliary cholangitis (PBC), autoimmune hepatitis (AIH), and their overlap syndrome (OS), involve immune-mediated liver injury, with OS occurring in 1.2%-25% of PBC patients. OS carries a higher risk of cirrhosis, hepatocellular carcinoma, and reduced survival. While its pathogenesis remains unclear, gut microbiota dysbiosis and serum metabolite alterations may play key roles. This study uses 16S rRNA sequencing and liquid chromatography-mass spectrometry (LC-MS) metabolomics to compare gut microbiota and serum metabolites among PBC, AIH, and OS patients, and explores their associations with liver function. AIM To differentiate OS from PBC and AIH based on gut microbiota, serum metabolites, and liver function. METHODS Gut microbiota profiles were analyzed using 16S rRNA sequencing, while untargeted serum metabolomics was conducted via LC-MS. Comparative analyses were performed to identify differences in microbial composition and serum metabolite levels among PBC, AIH, and OS groups. Correlation analyses and network visualization techniques were applied to elucidate the interactions among liver function parameters, gut microbiota, and serum metabolites in OS patients. RESULTS Compared to patients with PBC or AIH, OS patients demonstrated significantly reduced microbial diversity and richness. Notable taxonomic shifts included decreased abundances of Firmicutes , Bacteroidetes , and Actinobacteria , alongside increased levels of Proteobacteria and Verrucomicrobia . Distinct serum metabolites, such as pentadecanoic acid and aminoimidazole carboxamide ribonucleotide, were identified in OS patients. Correlation analysis revealed that aspartate aminotransferase (AST) levels were negatively associated with the bacterial genus Fusicatenibacter and the metabolite L-Tyrosine. A microbial-metabolite network diagram further confirmed a strong association between Fusicatenibacter and L-Tyrosine in OS patients. CONCLUSION OS patients show decreased gut microbiota diversity and unique serum metabolites. Multi-omics linked AST, Fusicatenibacter , and L-Tyrosine, revealing OS mechanisms and diagnostic potential.