Dysbiosis of the Oral-Gut Microbiome Axis in Autoimmune Diseases: Shared and Disease-Specific Patterns in primary biliary cholangitis, ankylosing spondylitis, and systemic lupus erythematosus

Autoimmune diseases (ADs) are associated with alterations in the oral and gut microbiome. However, methodological heterogeneity across studies has obscured the shared and disease-specific features of dysbiosis, and the relationship between the oral and gut microbial niches remains poorly characterized.This study performed integrated analyses of the bacteriome and mycobiome in matched saliva and fecal samples from patients with primary biliary cholangitis (PBC), ankylosing spondylitis (AS), and systemic lupus erythematosus (SLE), alongside healthy controls. We identified both shared and disease-specific dysbiotic features across these ADs. A core set of taxa, including enriched Escherichia-Shigella, Faecalibacterium, and Streptococcus gordonii in saliva and depleted Aeromonas and Cetobacterium in feces, was common to all three diseases. Notably, the Oral-Intestinal Microbial Translocation Index (OIMTI), quantifying the proportion of oral-derived bacterial strains in the gut, was significantly elevated in patients (PBC: 10.66%; AS: 5.58%; SLE: 10.70%) compared to healthy controls (1.61%), with disease-specific taxonomic profiles of the translocated communities. Furthermore, dysbiotic features, particularly in the salivary microbiome of AS patients and the gut microbiome of SLE patients, showed strong correlations with clinical disease activity and immune markers. Our findings underscore the oral-gut axis as a critical frontier in AD pathogenesis and highlight OIMTI as a promising, novel biomarker for assessing microbial translocation, with potential implications for future microbiome-based diagnostics and therapeutics.