Rheumatoid arthritis (RA) is a systemic autoimmune disease driven by complex interactions between host genetics and environmental factors. While taxonomic dysbiosis of the gut microbiota is well-documented, species-level abundance often fails to capture the high-resolution functional nuances required for clinical stratification. Microbial structural variations (SVs), including deletion (dSVs) and variable SVs (vSVs), offer sub-genome level resolution of bacterial function and harbor genes critical for host-microbe interactions. However, the specific contribution of microbial SVs to RA pathogenesis, particularly their causal relevance across different populations, remains largely unexplored.

We performed a cross-cohort meta-analysis integrating gut metagenomic data from four independent clinical cohorts, totaling 491 individuals from diverse geographical backgrounds. Microbial SVs were systematically identified using the SGV-Finder framework and integrated with host genetic data via two-sample Mendelian randomization (MR) to evaluate potential causal relationships with RA susceptibility. To characterize functional consequences, we implemented a multi-layer interaction network mapping SVs to Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, three-dimensional structures of candidate causal proteins were predicted using AlphaFold2, followed by automated molecular docking simulations (AutoDock Vina) against a library of systemic antibacterials curated from the DrugBank database.

Our meta-analysis identified a robust consensus signature of 59 RA-associated SVs (34 vSVs and 25 dSVs) across 49 differentially abundant species. Notably, a trans-ethnic causal association was established between a specific structural variant locus (2479_2481) in Faecalibacterium prausnitzii and RA susceptibility (FDR < 0.05), which was consistently observed across both East Asian and European populations. Functional profiling revealed that RA-associated SVs are non-randomly distributed, predominantly impacting modules involved in cell wall biogenesis, carbohydrate metabolism, and inorganic ion transport. The causal F. prausnitzii locus specifically perturbs a gene encoding a relaxase/mobilization nuclease domain protein (HMPREF9436_01231). Molecular docking simulations demonstrated that several classes of systemic antimicrobials—specifically third-generation cephalosporins, tetracyclines, and fluoroquinolones—exhibit high binding affinities (energy values < -7.0 kcal/mol) for the active site of this relaxase protein.

These findings represent a paradigm shift from observational dysbiosis toward high-resolution causal inference in RA research. By identifying a specific microbial protein as a fundamental "hit" in RA pathogenesis and demonstrating its vulnerability to common antibiotics, this study provides a novel structural biology perspective on how antibiotic-driven dysbiosis modulates host inflammatory susceptibility. This research paves the way for SV-based precision diagnostics and the development of targeted microbiome-directed interventions, such as "ecological shields," to preserve the gut-immune axis in rheumatoid arthritis.