The human microbiome shapes immune development and maintains homeostasis. Cumulative evidence has linked dysbiosis to the initiation and progression of autoimmune diseases. In this review, we summarize disease-specific microbial signatures and immunologic axes of rheumatoid arthritis, axial spondylarthritis, systemic lupus erythematosus, inflammatory bowel disease, and type 1 diabetes. Despite the promise of microbiome-based therapeutics, including probiotics, next-generation probiotics, engineered live biotherapeutics, and fecal microbiota transplantation, their translation into clinical practice is limited by heterogeneity, low-biomass contamination issues, and reliance on relative abundance metrics. We highlight the requirement for standardized sampling/analytics and absolute-quantitative approaches, multicenter validation of biomarker panels, and mechanism-driven interventional trials. The integration of microbial, metabolomic, and host immune response aspects is a pivotal step in the transition from association to causation and in the development of precise and safe microbiome-based diagnostics and therapeutics for autoimmune diseases.
Kim et al. (Sun,) studied this question.