The role of microbiota in autoimmune disease pathogenesis: Mechanisms and therapeutic implications

The role of the human microbiome in autoimmune pathogenesis. This review is intended to explore the cause-effect phenomenon in the interaction between microorganism and autoimmune disease through reference to data during 2000 till 2025. We discuss the influence of early-life colonization of the microbiota on immunological programming and discuss the possible relevance of sex-specific microbiome differences in the context of female bias in autoimmune diseases. Disrupted resident communities and translocation processes of microbes in systemic autoimmunity are discussed. We discuss microbiota-dependent molecular mechanisms, including epigenetic modifications, that are linked to regulation of B cell differentiation and autoantibody expression and differential regulation of T helper cell subsets. Segmented filamentous bacteria and mycobiota are highlighted for disease induction. In this review, we talk about the immune-modulating capabilities of microbial metabolites, and more specifically short-chain fatty acids, and discuss to what degree dietary alterations in the microbiome may influence disease course. By establishing the groundwork for these concepts, we reveal exciting avenues for the application of microbiota-based therapies, including dietary therapy, prebiotics, probiotics, fecal microbiota transplantation, and more sophisticated biotechnological approaches aimed at restoring our control over autoimmune disease.