Association between autoimmune diseases and the gut microbiome

The gut microbiome has emerged as an important environmental factor in the pathogenesis of autoimmune diseases. Advances in high-throughput sequencing technologies have enabled comprehensive characterization of the gut microbiome, providing detailed insights into its composition and functional potential. These approaches have been widely applied in autoimmune disease research, revealing disease-associated alterations in the gut microbiome of patients with conditions such as rheumatoid arthritis and systemic lupus erythematosus. In addition, microbiome sequencing data can be leveraged to investigate the gut virome, including viruses residing in the intestinal ecosystem. This review summarizes current evidence linking autoimmune diseases and the gut microbiome, with a particular focus on studies employing microbiome sequencing-based analyses.