Role of the intestinal microbiome in autoimmune diseases and its use in treatments

•Intestinal microbiome and their metabolites play a critical role in determining the immune system.•Gut commensals and derived byproducts may be used as biomarkers for inflammatory status.•Probiotics like gut commensals can modulate gut microbiome and generate homeostasis. The role of the intestinal microbiome in the pathogenesis of autoimmune diseases such as rheumatoid arthritis, multiple sclerosis, and type 1 diabetes is being increasingly appreciated. Many studies have reported that the compositions of the intestinal microbiomes of patients with these autoimmune diseases are different from those of healthy individuals. Analyses of the intestinal microbiome of humans suggest that various factors affect the composition of the intestinal microbiome, including, but not limited to: geographical location, diet, sex, and age. However, patients with rheumatoid arthritis and type 1 diabetes show unique intestinal microbiome profile even after considering these confounding factors. This review will describe the known differences in the microbial composition for each of the aforementioned autoimmune diseases, how it impacts the immune system, and how these compositions may potentially be modulated by treatments with probiotics, prebiotics, and other microbiome altering therapies.