A study from the Mayo Clinic published in the PloS ONE in June of 2012 showed that the gut microflora regulate the immune system and may be directly related to autoimmune disorders such as ulcerative colitis, and diabetes. In fact, the gut microbiome may be used as a biomarker for this predisposition and it may be possible to prevent autoimmune diseases by manipulating the balance of the microflora.
Imbalance of the gut microflora, known as dysbiosis, can lead to increased permeability of the gut lining, a condition known as leaky gut syndrome (LGS). The authors suspect that LGS catalyzes the development of autoimmune disorders.