Microbiota — an amplifier of autoimmunity

•Commensal dysbiosis is associated with autoimmune diseases.•The gut microbial ecosystem is shaped by the host through the immune system.•The gut microbiota may act as an acquired endocrine organ.•Barrier dysfunction, microbe translocation and metabolites compromise self tolerance. Many studies describe dysbiosis as a change in the microbiota that accompanies autoimmune illnesses, but little is known about whether these changes are a cause or consequence of an altered immune state. The immune system actively shapes the composition of the microbiota, with divergent outcomes in healthy or autoimmune-prone individuals. The gut microbiota in turn acts as an acquired endocrine organ, influencing the physiology of the host via release of nutrients and chemical messengers. Dysbiosis arising from abnormal immune function can initiate or amplify autoimmunity through multiple mechanisms. We examine how the bidirectional relationship between resident microbes and the immune system contributes to autoimmune diseases.