Human beings assemble and maintain a diverse but host-specific gut microbial community along the longitudinal axis of the intestines. Helped by a functional tight junction, the default response to commensal microbes is tolerance, whereas the default response to pathogens is an intricately orchestrated immune response, resulting in pathogen clearance. Nutrients and industrial food additives were suggested to impact the intestinal ecosystem and to breach tight junction integrity. Taken together, certain nutritional components, increased intestinal permeability, disease specific dysbiotic pathobionts and their capacity of post translation modification of proteins, are luminal events that impact autoimmunogenesis. The present review expands on the multi gut originated axes and their relationship to remote organ autoimmune diseases. Brain, joint, bone, endocrine, liver, kidney, heart, lung and skin autoimmune diseases are connected to the intestinal luminal compartmental deregulated events to form the gut-systemic organs axes.