By defining the patients as being eubiotic or dysbiotic, we demonstrate host–microbiota interactions that are putatively dependent on intestinal dysbiosis, including the genes involved in immunological tolerance and prevention of autoimmunity (e.g. bifidobacteria and FOSL1/KLF2 expression), colorectal carcinogenesis (e.g. Anaerostipes and SMAD4, Akkermansia and YDJC) and inflammatory signaling (e.g. Oscillibacter and OSM expression). The gene discussed is SMAD4; the disease is Autoimmunity.