The invention is related to a system for treating irritable bowel syndrome, Crohn's disease, ulcerative colitis (collectively, inflammatory bowel disease, or “IBD”) by determining a number of indicators, including genetic markers, gene expression levels, levels of certain compounds in the gut or feces, hydrogen and/or methane levels, and concentrations of particular bacteria in the gut or feces, and correlating one or more such indicators with symptoms in test subjects with IBD; and correlating diet, drugs, supplements or other therapy, with alleviation of IBD symptoms. The correlations established in the test subjects are confirmed or refuted for individuals suffering IBD, and the treatments established as reducing symptoms are supported through messaging and compliance is verified by monitoring the indicators.