Intestinal microbiota – host interactions play a major role in health and disease. This has been documented at the microbiota level (“dysbiosis” in chronic immune-mediated diseases) and through the study of specific bacteria – host interactions, but rarely at the level of intestinal ecosystem dynamics. Yet, understanding the behavior of this ecosystem may be key to the successful treatment of disease. We recently postulated that health and disease represent alternative stable states of the intestinal ecosystem (different configurations that can exist under identical external conditions), which would demand for adapted strategies in disease treatment.