The intestinal hologenome lies at the center of intestinal homeostasis and disease. It is the sum of the host genome and the intestinal microbiome. During the last decade we came to appreciate the pivotal role of the microbiome in intestinal inflammation and concomitant diseases. Moreover environmental factors, predominantly diet, affect the microbiome and the host immune responses. Thus manipulation of intestinal microbiota and environmental factors are rightfully the focus of current research. The study of the hologenome necessitates not only clinical assessments but also the use of model organisms, for example, mice and flies. Despite the limitations imposed by the evolutionary distance between flies and mammals, Drosophila research provided us during the last few years with a wealth of information regarding intestinal inflammation and the role of microbiota. Conserved aspects of intestinal homeostasis and disease between flies and mice, for example in signalling pathways, the intestinal defence responses and the role of microbiota, consolidate and may advance the principles that govern intestinal inflammation in humans.