Variation in the composition of gut microbiota is of relevance to human diseases though the factors that induce and/or maintain such variation are still poorly understood. Understanding whether, and if so how, the genetic make-up of the host affects the composition of the healthy human microbiota is now of great interest. This will be approached by comparing host genome with microbiome. Also relatively novel is the potential to correlate microbiota variation with human bowel behavior both in terms of stool frequency and consistency (as surrogates of gut function). Based on these, we aim to establish computational models to describe and predict how these three elements (host genome, gut microbiome and gut function) are functionally and causally related in gastrointestinal health and disease. For these objectives, our main focus is on the general population, and on patients suffering from irritable bowel syndrome (IBS) and/or inflammatory bowel disease (IBD).