The intestinal microbiota is of great importance to our health and wellbeing. Modulation of the intestinal microbiota by exogenous and endogenous substrates can be expected to improve various physiological functions of our body, not just those in the intestine. Recently, new targets such as immune function and areas outside the colon have been considered to be influenced by the intestinal microbiota. Novel approaches might include the application of prebiotics in different combinations or the provision of nutrients to different bacterial groups and to different parts of the intestine.