The gastrointestinal tract can be considered as a small, but complex, ecosystem that includes abiotic (physical and chemical characteristics) and biotic (resident microbiota) components. Many of the ecological principles known for river systems are shared by the GIT and are useful for understanding the influences of dietary inputs. Although each species has a genetically programmed sequence of postnatal changes in GIT structure, functions, and the resident microbiota, the patterns can be manipulated by dietary inputs. Important questions remain to be answered before dietary inputs can be effectively used to "manage" postnatal development of the GIT and thereby optimize health and development of animals.