The gastrointestinal tract of mammals contains a complex microbial community that influences numerous aspects of health and development. It is postulated that establishment of this community during early life has long-term consequences on the health status of adults. Potential influences on colonization are expected to include environmental microbes, diet and the developmental changes of the host. Denaturing gradient gel electrophoresis was used to follow the individual community dynamics of 24 piglets over the period of 3-36 days after birth. The community of piglets older than 31 days was inferred to show high stability relative to the first 28 days post birth. The stable day 36 community showed significant correlation between cohabiting piglets, but not between siblings. This cohabitation effect was not observable in 1- or 2-week-old piglets but was strongest at either 3 or 4 weeks post birth. The onset of this change after 2 weeks is predicted to be after the development of key induction elements of the immune system and before significant levels of piglet sIgA were observable (4 weeks). The outcome is altered community dynamics that result in significant similarity between the stable communities that develop in cohabiting pigs. We conclude that for a finite period in their development, the outcome of gut colonization in piglets is greatly influenced by the immediate environment. The implication is that mammals have a developmental window, in which the developing host-gut microbiota interaction will be simultaneously more amenable to engineering and more susceptible to disturbance.