Microbial Imprinting in Gut Development and Health

SUMMARY The microbial community of the gastrointestinal system has an enormous impact on the vertebrate host. The relationship begins at birth or hatch and evolves to a stable ecosystem in which diverse, and unique, niches are created and inhabited by microorganisms. These microbial populations tend to be similar within a host species (and even across host species), but each system is a unique construct resulting from its individual history of mutual influence. The development of the system, both microbial and host, begins in the perinatal animal. The timing of this developmental process is suggestive of imprinting, the process of epigenetic evolution of somatic stem cells. (Imprinted changes are thought not to involve the germ line, i.e., are not inherited by the next generation of the host animal, but are genetic changes that can be passed on to the daughter cells of the imprinted proliferative stem cell.) This review briefly discusses the development of the gastrointestinal system, including both the microbiota and its perinatal host. The effects of the microflora on enteric and immune cells are described. Effects of attempts to restrict contact between the mucosal immune system and the microbiota are addressed, along with further data that would be required to demonstrate that the effects of the gut microbiota on mucosal immune development are restricted to an ontogenetic window. Finally, the consequences of a failure to achieve a relationship of mutual tolerance between the microbiota and the host and some mechanisms to facilitate this process are discussed.