Unraveling the Microbiomes Role in the Expression of Complex Host Phenotypes Requires a Biogeographical Understanding

Microbes are not homogeneously distributed throughout the gastrointestinal tract (GIT), yet all can contribute to the physiology of the host. Complex phenotypes like feed efficiency in ruminants and obesity in humans have been linked to GIT microbiota and shown to involve more than simply the varying capacity of the microbiota to increase the accessibility of nutrients in the rumen and colon. Microbial influences on GIT homeostasis and health appear equally important and can be mediated from less commonly considered regions of the GIT. The composition and biospatial distributions of microbes throughout the GIT also vary over time reflecting age, dietary transitions, host physiology, health, and therapeutic regimens. Biospatial delineation of the GIT is evident within 24 h of birth and, in ruminants, we have found that each GIT location is deferentially seeded by maternally- and environmentally-derived microbes. Following colonization, a dynamic succession ensues until a climactic state is reached ~120 – 180 days in ruminants and ~3-4 years in humans. This climactic state mirrors measures of immunological maturation in both species and appears less pliable than their pre-climactic state. It is, therefore, hypothesized that these earliest seeding and successional processes are the most important to the ultimate phenotype of the animal. Because of this, it is essential that microbiota are studied biogeographically (over space and time) to derive a complete understanding of their roles in modulating complex phenotypes of the host.