When we are developing in the womb, the gut structure begins forming somewhere around the second week of gestation. This simple tube is laid out with epithelial and endothelial cell layers delineating what is inside and what is outside the future body. At birth, we already have the basic folds and villi of the small and large intestine, but research is showing that these are not necessarily as complexly organized as once thought. While our human DNA has set down the hills and shores of our gut topography, it still must be shaped by forces that are not human. Microbes have to step in and cultivate the land mass into a productive landscape. The veritable land grab that ultimately shapes the adult gut begins at birth whether the baby gets a mouthful of vaginal microbes or of skin microbes. It is at this moment, our guts begin to change and mature into the central site of our metabolism.

Without the luxury of recorded history of cities like Seattle or Rome, scientists are attempting to recreate a history of gut inoculation and cultivation by seeing what is going on now and extrapolating back. As our techniques of sorting out who is living in a gut and what it can do are getting more advanced, we are learning that initial colonization as well as adult structures in the gut aren’t as clear-cut as we thought. Physiological truisms are not holding up. Babies may not be sterile in the womb. Further, the deep crypts in the small intestine—once thought a pristine haven for human cells to escape the riffraff of microbes—appear to house many species of bacteria and may serve as a gated community of sorts that protects our commensal microbes from unruly newcomers. Bacteria like B. fragilis have special skills in their genetic narratives that allow them to homestead on the mucus layer here, allowing it to creep into the crypts and build a community. Once ensconced there—like old money on Nob Hill, this bacterium uses the crypt as a place of protection to hide out and reseed any other colonies that might have been damaged by other microbes or antibiotics^[i]. There is a specific gene that is responsible for B. fragilis’ being able to do this specialized colonization. And B. fragilis uses its place of privilege to ensure functional diversity in its niche. If a microbe appears that is too similar in abilities, B. fragilis is able to stymie newcomer with defensive tactics. Conversely, if a microbe shows up that has an ecologically different niche, B. fragilis welcomes it to the community. The specific skills coded for in this gene allows B. fragilis to occupy and control a unique and limited niche in the gut landscape and dictate who else gets to live there too.

^[i] S. Melanie Lee et al., “Bacterial Colonization Factors Control Specificity and Stability of the Gut Microbiota,” Nature 501, no. 7467 (September 19, 2013): 426–29, doi:10.1038/nature12447.