As the first organ to evolve, the gut is actually the most advanced structure in our bodies. It has had millions of years of environmental pressure shaping it into the control center for our engagement with the outside world. Our guts possess their own nervous system with the vagus nerve serving as a direct conduit to our brain. When the ancients examined the guts of animals, they viewed them as being portals to the minds of the gods. Thus, in the loops and folds of the GI tract, they thought that one could literally see the future being created as well as the effect the past had on that future. Today, we know that the direct connection of our guts to our minds does indeed affect how we behave as well as our moods . Though we may not read the future in our guts as coming from the minds of gods, we can indeed find signs of humanity’s future in addition to a record of our checkered past based both on the structure of our guts and the microbial inhabitants that thrive there.
In any ecosystem, we can’t discount the actual physical landscape and its effects on its inhabitants. The gut is no different. The complex topography of the GI tract serves as the main meeting ground between a diverse grouping of organisms—human, viruses, parasites, and microbes—as well as the main thoroughfare for energy to flow in and out of our bodies. In our internal exploration of ourselves, it could be helpful to imagine our guts as great underground river valleys, attracting many civilizations that have developed survival tactics necessary to survive in a specific environmental location. The biogeography of the gut ensures that epic environmental changes can occur millimeters away from each other, thus creating specific and unique niches in very close proximity.
For any biont to initially settle a landscape, three things need to happen; each builds and expands upon the other, causing niche and species stratification within the ecosystem. First, a settler has to have (or develop) skills that are suited to that environment. In the case of our microbes, scientist call these skills fermentative abilities (which is the equivalent to the ability to process an energy source), but I would like to expand these skill to include ability to communication with the immune system (bargain with the locals), ability to establish a hold on the mucus layer (set up a homestead), and outcompete other microbes (fight off claim-jumpers). Second, a settler needs to be able to find food. Microbes have nutrient processing mechanisms that are very specific to certain types of food, so even if it seems like everything we eat is nutrient energy, some microbes will starve while others will feast. Finally, a settler has to be able to avoid getting killed by the local predators. This last element may seem to fit in with the first, but in the microbial world, viral predation on microbial cells has a huge influence on how our gut civilization stratifies. We’ll talk more about these elements later, but now, like good explorers, we need to familiarize ourselves with the biogeography of our internal ecosystem.