In our discussion of this first step of colonization, we are talking a lot about food energy, and we’ve listed types of food energy as being part of the second step. Are we essentially talking about the same thing and just separating it into two steps? Yes and no. The basic skills of a colonizing microbe does have a lot to do with food energy, but it’s specifically about that energy in the form of electrons and where those electrons come from rather than larger nutrient categories (fiber, carbohydrates, protein, fats) that we are familiar with. Those larger nutrient categories are important influencer of our microbial communities as we’ll get to in later sections; however, the processing skills of those larger nutrients (how to get that electron energy) is the first factor that dictates which microbes settle where in our ecosystem.

Fermentation, more specifically, is the ability of an organism to use something other than oxygen as an electron energy source to run cellular metabolism^[1]. Different molecules have varying levels of electron accessibility, oxygen’s being the easiest. However, microbes can get really creative when it comes to snatching up electron, often using the waste products of other microbes. In a chain of energy transfer, our microbial inhabitants will grab at the energy source they prefer and then pass the byproducts of their metabolism down to another microbe. In a city, you may have a person who grows cotton (okay so maybe not in the city); someone takes the cotton and spins it into cloth; this cloth is passed to a dyer who makes each piece a different hue; another person buys all the red cloth and makes tee shirts out of them; yet another takes the tee shirts to a swap meet and sells them; another grabs used tees and drops them off at a consignment store; finally, a freegan finds the tee in the trash, wears it until it is in shreds then processes the fabric into toilet paper. In each step, energy is used to transform the material into another.

The same sort of hand it down structure happens in the gut as one microbe grabs a particularly nice string of oligosaccharides (nutrients) and, using a molecule like nitrate for electron energy, processes the string, releasing wastes in the form of short chain fatty acids (SCFA) and other side products (such as other molecules for electron energy). Our human cells love SCFA as an energy source while another nearby microbe may use the other side products to produce its own energy. There are microbes in our guts that can use methane, sulphur, and many other surprising components to get that valued electron. The farther down the processing chain a microbe that derives energy from the wastes of other microbes might be dictates how much energy that particular microbial population has access to: those on the bottom get less than those on the top.

Thus a system is set up in our guts where almost nothing goes to waste from food and gut mucus to sloughed human tissue and dead microbial cells. Each factor potentially contributes more and more diversity in the gut, as microbes build upon each other’s niches. The advantage to this stratification is that, like in biofilms, one type of cell doesn’t have to do all its metabolic work; it can specialize because other cells are performing other functions. One microbes’s shit is another’s dinner.

^[1] Everything in the colon is potential energy currency because everything can be broken down into basic atomic components. What drives cellular metabolism is the accumulation of electrons that can be used to make molecules of adenine triphosphate (ATP) from adenine diphosphate (ADP) in a cell. It is the endless cycling of ATP and ADP along with some essential amino acid building blocks that keeps organic life alive. This cycling depends on electrons which constitute the basic unit of energy. Because cells need electrons, they look for energy sources that are good sources of electrons. Oxygen is the preferred source of electrons, so oxygen-rich environments teem with microbial communities. When the oxygen gets used up or becomes absent, a different class of microbe takes over: one that can processes energy and make ATP without oxygen as an electron source.