Our first inoculation (whether with vaginal or skin microbes) initially operates based on fermentative abilities of the colonizing microbes, setting up a micro-biont social class system that is important for the health of our holobionts. First facultative microbes move in; then obligate anaerobes slide into the functional niches made as the oxygen gets all used up[i]. These are the microbes in your colon that do all that fermentation of impossible-for-humans-to-digest nutrients, passing on the byproducts of fermentation in convenient energy-available sources that also influence epithelial cell permeability (called tight junctions)[ii]. In first world countries, caesarean birth and fairly clean environments tend to delay the initial colonization of these microbes. Whether this delay has later ramifications has yet to be concretely determined. But in the race to find a niche in a cut-throat and busy ecosystem, delayed colonization of these micro-bionts could mean a delay in setting up a healthy thriving gut which then translates into a delayed or even faulty setup of our metabolism.
The distribution of gut microbes changes throughout the GI tract as microbes find and develop their habitat or niche. Just like human society became stratified based on how a certain human gathered and produced food energy—hunter/gatherer, nomad, farmer, fisherman—certain microbes occupy certain places in our gut based on how they process food energy (fermentative abililities). Microbes have special proteins on their surface called ectoenzymes that grab and process the energy that flows through the gut ecosystem. One of the first step colonization factors is whether a microbe needs oxygen or not to survive. Our mouths, particularly our teeth, are covered in abundant mats of microbes called aerobes on the outside with anaerobes next to our gums and teeth. If there is abundant food energy available, microbes will eat it so fast that they use up all the oxygen. This gluttony creates an oxygen-free layer below the happily growing, aerobic microbial community. This oxygen-free layer serves as habitat for anaerobic microbes, which use other metabolic pathways to breakdown food. Here we see our colonizing microbes restructuring the environment in such a way that a new environment emerges—they are changing the desert into a sandy beach (scientists call this system properties). By using up all of the oxygen, the microbes are actually creating an environment that didn’t exist before the aerobic microbes moved in. Ancient man did the same to the Fertile Crescent. By irrigating, humans were able to settle and grow grasses that produced a huge nutrient load which in turn allowed more humans to move in and establish urban centers which had never existed before and had a huge impact on the landscape. In these urban centers humans who acted in roles other than food producer could thrive. You ended up with potters, priests, and prostitutes. Which led to the necessary jobs of bankers and brewers.
This arrangement of aerobe overlying anaerobes serves as a basis for how microbes colonize our GI tract and shape it so that some metabolic processes occur that wouldn’t have without microbial introduction both ten thousand years ago and when you were first inoculated at birth only a (relatively) short time ago. Because this first step of colonization introduces microbial stratification based on their skills, our gut inhabitants can utilize some nutrient energy that would normally slip down the river. This creation of an oxygenless environment means that our gut ecosystems can support more types of microbes with more and more specific niches. The holobiont gains more functional diversity.
 Anaerobes don’t need oxygen to fuel their cellular metabolism. Some anaerobes are obligate and will die if oxygen is present. Others are facultative and can process energy with our without oxygen.
 Some medical authorities are now discussing the benefits of inoculating caesarean-born infants with vaginal microbiota post birth. At the moment, we aren’t convinced that this practice is necessary; but also, we are done having children and it’s too late for those we have.
 Ectoenzymes were first discovered in marine holobionts and are vital to microbial processing of energy. However, in addition to serving a vital role in energy for the cell, they also serve as the handles by which bacteriophage find and bind to their prey. We will talk more about that role in a later chapter.
 Aerobe means air loving. These microbes can only survive and process energy in the presence of oxygen. Like our human cells, these microbes will die without oxygen.
[i] I Adlerberth and A E Wold, “Establishment of the Gut Microbiota in Western Infants,” Acta Paediatrica (Oslo, Norway: 1992) 98, no. 2 (February 2009): 229–38, doi:10.1111/j.1651-2227.2008.01060.x.
[ii] Renu Sharma, Christopher Young, and Josef Neu, “Molecular Modulation of Intestinal Epithelial Barrier: Contribution of Microbiota,” Journal of Biomedicine & Biotechnology 2010 (2010): 305879, doi:10.1155/2010/305879.