Systems (ecological or otherwise) that change over time are called dynamic systems. The human holobiont is a dynamic system that continually changes. So not only is every human gut a completely unique version of a tiny metropolis with its own topography and nutrients, within the individual gut there is also constant movement and shift as we eat a bacon-donut sandwich one day and kale salad the next, run three miles one day then watch TV all day the next, are healthy one day and fight a cold the next. Further, as microbes move into the ecological niches of our guts, viral predators of those microbes called bacteriophage or phage also move in. Phages actively hunt for microbes, causing them to further stratify into other niches in order to evade attack. All it takes is one daughter cell become genetically different from those in her colony and, like that, a whole new microbial population arises. Just like the change in civilization is evident in the architectural layers of ancient cites like Rome or Bagdad, layer upon layer of microbial populations shift and change as various pressures from nutrient change to predator change occurs. This flux happens at an extremely rapid rate; changes in microbial population can occur in as little as 24 hours. Therefore, between human holobionts, more and more individual factors go into the many differences between individual gut compositions.
Despite all this flux, the general make up of our gut ecology remains remarkably stable. We’ve lived with our current gut inhabitants for thousands of years. This sustained partnership is mostly due to the fact that since the agricultural revolution, there hasn’t been a huge change in our species’ diet as a whole (a fact that continues to this day in many developing countries)—until this last Century, that is. With the advent of mechanized, industrial mono-farming techniques in the Western world, excessive use of antibiotics, and almost total globalization, we have embarked on a grand experiment with our holobiont health. One that is proving to be fairly harmful to our holobionts in the short term—both individually and as a population.