Human guts are inhabited by trillions of bacteria. However this is not a random selection. Why is it that only some bacteria are able to stably colonize our gut while others cannot? What is the molecular mechanism for this selection?
The chemical environment is the primary selector. Each person's internal chemical environment is different, resulting from diet, age, and genetic factors. In this way each person is a unique ecosystem, although there are some dominant bacteria. Couples and families have more similar microfloura than two unrelated individuals, almost certainly from frequent exchange and a similar diet.
Think of your guts as an exercise in evolution. Survival of the fittest. Those microbes (not just bacteria) that can most readily convert the nutrients provided by your diet into cell growth and replication while overcoming the onslaught of hazardous metabolic byproducts are the ones that will do the best. Brian is absolutely right, the chemical environment and the ability of each microbe to withstand and proliferate will dictate which ones stably colonize your guts.
The mechanism is simple. However, the players involved are complex. You must consider the diet, other microbial populations and immune system of host (especially if inflammation occurs in the gut). Changing diet, taking antibiotics, eating microbes that secrete antimicrobial products (most antibiotics are derivatives of natural chemicals used in microbial warfare) are all ways to change the profile of bugs in the guts. Switching from meat to veggie diet stimulates proliferation of different microbes, for example.
The mechanism is survival of fittest (Natural selection) and acclimatization to the existing environment (pH, temeperature etc). Just for example some microbes can survive in extreme conditions and others cant. Its just like that. Some bacteria can adapt themselves in human gut and while others fail to do so. I hope that helps. Cheers
The gut harbors various microorganisms. The selection and succession of microorganisms vary in individuals. Factors playing a role in succession include age, diet, geographic location and certain environmental conditions. Bacteria such as Bifidobacterium and Lactobacillus are natural habitats of the gut (specifically the colon). The colon is a target area for these natural flora to exert health benefits. Their ability to ferment food in the colon produces end products like acetic and lactic acid, which are responsible for inhibiting other microorganisms (which may become pathogenic).
You could also consider in more specific selection model, such as r- and K-strategy theory:
Andrews, J. H., and Harris, R. F. (1986). r- and K-Selection and Microbial Ecology. In Advances in microbial ecology Advances in Microbial Ecology. (Boston, MA: Springer US), pp. 99–147.
Actually, I am more interested in molecular mechanisms, such as membrane protein receptors, genes for colonization, resistance to host immunity, host-bacteria interactions as well as bacterial life styles that allow them to live in the gut.
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