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I am studying horizontal transmission of primary symbionts in insect reproduction. This reminded me of an earlier question I had asked, in which I learned that humans analogously acquired their particular microbiomes. It is also known how the human gut can be stratified in microbial content along the digestive tract. My question is what mechanisms are employed in ensuring that organisms acquiring their microbiomes from outside sources via horizontal transmission acquire the correct microorganisms in the correct parts of the gut? As the human gut metagenome does show "homology" between individuals, it can be safely assumed that the process can't be due to random chance.

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Initial gut microbiota development is influenced to an unknown degree by the fact that human milk contains oligosaccharides that promote the growth of certain strains of Bifidobacteria (see ncbi.nlm.nih.gov/pmc/articles/PMC2596198). –  Chinmay Kanchi May 24 '13 at 18:13

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