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I have a biology degree, but am A: plant focused and B: now a manufacturing engineer, because of you wanna do plant biology in the Midwest it's corn or soy time. And those are boring. So only marginally more applicable.
You're pretty spot on. The vast range of skin biomes directly impacts what sorts of organisms can live there. Even between a human arm, armpit, nose, and intestines you'll have different organisms making up the majority of the biome, and potentially even organisms unique to that biome.
Changes to the region or loss of competitors in other connected biomes can allow normally less dominant organisms to gain a foothold. Absolutely how one gets a yest infection. You can even just KILL EVERYTHING and still different organisms might colonize the area faster, resulting in a difference that's noticeable even at our comparably massive scale.
I didn't particularly know what organisms prefer the fur, feather, or scale coated regions of animals, but they very much would have the same type of dynamic populations.
Ballpark guess, given how there's a Salmonella risk associated with reptiles, I'd assume they have some biome that allows Salmonella to survive, if not directly thrive. Similarly with some varieties of Armadillo carrying leprosy.
Are biomes fighting to take over when we have sex? I have a friend who was getting multiple uti's after having sex with her now-ex. Is that a result of clashing biomes?