The lungs, mammary glands, uterus, ovaries, vagina, placenta, semen, eyes, skin, and nasal cavity all have their own documented microbiome so far, and we've been finding out about new microbiomes about once a year. They are not a thing that is reserved for the digestive tract.
If you were to simplify the human body to a sphere (or torus... or whatever corresponds with the number of orifices that a human has), then all of the microbiomes you've listed would be on the exterior. The brain (and heart and kidneys and liver and bones and...) would not be.
The microflora would need to have gotten there somehow, something analogous to endosymbiosis. But unless they're somehow getting from brain-to-egg-to-brain that's hard to explain. As for the others, they're easier, all being along the surfaces. Even the gut is on the "outside" in that membranes need not be crossed in order to access it.
Although counterpoint: the same argument would apply to a fish so I guess it's not impossible. Just more surprising.
> But unless they're somehow getting from brain-to-egg-to-brain that's hard to explain.
There are pathways from the outside to the brain - most notably the nose and the eyes. The former have a known pathogen pathway (naegleria fowleri, a virtually 100% fatal parasite), the latter are actually an immunoprivileged site [1] and investigations are ongoing what the role of eyes is in the transmission of H5N1 bird flu.
We already know of harmful pathogens that can infect the brain, such as Borreliosis. The only jump now is the fact that there could also exist harmless bacteria.
Spirochetes are much more efficient than most bacteria at moving through very viscous media, which include the obstacles encountered when moving through an animal body.
Thus, both the spirochetes causing Lyme disease and those causing syphilis have high chances of reaching even the brain, while traveling through the body.
Fortunately, for the bacteria employing other means of locomotion it is usually more difficult to pass through many of the internal body tissues, as long as those are intact.
The brain is _unusually_ protected though. There's nothing like the blood brain barrier basically anywhere else. Most the the tissues you mentioned are exposed to the environment in some way. There aren't many ways to reach the brain without getting inside the body first(sensory organs being the obvious pathway, but even that is a stretch).
Not saying it's impossible, just that the skepticism is warranted.
Indeed, those organs expose to the outside world have reason to cultivate friendly bacteria for no other reason than to take up space, to stop hostile bacteria having a place to take hold.
