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.
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.
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.
[1] https://www.aao.org/eye-health/tips-prevention/eye-immune-pr...
[2] https://www.unmc.edu/healthsecurity/transmission/2024/06/04/...
Not saying it's impossible, just that the skepticism is warranted.
There is. The placenta and, oddly, prostate as well.
For the more internal organs, bacteria would have to travel across a skin of digestive tract barrier.
Unless they're present in the womb as the fetus starts growing, I guess.