[pazimzadeh]

Our defenses are also crazy. For example, the inner mucus layer of the colon is able to keep trillions of bacteria at bay the vast majority of the time (unless there is inflammation or takeover by specific mucus-eating bacteria). Many of the proteins in the secreted mucus layers are still unknown in function, like FCGBP which comprises up to 40% of the protein content of mucus.

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria https://pubmed.ncbi.nlm.nih.gov/18806221/

Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis https://gut.bmj.com/content/63/2/281

So I think without trillions of bacteria to exclude, in the absence of any other issues excluding bacteria from the brain seems pretty doable.

Many viruses infect neurons, but they are way smaller than bacteria.