Dangerous bacteria

Just about any bacterium can pose a potential health hazard if it is in the 'wrong place', which is a rather vague term.

 

It's useful to think of humans as a sort of misshapen, hollow cylinder where the outside surface of the cylinder is our skin, the inside surface is our digestive tract, and the stuff in between is our internal organs. If you think of us this way, you'll see that our digestive tract is topologically part of our outside, and is a place where things in our environment interface with us, just like our skin. This is one reason why it's not troublesome to have bacteria and other microbes living in our gut; our body treats it as if it's part of the outside world and maintains barriers to protect itself from these microbes. Because our body keeps bacteria away from our true insides, you won't find any bacteria whose natural habitat is say, the liver or any other internal organ.

 

The idea in Ygggdrasil's post, although not explicit in the matter, covers the respiratory tract as well. As we are constantly breathing, all tissues and organs involved with respiration are interacting with the outside world constantly. It only makes sense that some bugs would find themselves a nice home at different sites which are still "part of the outside" so to speak. Compare, for example, the difficulty of a bug getting into our lungs versus a bug getting into, say, the liver or the brain. Or compare the microorganisms found in our intestines with those found in the peritoneal cavity.

 

Yes, there will certainly be examples of native microflora in some regions (for example, the gut) causing disease if they colonize a different area (like the nasal cavity or urinary tract). My point was just that many internal organs (like the liver) will not have bacteria in their native environments.