Most microbes (bacteria and viruses) are cleared out of our system and they never get very far in the respiratory track and our lungs are free of microbes. Only a selected few microbes can infect the respiratory system because they can colonize there and our own defense is not effective in clearing them out.

If microbes get into our stomach, which happens all the time, most don't survive there because of the low pH in the stomach. The few that manage to survive get into the digestive track which is full of resident microbes. So the alien microbes can't compete with them for nutrients and won't be able to propagate much. Most will die because of starvation, killing by other microbes or our own defense mechanisms.