Typically, we can tolerate microorganisms, depending on the type.

We have quite a few different bugs in our intestine, on our skin and in our mouths, and for the most part they do no significant harm. However, many bacteria and fungi grow a colony on a food source and produce a toxin to prevent other microorganisms from growing. Botulism food poisoning isn't actually caused by the bacteria, it's the toxin that the bacteria produces to "protect its turf." The bacteria is quite harmless and easily killed but the toxin is quite resistant. Same with yeast. It converts sugar (food source) into alcohol as a toxin to protect it's turf. Same with Pennicillin and almost every microorganism you can immagine.

Harmful or Pathogenic Microorganisms

Pathogenic means capable of causing disease. An actual harmful effect of a microbe to the body depends on:

microbial virulence - a relative ability of a microbe to cause a disease; for example, a certain, higly virulent subtype of influenza virus may cause a bird flu, which is deadly in a high percent, while usual influenza virus is not. invasion through the bodys barriers; staph bacteria might not cause any harm to a person with an intact skin, but can cause a severe infection of a skin wound. amount of microbes; eating few bites of food contaminated with staph bacteria may go unnoticed, while eating the whole portion of the same food may cause a severe food poisoning. bodys defense (immune) system; patients with a weak immune system, like those receiving corticosteroids, often get oral thrush (candida infection of the mouth), while otherwise healthy people do not.