There is actually two different types of foodborne disease, infection, and intoxication or poisoning.
On the case of infection, the bacteria has evolved over time to be able to survive the harsh environment of the stomach and make it to the intestines, where it can colonize and grow. E. Coli O157:H7 is a bacteria that makes you sick in this manner.
For intoxication, the bacteria have actually grown in the food and created a poison before you ever eat the food. The toxin produced is extremely hard to remove or degrade to where it is no longer harmful. One of the major concerns in canned food, clostridium botulinum, causes illness like this. Your stomach will kill the bacteria itself, but it won’t have any effect on the toxin or spores if they have already been produced.
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