In addition to bugs that can survive the pH of your stomach, there's also toxins in the food.

E-coli and such will produce toxins that remain in the food even if it's cooked/prepared in a way that kills all the live e-coli. That's why sometimes you get very sick after eating something but it passes quickly - you're just sick while your body purges the toxins out of your gut, but there's no live bacteria/viruses that take up residence in your body.

The stomach has a pH of ~1 to 3, which is acidic enough to kill some of the microbes/toxins present in bad food.. but some microbes (ahem, Salmonella and E. coli) can survive this acidic environment because of a protective layer called a biofilm.

Some bacteria can be resistant even to incredibly hostile environments (like your stomach, a volcano, or freezing temperatures, etc.). So your stomach's acid might not be enough to kill some kinds of bacteria that may have grown on/contaminated your food.

There are two forms of food-poisoning: too many pathogens that then grow in your body and make you sick out both ends while your immune system fights the growth, and toxins from spoilage that will have a more immediate rejection from the body.

The ones that grow in you have pretty good resistance to acids. (All are slightly different) And toxins just are, so acid won't necessarily break them down.

your stomach can destroy most, but not all. furthermore, it doesn't always destroy the toxins that these germs produce, either in life or as they die. food poisoning caused by salmonella, botulism, and E Coli are often results of the toxins they leave behind rather than the bacteria themselves.

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