A small addition for interest:
Other commenters are right that the bacteria die and break in to little bits and the little bits are still in the water, they don’t “go” anywhere, they’re just pretty harmless. When the bacteria are alive they multiply and multiply and multiply and can make you sick. When they’re dead and all broken up in to bits they don’t do this. And stuff that goes in to your stomach is broken down and destroyed even more by acid. But the stuff in your stomach isn’t *inside* your body in the same way that your blood and bones and stuff are. The food and stuff is in the “bag” that is your stomach
Even the tiny bits of dead bacteria are dangerous if they get truly *inside* your body. To make something safe to *inject* in to you, boiling won’t even nearly do the trick. Exactly because the “corpses” haven’t gone anywhere after the bacteria are dead. You have to do a *lot* more to destroy the dead bacteria bits *even more*, which uses special technology.
If there aren’t a *lot* of bacteria, boiling can make something safe enough to drink, but it would still be dangerous to get in to your body another way, precisely because the dead bacteria don’t “go” anywhere, like you said. So it’s a good question. The bacteria “corpses” are a real problem in some instances, like making injections.
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