The temperature of the water makes most of the structural molecules and proteins to dissolve (denaturate), making it into a liquid. Since there is nothing more resistant to heat like bones, you cannot find any remains.
There are other organisms of the same size that have capsule-like protections that can resist heat, like the silicon shells of diatoms (algae) and some spores from fungi and plants.
They stay in the water and get dissolved. So basically anything you eat that has been cooked has some dead bacteria as part of the food. Enjoy!
Bacteria bodies are completely harmless and make up a very small amount of the substance so it’s really not a concern. Only problem can be that some bacteria produce toxins and those toxins don’t go away so if you have something that has been really infected by bacteria then it’s probably not safe to eat even after removing the bacteria.
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