The bacteria may not all die in cooking, just be reduced to a safe level if we’re talking fresh food.
For expired food, the bacteria levels may have grown so that the proportional reduction by cooking still leaves too high a number (say 1/100,000 left in fresh, 100/100,000,000 in expired) . There’s also accumulation of the byproducts of the bacteria digesting the food that may be toxic- in some booze making processes, for example, the yeast stop when they’ve made enough alcohol to kill themselves if left long enough.
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