Two main reasons: 1) Most of the bacteria living in your body are helpful to it (e.g. e. coli in your large intestine helps absorb water and produces vitamin K that your body can’t make for itself. Killing off these bacteria will harm your body.
2) You don’t kill ALL the bacteria; some have mutated to have some drug resistance. If you kill off all the non-resistant ones, the resistant ones multiply rapidly to fill all the space you’ve created for them by destroying the competition. Now you have a colony of drug resistant bacteria in your body and antibiotics are useless.
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