They are living, they reproduce. Damaged ones die off.
That's why you're told to take yogurt/other fermented foods after taking antibiotics, to provide a reproductive environment for them to grow.
However it's still a risk you could kill off a whole species and lose their function, so probably best not to take antibiotics unless you really have to.
It's an easy analysis process though, you try to recover for a couple days, if you cannot and no virus is detected, you take antibiotics.
If it's a bacterial infection and it's spreading you have to take antibiotics, otherwise you die and all of your microbes die with you.