There's no way you can take a few quantity of antibiotics and make the good bacteria to survive.
antibiotics do not differentiate between "good" bacteria and "bad" bacteria, thus killing both indiscriminately. This means that the bacteria that were helping your normal bodily processes are gone, which can lead to problems. The absence of "good" bacteria in your gut and elsewhere also leaves you vulnerable to repopulation by "bad" bacteria, which can cause some problems. It's why you'll often be told to eat some yogurt or something when taking antibiotics, because it'll repopulate your gut with "good" bacteria.