Antibiotics tend to kill all bacteria, not just the ones that are bad for you. The good bacteria in your gut are vital for your health, and their destruction can wreak havoc with your immune system, as well as with your digestion. If a doctor places you on an aggressive antibiotic for two or more weeks, then even if you take probiotics daily, your gut might need a year or more to recover from the damage. Some guts will never be the same, even if the antibiotic is administered intravenously.