Your question is a very sensible and well thought out one.Whether it's in humans or animals,antibiotics do kill of friendly gut flora as well as harmful ones,and you're right to consider this.I got some acidophillus capsules from my health Store,and gave them(at a sensible dosage rate of course) with a syringe,using a little honey to make it easy to swallow.It's just a safeguard,and even though the Baytril may be well tolerated,it could still affect his digestive system. Keep thinking outside the box
Yes, some antibiotics can be very harmful to a rabbits gut bacteria. Like the penicillin group of antibiotics, if given orally can lead to fatal antibiotic induced enterotoxemia. Other antibiotics like enrofloxacin, are usually well tolerated when given orally as they don't normally disrupt the good bacteria in the rabbits digestive tract. It has to do with the spectrum of antibacterial activity for each antibiotic and it's acting affect on aerobic and anaerobic bacteria in the gut.