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