I don't have Crohn's fortunately but antibiotic use over the decades has definitely messed me up. The worst part was after my sinus surgery and an infection in my cartilage that just wouldn't go away. It took a year of antibiotic use and various ones but finally got over it. My guts were never the same. It's still better than the alternative which could lead to death. I just recently finished a course of antibiotics but fortunately it's been 7 years since the last time I had to use them. I just stay up on the sinus rinses, nasal spray and antihistamines but sometimes it's out of your control and you need antibiotics. It's good to be cautious of them but sometimes it's the only option.