I took omeprazole for 1 month for gastritis, GERD. Will this antibiotic cause any harmful long term effects to my body?

No. Omeprazole, which is not an antibiotic, by the way, is usually well-tolerated and will not cause permanent harm to your digestive tract. Any side effects will be gone shortly after stopping it. Some people require Omeprazole long-term for their GERD, and most people do not have any side effects while taking it. Good luck.