With my first two pregnancies, my GI and my OB chatted and agreed that it's not good to take (Cipro and Flagyl) until 2nd and preferably 3rd trimester. I took it in my last trimester with my first and once in my 2nd trimester and once in my 3rd trimester with my second.
I do find eating a low residue diet and staying away from deep fried things, chocolate and dairy helps so much! (I'm currently 16 weeks with my 3rd and am making due without taking antibiotics....but the pouchitis still looms here and there and is not taken care of by diet alone.
That said, for this pregnancy my GI referred me to a FRAME specialist who basically reads up in every study of the medications in question and tells you the risks of them to a fetus. This enables me as the patient to decide if taking the medication is worth the risk for my baby.
Keep in mind that feeling better allows your body to absorb more nutrients so sometimes you have to weigh the pros and cons.
If memory serves me correctly, the only thing she could find as a risk for Flagyl was that long ago there was a study where some babies were born with cleft palates. This was not found in all of the studies. This would have also been on women using Flagyl, then found out that they were pregnant so it would be used VERY early in pregnancy. I'm sorry I don't remember more details if the article but I'm sure you can look it up.
Im so happy that you were able to conceive! We tried for a year for our first as well and my second and third came soon after (they are 18 months and will be 20 months apart) and my GI is astounded that each time I come for an appointment I'm pregnant again! It's such a blessing. When I had my surgery 10 years ago, I specifically asked my GI at the time if I would have any issue getting pregnant and he said, no issues....it will just take twice as long as the average person. My current HI tells me that we only have a 1 in 4 chance of ever conceiving....that's crazy! I certainly hope more women will be blessed as we've been! Take care!