Krika,
The baby is really not exposed to your germs in your colon during birth. Not sure where you read that but the colon is a sealed system totally seperate from the vaginal canal. If you are worried ask the nurses to cleanse your bottom with some betadine or whatever cleanser they use right before the baby come out. that way if there are any germs lingering in the rectal area they will be cleaned away right before baby comes out.