Do births by caesarean section reduce bacterial immunity?

There haven't been a huge amount of studies done comparing caesarean and normal birth, but I think if at all possible, then a normal birth is actually preferable because as you say, the baby is sampling the mother's bacteria as it's being born. It's also immediately encountering the mother's skin bacteria as well as soon as it's put to the breast and things, and that is definitely an advantage. I think in the greater scheme of things whether it has a long term effect on the health of the child, that's really still up for debate.