The question of whether the fetus is sterile has come up on a few occasions recently, so for those of you interested, here is some of the evidence out there on the controversial topic. One research group in particular takes the stance that bacteria colonize the gut before birth.
In one of their studies, they looked at the presence of bacteria in human newborns and cultured species of Enterococcus, Streptococcus, Staphylococcus and Propionibacterium from umbilical cord blood from 9 of 20 healthy neonates born by caesarean section. In another study, they looked at the meconium of neonates (your first poop) born by vaginal delivery or ceasarean section and cultured similar species from all samples.
They also tested their theory in mice. Using a genetically tagged strain of Enterococcus fecalis, they orally administered the bacteria to pregnant mice and looked for its presence in the amniotic fluid and meconium of fetuses following caesarean section. They recovered the tagged strain in cultures from both the amniotic fluid and meconium in all samples, suggesting that bacteria of maternal gut or oral origin are able to cross the placental barrier and act as the initial inoculum for the gut microbiota in the fetus.
So perhaps our notion that the environment in utero is sterile is no longer sound and in actuality our exposure to the microbial world begins much sooner than we thought.