But, before your baby is born, they are in a sterile environment inside of your bag of waters. There are no bacteria present in the amniotic fluid, and so your baby is practically void of all bacteria. After your water breaks, this sterile environment is broken. This is why it is a good idea to not have too many vaginal exams after your water breaks, and if it's been broken for a long time, your OB or midwife may want to get things going. Once the barrier of your bag of waters is gone, there is an opportunity for bacteria to travel up and reach your baby. This is not what we want.
During pregnancy, if the mom takes probiotics, some studies have shown that this can be helpful, especially if the mom has a condition that may get passed down such as obesity or asthma. This affects the baby because when mom's bacteria are healthy, she will then pass on healthy bacteria to her baby when he/she is born.
Old school practices dictated cleaning and shaving the perineal area before birth, but this is not practiced many places anymore. Science has now told us that it's not necessary, we actually want the normal bacteria that is present on mom to reach baby as they come into the world. Your baby passes through the vagina, which is located next to the rectum. This anatomical location where birth takes place leads itself to your baby being introduced to bacteria from your gut as it's being born. These bacteria travel into your baby's previously sterile gut and start to take up residence-this is a good thing. The bacteria passed from mom's gut to baby are friendly gut helpers- they will help your baby digest their first meal of colostrum.
During a cesarean birth, your baby will not be exposed to the bacteria in your vagina or in your perineal area. We are just beginning to grasp the complexity of our relationships with the multitude of species which inhabit our bodies. The differences in the bacteria present in a baby born vaginally versus by cesarean are big, and may have lasting health effects. To combat this, a practice many hospitals have adopted is to put baby on mom's chest very first thing after they are born. This way all the friendly bacteria on mom's skin will get transferred to baby. But this is still a different set of bacteria than what vaginally-born babies get exposed to. In some hospitals, a piece of gauze will be put in mom's vagina to chill there for a while, then when baby is born by cesarean, the gauze is wiped on baby's face, eyes, and mouth. How interesting is that?
Your baby's microbiome is complex and fascinating and we are only just beginning to understand its development.