The current thinking is that babies are sterile in the womb, although traces of bacterial DNA have been found, that is not the same as finding bacterial communities, so the intial set up of the microbiome starts at birth.
In a vaginal birth the baby passes down the birth canal to be born. Here, as baby slowly makes it’s way out, the baby is coated in bacteria picking up vaginal microbes, even swallowing some. As babies are born they rotate on the perineum and pick up some gut bacteria while they are there (it’s not an accident that the birth canal and rear passage are close or that often women will have a bowel movement before the birth!) all this acting as a ‘starter kit’ of microbes for the baby. As soon as the baby is born they will ideally be put onto mum’s bare chest for skin to skin thus transferring skin microbes to the baby.
Where this happens makes a difference; home or hospital will result in different microbes being present in the air, on the bed, on the bedding etc
Who handles the baby in those first few minutes and hours matters as they are all passing microbes to the baby.
Feeding makes a huge difference to the establishment of the microbiome, breastmilk is packed full of microbes but also food for the microbes (yes you read that right! Breastmilk contains about 200 human milk olygosaccarides, non-digestible carbohydrates that are there JUST to feed the good microbes), if the first food is formula, then the microbiome will establish differently (different is not necessarily bad!).
All these intital encounters make up the inital formation of the microbiome in an infant. This matters as the first microbes in are the ones that ‘train’ the immune system, letting it know which bacteria are ‘friend’ or ‘foe’. A study in 2008 by Martinez and all found that the first types of bacteria to colonize the gut of mice have a lasting impact on their microbiome, so what happens at birth matters.
In fact when scientists look at microbial make up of newborns, a home vaginal birth was found to have the highest levels of beneficial bacteria
Differences in the fecal microbiota of neonates born at home or in the hospital (Dominguez-Bello 2018)
A 2004 study found no difference to the microbiome when baby was born in water versus out of the water
“WE NEED THE RIGHT BACTERIA AT THE RIGHT TIME AND IN THE RIGHT ORDER”
When birth is vaginal, there is immediate skin to skin and mum breastfeeds, you don’t really need to think too much about the microbiome, (unless antibiotics are used) it’s when that transmission (known as vertical transmission) from mum to baby is interupted that you really need to have the microbiome in mind, for example if mum needs a caesarean birth.
“we need the right bacteria at the right time and in the right order”