Research on the gut microbiome is still considered relatively new to the science industry. Research on the infant gut microbiome is therefore even newer and there is still plenty of research that needs to be done in order to thoroughly understand what are the implications of a vaginal and Caesarean births on children’s health development from a microbiome point of view and how we can best support an infant’s gut microbiome development.


The human microbiota is a particular community of microbes residing in and on the human body including bacteria, archaea, viruses, and very tiny eukaryotes. Due to some technical limitations, most of the research is actually focused on the bacteria. The most important areas that host a distinct microbial community are the mouth, the skin, the gut and, in women’s case, the vagina. Each individual is unique and there’s no exception when it comes to our gut: our microbiome is less than 10% similar to that of anyone we know.


This depends on how the baby enters the world.

If a baby is born vaginally, a baby’s first microbes will primarily come from his or her mother’s birth canal where the vaginal microbiome sits. Lactobacillus is what primarily constitutes a healthy woman’s vaginal microbiota, which is a type of bacteria very important for human health.

If a newborn is delivered via C-section, the baby’s first microbes will look more to those found on the human skin. Which is one of the reasons why immediate skin contact is extremely important. We know that Caesarean births are correlated with higher rates of different types of diseases, asthma and food allergies being some of them. But whether there are any health implications for babies with a skin-like microbiome is still to be researched.

What’s currently known is that, depending on the type of delivery, there are not only differences when it comes to the type of bacteria (those found in vaginally born babies are considered more health protective), but the intestinal microbiome of babies born surgically show less diversity compared to vaginally delivered infants. And both in infants and adults, an increased diversity of microbes within the gut is considered protective.

It’s important to know that, regardless of whether babies were eventually delivered vaginally or via C-section, if they were exposed to the vaginal microbes during a trial of labour, they’ve had a degree of exposure to mothers’ bacteria.

What’s interesting is that different options to expose newborns delivered via elective or unplanned C-sections to the mother’s vaginal microbiota are currently being researched and tested. One of them is called vaginal seeding, but at the moment this is only being performed under the scope of research. I am particularly interested to see how this area of research will develop. 


A newborn’s gut microbiome is less diverse than that of an adult. Contrary to adults, a baby’s microbes will be similar across all body sites, because their microbial communities are not yet developed. But the infant gut changes over time and there are a few factors that influence its development. It seems that during the first three years of life, the gut microbiome’s development is highly influenced by maternal exposures – stress, infection, obesity – and by neonatal exposures – mode of delivery, feeding patterns and antibiotic exposure. Additionally, if babies are separated from their mothers after birth for an extended period of time, they may also miss the opportunity for immediate colonisation with the maternal skin microbiome.

Exposure to antibiotic therapy will have an impact on the infant’s microbiome not only after birth, but also while in utero. One of the often cases of antibiotic administration during pregnancy is to treat group B Streptococcus. Research shows that infants born to mothers receiving antibiotics prior to delivery show a significant decrease in Bifidobacterium.

Feeding patterns are an important factor when it comes to the development of infants and children gut microbiome development. Studies have shown that different bacteria dominate breastfed infants and formula-fed infants. One research concluded that “the prevalence and counts of C. difficile as well as E. coli are significantly lower in the gut microbiota of breast-fed infants than in that of formula-fed infants, whereas the prevalence and counts of Bifidobacterium spp. is similar among both groups.” The implication here is that a greater abundance of C. difficile in the gut microbiome of formula-fed infants can mean “a higher risk of developing several atopic symptoms, including eczema, recurrent wheeze, allergic sensitization, and diagnosis of atopic dermatitis.”

Diet plays a primary role in the composition and diversity of the microbiome during the first three years of life – and beyond. Transitioning to solid foods is therefore an important aspect for this topic. Basically, as solid foods start to increase in infants’ diets, the bacterial flora of both breast and formula-fed babies approach that of adults.


Diet is also one of the aspects that we can, most of the times, most easily influence from all the other aspects mentioned above. The amount and diversity of beneficial bacteria living in a baby’s digestive tract greatly impacts the strength of their digestion and their overall wellbeing.

Probiotics have an important role to play in every infant’s diet, but are especially beneficial for babies born C-section or en caul, are formula-fed or have been either maternally (during pregnancy, labour or while breastfed) or directly exposed to antibiotics. Furthermore, probiotics can be of great support for babies that suffer from constipation, colic, acid reflux, gas or other tummy troubles.

That is why, once a baby has begun solid foods, introducing small amounts of fermented food as soon as possible will be highly beneficial. These should nevertheless be introduced slowly and starting with very small amounts in order to provide enough time to a child’s digestive system to adjust.

Some fermented foods that you can incorporate into your baby’s diet are sauerkraut, probiotic applesauce, fermented root vegetables, coconut kefir, milk kefir or yoghurt (if dairy is well tolerated and has been safely introduced).

If you need help starting your baby on solids or need to holistically support their gut, let me know.

Links to research studies:

1 thoughts on “The development of the infant gut microbiome

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