Childbirth & the microbiome – “What every becoming mother should know”

Microbes during “Natural Birth”

In the first few hours of a child’s life, microbes play a very significant role. From bathing in the mother’s warm secure womb, a sec of amniotic fluid inside the uterus, the baby is protected from the microbes of the outside world.

Once the water break, the colonization begins! The microbes the baby encounters are not antagonists, but friends. It’s a ride coating the previously almost sterile baby in a smear of vaginal microbes. And as the baby comes to life, it gets another set of microbes from faeces which is very natural since pressure cause most women to defecate. 

A baby tends to come to life head-facing towards their mother’s bottom, pausing for a moment with its head and mouth in prime position, whilst the mother is waiting for the next contraction to help ease out the rest of the child’s body. In this process every mother gives her child a simple and safe bacterial birthday gift, consisting of vaginal and faecal microbes.

Lactic Acid Bacteria in Kimchi Reduce Cholesterol in Blood

Our good old friends Lactic Acid Bacteria

So, we basically start all of with mums’ bacteria which is there to protect us and help us to build our immune system, breaking down proteins and enzymes etc.

The most populated bacteria hereby are from the family Lactobacillus and Prevotella which specifically come from the vaginal and faecal area.

Where there are Lactobacilli, the thinking goes, there are no pathogens (such as Streptococcus, C. diff, or Pseudomonas). The Lactobacillus species simply crowds them out and next to that produces antibiotics of their own (called bacteriocins).

Furthermore, Lactic acid bacteria are milk-eaters which take the sugar found in (breast)milk – lactose – and convert it into lactic acid, creating energy. Babies are milk eaters converting lactose into glucose and galactose absorbed by the small intestine. What is not absorbed feeds into the large intestine where lactic acid bacteria is waiting to further break down.

A mother’s gift (natural birth)

The microbiota begins with a simple selection of lactic acid bacteria, partially transferred by the mother onto the child. These bacteria play a role in cultivating the baby’s metabolism & educating the immune system (Thanks mum). After a few months the child’s microbiota grows in diversity and complexity – ecological succession.

Researchers believe that another set of bacteria, which is stored after giving birth in the baby’s gut-microbiome, is given by the mother to her child for later life development. This set of bacteria is thought to be designed especially for digestion and immune system related growth.

C-section birth

Here comes the C-Section

But what about the millions of babies who each year come to life without going anywhere near their mother’s vagina?

The Caesarean sections have been used for centuries, usually to save a stuck child from being pulled under by its dying mother. In the last century though, with enhanced surgical techniques and anaesthetics we managed to not only save child but mother as well. 

C-sections are a crucial alternative to vaginal delivery in certain medical circumstances – some women have no choice but to give birth this way. But since the 70s we see an upward trend in C-sections across many countries around the world. The WHO estimates that the optimal rate of C-Sections should lie around 10-15% of all births (A. Collen, 2015).

In reality though, as an example, we see numbers in some hospitals in Brazil up to 90% (in the US up to 70%) of births given via C-section. And Brazil is not alone in this! Argentina, Iran, Mexico, Cuba, and in many parts of our Western World, hospitals are specializing on giving birth via C-section as the “fast and safe way out”.

Why the increase in C-section births?

It seems that giving birth naturally is considered too time-consuming and unpredictable for many health care facilities around the world. Women are also told that it's once a C-section, always a C-section (because the scar in the uterus could rupture under the pressure of contractions). Research shows that there is no significant extra risk to giving birth vaginally after up to 4 C-sections births and many women have a natural birth even after having had a C-section birth with their previous child (A. Collen, 2015).

C-sections are not the safest way out


In France, for example 4 in 100.000 previously healthy women die giving vaginal birth, but 13 in 100.000 die after a C-section. “Even in non-fatal circumstances, C-sections are more dangerous than vaginal deliveries: infections, haemorrhaging and problems with anaesthesia can occur – all risks of any abdominal surgery” (A. Collen, 2015).


Lots of women suffer after giving C-section birth because it is an intense surgical process. Furthermore, Psychological scarce can be left with the mother and child influencing their life in various degrees (further research needed towards the topic mobility).

Cesarean Section Scar and Cosmetic Disfigurement - Dolphin Neurostim | MPS  Therapy

C-section children and the development of the microbiota

Once assumed to be a harmless alternative to “natural birth”, C-sections are now increasingly recognized as a possible risk carrier to the well-being of both mothers and their children.

In the early days, for example C-Babies are more susceptible to infection (up to 80% of MRSA infections in infants occur in those born via C-section). They are also more likely to develop allergies. Babies born to allergic mothers are 7x more likely to be allergic themselves.

Science also shows that C-section babies are more likely to be diagnosed autistic. People with obsessive-compulsive disorder are twice as likely to have been born by C-section.

Type 1 diabetes and coeliac disease are more likely in children born by C-section and even obesity is associated with having been born via C-section (A. Collen, 2015).

Do you see the connection here?

These are all 21st century illnesses and even thought each one is multi-factorial, coming from many risk factors and genetic predispositions, the connection between C-Births and an increased risk of these illnesses is conspicuous.

Vaginal Seeding

There is plenty emerging research on how exactly these differences in the gut microbiota translate into the health consequences associated with Caesarean birth. For example, trials have been conducted where the vaginal bacteria are rubbed first into the babies’ mouth, then across its face and body after giving birth via C-section. But for now, we can only guess what the outcomes of these studies will be.

Childbirth and the microbiome


The trend to switch to the fast delivery method C-section only for convenience, financial, or cosmetical reasons is noticeable but definitely not a positive trend. Ongoing research continues to confirm that the protection layer given to the child by its mother via natural vaginal birth, plays a significant role in early life development.

As Alanna Colleen writes: “we are only 10% human and mostly microbes”, and this journey starts already in the womb.

We have an immediately available possibility to ensure our children with a healthy microbiome by taking care of our own bacterial diversity, especially during pregnancy and while feeding breast milk. Additionally, the microbiome from mother and father are given further via genes as well to their child, as shown by other emerging research.

As a mother, a diet rich in “cultured food that is alive”, pro- and prebiotics (no antibiotics), and a low-stress lifestyle, contribute to a healthy gut-microbiome. Ultimately, carefully choosing the way you’d like your child to see the light on this wonderful planet for the first time, is what you can take control of (in most cases, with exemptions).



  •  Alanna Collen (2015). 10% Human: How Your Body's Microbes Hold the Key to Health and Happiness. HarperCollins
  • Lisa F. Stinson,Matthew S. Payne, and Jeffrey A. Keelan (2018). A Critical Review of the Bacterial Baptism Hypothesis and the Impact of Cesarean Delivery on the Infant Microbiome. Frontiers in medicine. Doi: 10.3389/fmed.2018.00135

  •  Mayer, E. (2018). The mind-gut connection: how the hidden conversation within our bodies impacts our mood, our choices, and our overall health. HarperCollins.
  • Pia Huber (2020). Interview with Midwife from South-Germany. Co-Founder of Natural Birth House in Aichach.
  • Sara Allin, Michael Baker, Maripier Isabelle, Mark Stabile (2019). Accounting for the Rise in C-sections: Evidence from Population Level Data. NBER Working Paper No. 21022

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