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There are many reasons why a baby might need to be born by caesarean, from maternal choice to placenta previa (when the placenta blocks the cervix), it’s fantastic that caesarean births are an option, there are countless infants whose lives have been saved by them. On a personal note we might not still have our eldest if we couldn't have gone to caesarean to get him out when he needed it. I’m delighted and grateful that he could be born by caesarean! But if I had know more about the microbiome 19 years ago when he was born, I would have done more to protect his, which might have meant a life without the medical conditions he now lives with. 

When babies are born vaginally they pass down the birth canal and pick up this ‘starter kit’ of vaginal/gut bacteria, which establish baby’s microbial communites and help train the immune system, during a caearean birth this doesn’t happen so the baby potentially starts life with a different set of microbes and this matters.

Caesarean: Welcome


Dominguez-Bello 2010

Dominguez-Bello 2010
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"There is emerging evidence that babies born by CS have different hormonal, physical, bacterial, and medical exposures, and that these exposures can subtly alter neonatal physiology. Short-term risks of CS include altered immune development, an increased likelihood of allergy, atopy, and asthma, and reduced intestinal gut microbiome diversity. ”

The Lancet 2018

Caesarean: Quote

Increasingly though from being a little used, absolute emergency procedure, caesarean birth has become incredibly widespread; in 2015 worldwide an estimated 29·7 million (21·1%) births occurred by caesarean. This matters because babies born by caesarean are at increased risk of both short term and long term health alternations:

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The Lancet 2018

Data from individual studies have highlighted an association between birth by CS and:

– features of metabolic syndrome, including obesity, 

–increased blood pressure, 

–type 1 diabetes, 


–increased body mass, 

–changes to liver function, 

–immune-related conditions, 

–neurological and stress-related problems, 

–autoimmune gastrointestinal disease in childhood. 

Caesarean: Image

It is thought that while there is an epigentic element to this (the experience  of labour ‘turns on’ genes) but mostly alterations to the baby’s initial microbes are thought to be significant, because even though after a few weeks the microbiomes of caesarean and vaginally born babies look more similar, some differences remain . More importantly it is the training of the immune responses that happened at the start of life that can can have consequences throughout a lifetime. 

Training the immune system

To coexist with the trillions of bacteria we live around every day our immune systems have to juggle which are ‘friendly’ and which are ‘foe’. The fact that some are allowed to live in us is quite amazing as our entire immune system is designed to fight off foreign invaders.

 “Once you’re born, you’re assaulted by billions of bacteria, so if the babies’ [immune systems] responded in the appropriate adult manner, they would just be auto-inflammatory bundles,” says Grace Aldrovandi,  a professor of pediatrics at the University of California, Los Angeles. “The [question] then is: How does the immune system learn when to relax and when to respond?”

It is thought that the first microbes we encounter are the ones that ‘train’ the immune system - so what gets in first matters. If the immune system is incorrectly trained it can result in autoimmune responses such as asthma or allergies and later in life by more serious conditions.

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I know this might all seem a little scary but it is an  increase in risk, not a certainty.

However with around 30 millions caesarean births a year that is a LOT of babies facing a less healthy future.

So what can we do?

Firstly it’s important to know that there are differences between babies born by elective caesarean (before labour begins) and those born after labour has begun and importantly the waters have broken, exposing baby to the birth canal microbes (emergency).

Babies who have experienced some labour before the caesarean may well have had some exposure to the  birth canal microbes (or ‘seeding of the microbiome’ as it’s known) but they will still have the effects of the post operative antibiotics.

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Here are some suggestions for helping the babies bacterial start if they are born by caesarean, but the key step would be breastfeeding, even just once. Breastmilk provides microbes to the baby (not exactly the same as they would get in a vaginal birth but REALLY  beneficial). Everything possible should be done after a caesarean birth to help support a mum who wants to,  to breastfeed.

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If labour begins and the waters break, baby will be exposed to some of the birth canal microbes


Ask for skin to skin in theatre and do as much of it as you can in the early days


This is not evidence based and is in no way meant to disrupt that all important first breastfeed, but where babies have not passed down the birth canal breastmilk can provide them with microbes that they might not otherwise get. By harvesting it just before the surgery it will not be affected by post operative antibiotics

You can find out how to do this here:


This is the key after a caesarean birth. Breastfeeding actually gives babies both microbes and food for the most benefical microbes in their gut. It is an absolute wonder food for the microbiome. Even one feed makes a difference, if mum can’t breastfeed, consider donor milk from a milk bank.


The most beneficial microbiome is found in babies born vaginally at home so consider bringing in a baby blanket from home to wrap the baby in once you get to recovery


The best source of probiotics is food, so ideally eat a good gut friendly diet but you could consider a suppliment at this point.

The evidence is not strong on their effectiveness however sometimes, every little helps as they say. You should always consult your health provider before use.

If you need to take antibiotics then probiotics might help.

You should always consult your health provider before use.

We like: Synerbio Mother and Baby

or Synerbio Daily

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This is an exciting possibility to restore the vaginal microbes to baby’s microbiome after a caesarean birth.

While vaginal swabbing did make a difference in a proof of concept study, and is currently in a major multinational study at present it’s not evidence based as an appraoch and might inadvertently pass on harmful bacteria. It’s worth noting that women in the study were all tested and had negative results for the standard of care tests of STDs, including HIV, Chlamydia and Group B Streptococcus (GBS, standard test at 36 weeks by culturing), no signs of vaginosis or viral infections as determined by their obstetrician and a vaginal pH<4.5 at 1–2 h preceding the procedure. It is currently not evidence based, and so not recommended but if the research when completed finds it is safe and beneficial, it could be a game changer for caesarean born babies. 

See also the latest news on this at

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It's really important to remember that caesarean is a good, safe option for birth. Protecting the microbiome just helps redress any potential alterations and effects on the microbial start in early life. I am so grateful that my eldest could be born by caesarean when he needed it. 

This is just about doing better at every birth and giving every baby the best bacterial start.

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