CAESAREAN
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 a 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 25 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.
VAGINALLY DELIVERED INFANTS HAD BACTERIAL COMMUNITIES RESEMBLING THEIR OWN MOTHER'S VAGINAL MICROBIOTA.C-SECTION INFANTS HARBOURED BACTERIAL COMMUNITIES SIMILAR TO THOSE FOUND ON THE SKIN SURFACE
Dominguez-Bello 2010
"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 birth has become increasingly widespread — and the numbers have risen dramatically in recent years.
In England alone, 42% of all births are now by caesarean section — up from 29% just five years ago, and more than double the rate in 2002. For women aged 30–39, caesarean is now as common as vaginal birth, and for those over 40 it is the most common way their baby is born. Globally the picture is similar, with caesarean rates climbing steeply in many countries.
This matters because the scale is so significant — and because babies born by caesarean can be at increased risk of both short and long-term health changes.
Photo copyright Bridget Supple
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,
asthma,
increased body mass,
changes to liver function,
immune-related conditions,
neurological and stress-related problems,
autoimmune gastrointestinal disease in childhood.
It is thought that while there is an epigenetic element to this (the experience of labour can 'switch on' certain genes), it is mostly the alterations to baby's initial microbes that are significant. 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 very start of life that 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.
Antibiotics during birth — what the research tells us
Most women having a caesarean will receive prophylactic (preventative) antibiotics during delivery, and many women having a vaginal birth do too — particularly if they carry Group B Streptococcus (GBS).
This is important for preventing infection, but it does have an impact on baby's microbiome.Research from the CHILD Cohort Study — one of the largest and most detailed birth studies in the world — examined data from nearly 200 healthy full-term babies and found that antibiotics used during delivery, whether by caesarean or vaginal birth, were associated with a microbial imbalance (dysbiosis) in the infant gut at three months of age. Specifically, babies born to mothers who received antibiotics had lower levels of beneficial Bacteroidaceae bacteria.
The good news? Breastfeeding made a real difference. By 12 months, many of these differences had reduced in babies who had been exclusively breastfed for at least the first three months. This is one of the most important things you can do after a caesarean birth, and we'll come back to it below.
(Shafaghi et al, BJOG 2022)
DON'T PANIC!
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.
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.
Here are some suggestions for helping your baby's bacterial start after a caesarean birth. The single most important thing you can do is breastfeed — even just once makes a difference. Breastmilk provides microbes to baby (not exactly the same as they would get in a vaginal birth, but genuinely remarkable). Everything possible should be done to support a mother who wants to breastfeed after a caesarean.
IDEALLY LABOUR BEGINS AND THE WATERS BREAK
If labour begins and the waters break, baby will be exposed to some of the birth canal microbes before the caesarean takes place.
MAXIMISE SKIN TO SKIN
Ask for skin to skin in theatre and do as much of it as you can in the early days. It transfers skin microbes to baby and has so many other benefits too.
HARVEST COLOSTRUM
Expressing a little colostrum before your caesarean (antenatal expressing) means baby can receive it immediately after birth, before any post-operative antibiotics have passed into your milk. This is not evidence-based as a microbiome intervention specifically, and is absolutely not meant to replace that all-important first breastfeed — but it can be a helpful step. You can find out how to do this at: https://abm.me.uk/breastfeeding-information/antenatal-expression-colostrum/
SUPPORT BREASTFEEDING
This is the most important step after a caesarean birth. Breastfeeding gives baby both microbes and food for the most beneficial microbes in their gut — it truly is a wonder food for the microbiome. Even one feed makes a difference. If breastfeeding isn't possible, consider donor milk from a milk bank.
BLANKETS FROM HOME
The most beneficial microbiome is found in babies born vaginally at home, so consider bringing a baby blanket from home to wrap baby in once you get to recovery — it introduces home microbes from your own environment.
Is your caesarean medically indicated? Using BRAINS to help you decide
We know that a significant proportion of caesarean births are not medically necessary — and while caesarean is always a valid choice, it is worth knowing that you have the right to ask questions and explore your options, whatever is being proposed to you.
A simple tool called BRAINS can help you have those conversations with confidence:
B — Benefits - What are the benefits of this procedure for me and my baby?
R — Risks - What are the risks?
A — Alternatives - What are my alternatives?
I — Intuition - What is my gut feeling telling me?
N — Nothing - What happens if I do nothing, or we wait?
S — Space - Can I have some time and space to make this decision?
BRAINS isn't about saying no to medical care — it's about informed consent, understanding your options, and feeling respected in your birth. It can be used antenatally when making decisions about your birth preferences, or in labour if something unexpected is proposed.
You know yourself and your body. Asking questions is always your right.
Supporting breastfeeding after a caesarean — plan ahead
One thing that isn't always talked about in relation to caesarean birth is its potential impact on breastfeeding. The hormonal cascade of labour plays a role in triggering milk coming in — what is known as Lactogenesis II — and a caesarean, particularly one before labour has begun, can delay this process by a day or more. This doesn't mean breastfeeding won't work — it absolutely can and does — but it does mean that being prepared makes a real difference.
If you know you are having a caesarean, or think you might, it is worth seeking out infant feeding support before your baby arrives. Getting good guidance antenatally, knowing what to look for and who to call if you need help, puts you in a much stronger position in those early days.
In the UK The National Breastfeeding Helpline is one of the most accessible resources available — it's free, non-judgemental, and now open 24 hours a day, 365 days a year. That means support is there for you at 3am just as much as midday.
You can reach them on 0300 100 0212 or via their website at nationalbreastfeedinghelpline.org.uk. Support is also available in Welsh, Polish, Bengali and Sylheti.
VAGINAL SWABBING
Vaginal microbiome transfer — where has the research got to?
When we first wrote about vaginal seeding (or vaginal microbiome transfer, VMT) it was very early days — a proof-of-concept study had shown promise but the evidence wasn't there yet to recommend it. The science has moved on, and it's worth updating you on where things stand.
A 2024 systematic review brought together eight studies involving over 550 caesarean-born babies and found that vaginal microbiome transfer can partially restore key gut microbial communities in caesarean-born infants — in particular increasing levels of beneficial Bacteroides and Lactobacillus bacteria. However, it does not fully replicate the microbial transfer that happens during a vaginal birth, and results vary between studies.
A separate 2023 randomised controlled trial found that VMT also appeared to support infant neurodevelopment — babies who received the transfer had higher developmental scores at 6 months — though this needs further research before firm conclusions can be drawn.
Importantly, a large, rigorous randomised controlled trial funded by the US National Institutes of Health is currently underway (NCT03298334), looking specifically at whether VMT can safely transfer microbes from mother to baby and whether this benefits the metabolic and immune health of the child. We will update this page when results are available.
Should you consider it?
We do not recommend it. But this is very much a personal decision and one to discuss with your healthcare provider. If you are considering it, the key safety steps from earlier research still apply — testing negative for GBS, HIV, chlamydia, bacterial vaginosis and other infections is essential. It is not currently recommended as standard practice, and we do not recommend it , but neither is it the unknown quantity it once was. Watch this space — new research could be a game changer for caesarean-born babies.
(Wang et al, Journal of Infection 2024; Zhou et al 2023; NIH Clinical Trial NCT03298334)