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11 Minutes

The Gut: the organ that can help set up a baby’s health and defences for life…

Neurological and autoimmune conditions in our children are becoming an increasing issue in our modern times. The latest research is suggesting that focusing on building a healthy gut can be a very positive way to counteract this. Research also suggests that this process starts as early as during pregnancy. It also appears that the most crucial time is between this point and stabilisation around 2-3 years old. A massive opportunity.

This article is a deep dive look at the emerging science behind this. We look at how it works. Most crucially we look at how your actions can positively contribute. Not only to a healthy gut for your baby, but potentially positive implications for lifelong health, immunity and brain development.

There has been a huge leap forward in research over the last ten years on how important a healthy gut is. Both to the overall healthy functionality of your body but also the immune system. Crucially, we have learnt that the very earliest formation (from in the womb until stabilisation around 2-3yrs old) matters. Research suggests it has potentially lifelong consequences for the health of a baby. Science doesn’t understand everything yet, but here are a few things we are starting to realise.

What is becoming increasingly clear, is that disruptions to the gut microbiota have been linked to mood and neurological issues. It has also been linked to allergies/intolerances, autoimmune conditions, obesity and a propensity towards a number of diseases in adulthood.

What is the microbiota? This is the collection of bacteria, fungi and even viruses that live together. Disruption (as we understand it) is where there is imbalance or lack of diversity:

‘Various epidemiological studies have established a clear correlation between factors that disrupt the gut microbiota during childhood and immune and metabolic disorders later in life’ (1)

That’s why if you’re thinking of having a baby, are pregnant or have a very young child you need to read this.

So: how do we set this up for the healthiest start?

Research around the gut and its role remains ongoing. However, it had previously been assumed that the all important gut microbiota (the bacterial mix in our guts) starts to build at birth.

The latest research however is suggesting it starts even earlier than this: in the womb. Research is even suggesting that other microbiota in our bodies – specifically in our reproductive system – could play a role during pregnancy. Potentially impacting implantation and it has even been associated with risk around preterm birth with imbalances causing potentially damaging inflammation (click here to read more on this and why it can pose such a problem). (1).

The brain is another key area. We are all hearing more about the gut-brain link. Mayer et al noted in the Journal of Neuroscience that alterations in the gut microbiome could potentially play a role in human brain diseases including ASD, anxiety, depression and chronic pain. (2)

So – you can see that making sure you don’t have imbalances and have a microbiome which is as diverse as possible is crucial.

Unfortunately modern life doesn’t make it that easy.

So, what can we do?

Our knowledge of the microbiome is very much still evolving. We definitely don’t have all the answers yet. However, there was a phenomenal study released last year by the American Society for Microbiology looking at the earliest microbiome formation in babies. It focused on how crucial this formation is for future health, how it develops and what can knock it off. If you want to geek out hard, check out the link here. If not, here is what you need to know:

Key important points to consider:

  • How a baby’s own gut is built

  • What does a ‘healthy’ gut microbiome look like?

  • When does a baby’s gut development stabilise?

  • What are the factors that can influence this?

  • How can this cause allergy and autoimmune conditions?

  • What can we do ourselves to help it be as healthy as possible?

The earliest stages matter:

There have been a number of studies released that have gone against the long held view that a baby’s gut starts to build at birth. What we are seeing now (given more sophisticated research techniques) is more and more evidence that it starts while the baby is in utero (1). Meaning that the earliest pioneers of your baby’s own microbiota come from the mother.

Translation: while you’re pregnant. First thing to do: ensure that your own gut health is in tip top condition – click here to learn more on how you can optimise this.

We also know that the baby’s gut makeup changes a lot in the early stages. Generally speaking development only starts to stabilise around 2-3yrs old. This means: from conception to that point, you have a window of opportunity. This could potentially set a baby up for good health in the future if you’re mindful of how this develops.

So, what does a ‘healthy gut microbiota’ look like?

This is a very good question. Once again, for now the science is still learning and evolving here. We definitely do not have all the answers yet. However, we do know that everyone seems to have a different mix. Generally speaking however, we want greater diversity (more is better than less). We also want to ensure ensuring there are no big imbalances (particularly of pathogenic ie. disease causing bacteria).

In terms of individual strains: it appears that Bifidobacteria is an important one to have. Abnormal levels have been associated with disease in early life. They have also been noted to have protective and anti inflammatory properties. (1) This is why they are used so much in many store bought Probiotics (click here to learn why you should be a bit careful with these).

So, what influences how a baby’s gut gets built?

We have learnt that a number of factors shape how a baby’s gut is built at the earliest stages:

  • Mode of delivery (C-Section or Vaginal)

  • Type of feeding (breastfeeding or formula)

  • Antibiotic use

  • Diet

  • Fetal age at delivery (pre or full term)

  • Genetics

  • Lifestyle

Method of birth: Personally, this is something I wish I had known before (my baby was born by C-Section). However, what the research shows is that when it comes to building a solid gut microbiota how a baby is born matters. Most of us cannot control this of course. Often a C-Section birth is lifesaving and necessary for both mother and child. However, it is important to be aware of. The good news is that once you’re aware, if you cannot have a natural birth there are lots of other things you can to put yourself in a good position. So do not worry. Knowledge is power.  (click here for more on this).

Why does this matter/play a role?

During a normal vaginal birth the baby picks up the bacteria present in the birth canal. Sounds obvious. However, this is the first major exposure to bacteria and this tends to make up the first colony within the gut. A C-Section baby, doesn’t get this. Instead, the initial bacterial colony comes from the mother’s skin microbiome, the hospital environment and the Colostrum (first milk). This has some consequences:

Here is what the research says when we compare the gut of a baby who is born via C-Section vs one who has been born vaginally:

  • Lower complexity of bacteria in C-Section babies (remember we want diversity) until around a year old.

  • Lower initial numbers of what we think are ‘good’ bacteria (Bifidobacteria and Bacteroides)

  • Lower Cytokines (what is a Cytokine? Small proteins that are important in cell signalling ie. the affect the behaviour of cells around them)

So, from a gut perspective, its not ideal to be a C-Section baby. However, the good news is that these differences do seem to diminish over time. Further, the research has linked (although causality has yet to be proved) C-Sections with higher propensity towards autoimmune conditions, asthma, Type 1 Diabetes, allergies and obesity. (1) So it appears that the early colonization really does matter. However, once again please do not stress if you cannot have a natural birth. There are lots of other positive things you can do. Awareness is an empowering thing, not something to make you feel bad.

So what else can you do?

Type of Feeding: There are many reasons why the ‘Breast is Best’ mantra really is true (click here for the real story on that). It’s tricky, as it is not easy for everyone. Personally I had a really hard time the whole way along. However, this is a subject that is well researched and from the perspective of building a healthy gut: the science increasingly suggests it really does matter. Here is what it says when it comes to the gut and its development:

  • Breastfed infants have higher Bifidobacteria (which appear protective)

  • Breastmilk contains promicrobial and antimicrobial agents (what does that mean? Well it appears to be a natural way to promote balance)

  • Appears to contain IgAs (what is this? A type of antibody – interestingly enough low levels are associated with heightened risk of infections, allergies and autoimmune diseases).

  • Contains natural prebiotics or Oligossacharides (what is that? Click here to learn a lot more but essentially this ‘feeds’ the bacteria in the gut)

  • Different levels of SCFA (again click here for more on why that matters)

Click here for more on this.

Once again. If you cannot do this, do not stress, there are other things you can do. More of which to come. It is just worth knowing that if you can do it, it is worth ploughing on. Motivation for those 3am feeds! 

Antibiotic use: Antibiotics of course kill bacteria. Including those in the gut. There are two things to consider here. Prescription antibiotics (which often you cant help) and over disinfecting and antibiotics in food (which we have more control over).

We want to focus on what you can control.

When it comes to antibiotics: overuse in the early stages have been linked to metabolic disorders in later life, obesity and allergies. All things that are becoming an increasing issue globally. Of course, this can be something that is hard to control. For example if you have a serious infection you absolutely have to listen to your doctor. This can be lifesaving when used in the right way. The antibiotics we are talking about are those that are unnecessary and that you can avoid. Remember: always listen to your doctor on this.

The things we can do however, is to be aware of antibiotics than can sneak into our systems. Sometimes this can happen without us even realising.

What do we mean? Even being conscious and avoiding small every day things like reducing ingestion of farmed fish, meat, milk products that are not organic is wise. Why? Unfortunately these days these are often treated with antibiotics. It is also worth being less ‘hyper-clean’ with overuse of antibiotic hand-gel/sanitiser etc. Now of course this is about being sensible. The very start of a baby’s life when immune system is low is a time for vigilance. It is just important not to overdo it for too long. Some germs are good!

Here is what the science says as to why this matters:

‘considerable attention has been drawn to investigating the role of early-life antibiotic therapy in being an important driver for subsequent development of metabolic diseases. Several analyses have shown that altering the gut microbiota with antibiotics during early life will have long-lasting metabolic consequences, including adiposity (excess fat tissue), weight gain, insulin resistance, type 2 diabetes, and liver disease.’ (1)

Translation: be aware. Avoid antibiotics where you can. Listen to your doctor. Don’t overdo the sanitisation!

What’s interesting is that countries where there is the heaviest use of disinfectants, antibiotic and over use of prescription drugs as well as processed food and heavy pesticide use are typically the countries that are seeing the most rampant rise in things like autism and allergies. Is there a connection? Hard to say conclusively, however, Evrensel and Ceylon (amongst many others) make a link between this and the gut microbe:

‘Effects of growing up in a more hygienic environment and changes in diet are mainly observed in developed countries, where the incidence of allergic diseases and autism is increasing….The diversity of the gut microbiota can change under the influence of drugs, diet and stress’. (3)

Weaning: there have been surprisingly few studies around this. However, given the fact a baby’s gut is still in a state of heavy flux at this stage it makes sense to safeguard this as much as possible. Organic, diverse whole foods without preservatives are the simple, smart way to go. Meat stock (click here for more) is also recommended by one of the pioneers of gut health: Dr Natasha Campbell-McBride. Food naturally rich in prebiotics (click here for more) is another smart choice. Think fibre!

What about probiotic supplements? Click here for much more on this. However, the short version: the jury is still out. The reality is at this stage we just do not know enough. Everyone’s gut mix looks different. Plus, the type you can buy over the counter is pretty unregulated so often you dont really know what you’re getting. There is some emerging research about using very specific targeted strains for example with babies who suffer from colic/regurgitation. Click here for more. It is still very early days though. It does look increasingly likely that the future is about using a specific/targeted approach. We are just not there quite yet. For now, science at this point still points to a simple approach. Eating a balanced diet of pre and probiotic foods, whole foods, organic and avoiding too much stress. Click here for more.

Bottom line? There is a decent chunk of evidence that how our guts are formed at the very earliest stage really does matter with lasting consequences for long term health and susceptibility to disease. Particularly when it comes to issues that are seemingly on the rise today. Things like allergies, autoimmune conditions, mood disorders, obesity. Awareness is the first step and the good news is there are lots of easy things you can do to ensure that you put yourself and your baby on the best possible path for optimum gut health. It’s not about doing a single thing, its about being conscious. Lots of little things all together. It is also never to late to start! 


1) MILANI C, DURANTI S, VENTURA M: The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota: Mirobiology and Molecular Biology Reviews: 2017 Dec: 81 (4)

2) MAYER E, KNIGHT R, MAZMANIAN SK, CRYAN J, TILLISCH K: Gut Microbes and the Brain: Paradigm Shift in Neuroscience: The Journal of Neuroscience. November 12 2014: 34(46)

3) EVRENSEL A, CEYLAN ME: The Gut-Brain Axis: The missing link in depression. Clinical Psycopharmacology and Neuroscience: 2015; 13 (3): 239-244


This article is for informational purposes only. This article is not, nor is it intended to be, a substitute for professional medical advice, diagnosis, or treatment and should never be relied upon for specific medical advice. The information on this website has been developed following years of personal research and from referenced and sourced medical research. Before making any changes we strongly recommend you consult a healthcare professional before you begin.

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