The surprising link between your baby’s gut health and their future brain health

How early gut health could shape your child’s brain and long-term wellbeing.

Cheerful toddler girl enjoying picnic in nature

Published: April 15, 2026 at 1:25 PM

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With recent research finding that our rates of Alzheimer’s disease are impacted by the health of our guts, eating a healthy diet has never been more important, and not just for adults. The first 1000 days of a child’s life are incredibly important for establishing good gut health, and the eating habits parents instil in them from childhood can help them maintain a healthy gut for the rest of their life.

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It might sound quite serious, but cultivating a healthy gut microbiome as early as possible doesn’t have to be hard. MadeForMums spoke to Dr. Marion Sloan, a GP in Sheffield and chair of the Primary Care Society for Gastroenterology, about the links between childhood gut health and cognitive decline. We also asked Professor Willem M. de Vos, a microbiologist who co-founded Alba Health, a startup that provides gut health tests for children, about everything you need to know about early-years gut health.

What is good gut health, and how does it impact our risks of Alzheimer’s in older age?

When babies are born, they don’t have a gut microbiome, which is the trillions of microorganisms that live in our intestines and help us digest food. It is built up as microbes colonise babies’ guts during birth and for the first few years, until it stabilises at around two or three years old.

Not only does it facilitate the digestion process, but scientists have also recently discovered that the gut microbiome plays an important part in our general health, too. They think it has a hand in the functioning of our immune systems, hormone secretion, and even our mental health.

Mother kissing belly of baby girl lying on bed in an apartment

Having an unhealthy gut microbiome — meaning that there isn’t much diversity in the types of microbes in the gut — can lead to health issues later in life, such as irritable bowel syndrome and inflammatory bowel diseases.

Marion says that research suggests many types of dementia (including Alzheimer’s) are impacted by gut health, too, because they are linked to chronic inflammation in the body.

“A less diverse gut microbiome can promote a long‑term pro‑inflammatory state, which increases the risk of vascular disease in the heart, brain and other organs,” she says, as well as contributing to risks of developing dementia.

Scientists think that an unhealthy gut could also contribute to other chronic diseases like allergies, depression, obesity, and even certain cancers, although the research is still ongoing.

There are several key things in early life that affect your gut microbiome

Key factors like the method of delivery, whether they are breastfed or not, and if they have antibiotics can contribute to a baby’s gut microbiome.

Method of delivery

“Vaginally born babies are colonised by the mother’s faecal material,” Willem says. So, far from being embarrassing, it may actually be beneficial to your baby’s health if you pooed during labour!

This is because babies are exposed to their mum’s gut bacteria as they come into contact with her faeces during birth, which helps to populate their own guts.

Meanwhile, at four days old, babies born via Caesarean section have fewer helpful bacteria from their mums and more bacteria associated with the hospital environment, a 2019 study published in the journal Nature found.

But don’t worry if you’ve had a C-section — the differences lessen by infancy, and the life-saving benefits of the procedure are more important!

Breastfeeding

Breastfeeding can also help to colonise babies’ guts with beneficial bacteria. Willem says that breastfeeding for at least six months, but ideally for a year or more, can promote the growth of good bacteria.

In fact, some of the sugars in breastmilk can’t actually be digested by the baby, Willem says, but can be broken down by gut microbes.

If your baby is formula-fed, they aren’t missing out. The gut microbiomes of breastfed and formula-fed babies are very similar, thanks to the pre- and probiotics that are added to formula, according to a 2022 review of research published in the journal Nutrients.

Young mother breastfeeding your 2-3 month baby boy lying on blanket at home

Antibiotics

Antibiotics can have a huge impact on the gut microbiomes of babies, children, and adults.

In studies that Willem has been part of, done on children in Finland, he found that the children who had had more courses of antibiotics during their lives (sometimes up to 25 courses!) had their gut microbiomes “jeopardised” or at least “changed” a lot.

“The kids that had those courses of antibiotics had a very different microbiome. They had a reduced number of different bacteria, and they had a higher risk of getting asthma and allergic diseases later in life — and in some cases they were also more predisposed for higher BMIs or obesity,” he says.

He warned that this doesn’t mean that antibiotics directly cause higher risks of chronic diseases, simply that research is finding similar links.

So, you should always take antibiotics if doctors prescribe them to help your child’s health but don’t ask doctors for them unnecessarily.

How to take care of your child’s gut

Many of the factors above are unavoidable, and at the end of the day, it’s much better that babies are kept healthy, safe, and fed through interventions like C-sections, formula milk, and antibiotics than not having them at all.

Despite these early-life events being quite impactful for our gut health, it doesn’t mean all is lost after the age of two. There are lots of things you can do to give your child the healthiest gut possible.

“We have data to support that it is five years or maybe longer before you have the adult microbiota,” Willem says. “And then important changes also occur also in puberty as their hormones pick up, and their eating habits are changing.”

“It’s never too late to adapt and change” for better gut health, he says.

So, even into their teen years, you can help children develop healthy eating habits that will support their gut health in the long term.

Having better gut health can help with reducing risks of obesity and constipation, and increasing the likelihood of better immune health, metabolic health, brain health, and weight management, he says.

Eat a healthy diet and avoid processed foods

Willem says it doesn’t matter what cuisine children are brought up eating — as long as they are fed a healthy diet.

Cute toddler girl with pigtails eating broccoli at a table at home.

A healthy diet means a balanced one, with plenty of fruit and vegetables, enough protein and dairy, and few ultra-processed foods (UPFs).

UPFs are foods that have had a lot of different processes done to them, using ingredients and equipment that you wouldn’t use at home. They often contain added salt, sugar, and preservatives, and they usually don’t look like their ingredients. Think fast-food burgers, fizzy drinks, packaged snacks like crisps, and instant noodles.

A growing amount of research is linking them to increased risks of chronic health conditions such as certain cancers, depression, heart disease, and diabetes.

It’s very difficult to completely cut out UPFs in a Western diet because they are convenient and cheap. And some processed foods, like whole grain bread or fortified cereals, can actually be beneficial for health.

So, don’t stress yourself out by trying to provide a diet with absolutely no UPFs — just try to cut down on them where you can and replace them with whole foods (or single ingredient foods).

Here are some recommended swaps from Alba Health:

But remember, overall, fed is best!

Eat lots of fibre

“Regularly including high‑fibre foods and prebiotics, which support a thick, healthy mucus layer in the gut and help reduce low‑grade inflammation,” is great for our gut health, Marion says.

“We should eat about 30 to 40 grams of fibre per day, which is not easy,” Willem says. This is lower for babies and children:

But most adults are getting around 20g of fibre a day, and most children 16g a day, according to the NHS.

Getting enough fibre makes it easier to digest food and poo, as well as reducing our risks of heart disease, strokes, type 2 diabetes, and bowel cancer.

Fibre is found in most plant foods, but especially in the following foods:

Mario also suggests fermented foods to up your fibre intake: “Adding fermented foods such as kefir, live yogurt, sauerkraut, kimchi and kombucha, provides a mixture of fibres and bacteria that can improve immune responses and lower inflammatory markers,” she says.

Mother and daughter preparing fresh vegetables for cooking at kitchen. Both laughing

Lead a generally healthy lifestyle

Having good gut health isn’t just about what you eat. Willem recommended helping children to get enough exercise and avoid a sedentary lifestyle, as well as getting good amounts of quality sleep.

Leading a generally healthy lifestyle means that the body can perform all of its functions as best it can. But there are also more specific links being found between exercising, sleep, and gut health.

A 2023 study by researchers at The University of Queensland, for example, found that people who exercised more frequently had a higher variety of microbes in their guts — which is great for gut health. Researchers suggested this could be because of the changes in body temperature and blood flow that come along with exercise.

And researchers also suspect that sleep and gut health can impact on each other — one 2024 study published in the journal Open Life Sciences suggests that gut microbes are affected by the circadian rhythm. Another 2023 study by researchers at Kings College London found that irregular sleep patterns were linked to a higher number of microbes that are associated with health conditions like obesity and inflammation.

Get your child’s gut tested, especially if they have digestive problems

Willem’s company, Alba Health, has launched a gut health test for children, because digestive symptoms, allergies, and symptoms related to gut issues — like sleep disruption and crying — are all on the increase.

Alba’s tests entail sending a sample of your child’s poo to Alba, who test it for bacterial imbalances and send you a personalised nutrition plan with realistic guidance about what to eat and whether to take probiotics. MadeForMums likes Alba’s testing because they don’t sell customers their own products, meaning you’re getting personalised suggestions specifically for your child.

But it’s important to note that poo testing can only tell you so much — as with all testing, it will only provide a snapshot of the bacteria found in that specific bit of poo on that specific day, so can’t give you the full picture. And while poo testing can look for bacteria that we know causes disease, we don’t yet know for certain how the presence or lack of other bacteria affects our health because the research is still in its infancy.

The charity Guts UK has a good explainer on the benefits and drawbacks of gut health testing.

Don’t worry too much!

As we’ve seen, the choices that parents make can obviously have an impact on their child’s gut health. But if a child is born via a C-section, is bottle-fed, and goes on antibiotics, these things were probably done in their best interests even if they marginally affect the gut later down the line. And diet is not the only factor in determining someone’s gut health and/or risks of developing Alzheimer’s — genetics, environment and social factors, and life events all also play a part.

“Parents can't "guarantee" that their child will never develop dementia, but they can give them a strong foundation for lifelong gut and vascular health,” Marion says.

“Supporting a healthy microbiome in childhood is a positive, realistic step that also improves day‑to‑day health, immunity and wellbeing. Rather than focusing narrowly on dementia decades in the future, it is more helpful to think about building habits that support a robust microbiome, a strong body and a resilient brain throughout life.”

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“For parents, the most helpful approach is to focus on building a family pattern of eating "real food" from all the main food groups, enjoying plenty of plants and fermented foods, and keeping ultra‑processed products in the background rather than the foreground,” she says.

Authors

Serafina Kenny journalist headshot

Serafina KennyDigital Journalist

Serafina Kenny is a Digital Journalist at MadeForMums. She writes news and features and has expertise in health, nutrition, relationships, and history. She has previously written for Business Insider, Women's Health, Stylist, Men's Health US, The i Paper, Dazed, and more. You can contact her with tips and story ideas (or compliments!) at serafina.kenny@immediate.co.uk.

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