How to nurture infant microbiomes for a lifetime of good mental health

New parents have plenty to fret about – sleeping, feeding, the colour of their newborn’s poo – but their baby’s microbiome probably isn’t high on the list. According to experts, it should be.

“The first 1000 days of life are incredibly important for seeding your microbiome. Once it’s in place, it’s hard to change,” says Federica Amati at Imperial College School of Medicine. Early microbial colonisation doesn’t just shape physical health, it influences brain development, mental health through adolescence and even cognitive diseases in later life.

That’s a lot to put on new parents, I thought, when hearing this emphasised at the Goodwood Health Summit in Chichester, UK, this month. But after speaking with nutritionists, microbiologists and doctors, I left convinced early microbial seeding really does matter, and there are several simple, low-cost ways to help steer a child’s microbiome in the right direction.

Why your early microbiome matters

We’re used to hearing about how the trillions of bacteria, viruses and fungi that comprise your microbiome affect your body – they protect the gut lining and regulate inflammation, for instance. But they also affect the brain.

Microbial byproducts shape how brain connections form and are pruned in early life – a process critical for healthy brain development. Bacteria communicate directly with the brain via the vagus nerve, affecting stress and mood. Chronic inflammation from a leaky gut – which can happen when the gut microbiome goes awry – is also linked with depression and neurodegenerative diseases.

Then there’s research tying microbiome imbalances to Parkinson’s and autism. Children with autism have some distinct microbiome profiles, and there’s some early evidence that fecal transplants from non-autistic donors can improve their gut and behavioural symptoms.

How to grow the perfect microbiome

Seeding it well is vital, because once your microbial ecosystem has settled in, it’s hard to overhaul. “It’s like trying to turn an English garden into a tropical rainforest,” says Amati, who is also head nutritionist of the Zoe health app.

So what can we do to create the garden we want? Even before birth, your gut microbiome is beginning to blossom. Bacteria and fungi in the uterus are ingested by a fetus, and your child is gifted with more microbes if they pass through the vaginal canal at birth.

Babies born by caesarean section tend to have different gut bacteria, which has been linked with a slightly higher risk of asthma and eczema, though these differences largely disappear by the time babies are between 6 and 9 months.

A bigger influence comes from breastfeeding, because breast milk contains sugar-like compounds that promote the growth of Bifidobacterium that aren’t present in formula. If we’re still thinking of our microbiome like a garden, these bacteria shut the front gate, preventing more harmful bacteria from getting in.

Antibiotics are a major disruptor of early seeding, wiping out good bacteria as well as bad. Of course, they also save lives, so it is up to doctors to prescribe these judiciously to protect the developing gut, says James Kinross, a colorectal surgeon at Imperial College London.

After the first year, diet becomes the biggest influence. Diversity is key, says Amati, and that comes from whole foods not the ultra-processed snacks that are often aimed at toddlers.

The trouble, as any parent knows, is that toddlers are famously picky. “Food before one is just for fun,” says paediatrician Nancy Bostock, at The Croft Child and Family Unit, in Cambridge, UK, reminding us that toddlers don’t actually need to eat huge amounts. After that, persistence pays off. “Offer it twenty times,” says Bostock. I’ve tried this – serving salmon every Monday for six months, despite repeated resistance. My kids now genuinely enjoy it.

Eating whole foods doesn’t have to be expensive, either, says Amati: “tinned lentils, frozen raspberries, they’re all great options”.

The benefits of dirt

Another cheap and underrated way to boost early microbial diversity? Get dirty. Research has shown soil, plant and human microbiomes are more interconnected than previously thought.

Kinross says healthy soils – those that haven’t been degraded by over-farming or chemicals – teem with microbial life that produce more nutritious foods that nourish our microbiome. “We are completely co-dependent on the health of soil. The soil microbiome shapes the food we eat, which shapes our health every single day.”

But it’s not just an indirect association – working with soil can transfer microbes directly to our guts, and it’s thought this can have beneficial effects on our immune system. In one study, Amish communities who farm manually showed stronger immune systems than similar Hutterite groups who use industrialised farming. In mice, inhalation of dust from the Amish homes – but not the Hutterite homes – provided a protective effect against asthma, through microbes’ influence on immune signalling.

Likewise, families who garden together also carry soil bacteria in their guts that varies with the seasons, suggesting microbes are transferred from soil or home-grown food. The long-term impact on kids’ microbiomes isn’t yet clear, but gardening families in this study and others consistently show greater diversity of microbes in their bodies and healthier nutrition scores than non-gardening families.

You don’t even need a garden to benefit. Going outside or potting plants on your windowsill and eating what you grow is good for your microbiome, says Amati.

Getting dirty shouldn’t be confused with the “Hygiene Hypothesis”, the outdated notion that blames clean homes for inflammatory illnesses. In fact, the exposure we need isn’t to childhood infections that clean houses and washing hands help to avoid, but to beneficial microbes.

The “old friends hypothesis” proposes instead that we co-evolved with beneficial microbes from soil, animals and other humans, and that reduced contact with these “friends” as a result of behavioural changes – such as spending less time outdoors – has led to an increase in chronic illnesses.

Eating well for children’s mental health

Even after that crucial first 1000 days, the microbiome remains adaptable. Which is why we need to foster a love of healthy foods in children, says Amati.

Bostock, who specialises in treating children with mental health conditions, including eating disorders, warns against restricting certain foods. “Time and again I see parents saying their child can’t have pudding until they’ve eaten this or that.” This over-emphasis on “good” and “bad” foods increases the likelihood of eating disorders and obesity, she says.

Instead, she recommends persisting with offering a variety of foods, eating together around the table and celebrating what each food does – whether that’s giving you a quick burst of energy or making your bones stronger.

And don’t forget to teach kids about those bugs, says Amati. “Tell them what their microbiome does – they love it! They love feeding their good bugs.”