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

New parents have plenty to worry about—sleeping, eating, the color of their newborn’s poop—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 of Imperial College School of Medicine. Early microbial colonization not only shapes physical health, it affects brain development, mental health through adolescence, and even cognitive diseases later in life.

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

Why Your Early Microbiome Matters

We are used to hearing about how the trillions of bacteria, viruses and fungi that make up your microbiome affect your body – for example, they protect the intestinal mucosa and regulate inflammation. But they also affect the brain.

Microbial byproducts shape how brain connections are formed and pruned in early life—a process critical to 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 to depression and neurodegenerative diseases.

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

How to grow the perfect microbiome

It is important to sow it well, because once your microbial ecosystem is established, it is difficult to overhaul. “It’s like trying to turn an English garden into a tropical rainforest,” says Amati, who is also chief nutritionist at the Zoe Health app.

So what can we do to create the garden we want? Even before birth, your gut microbiome begins to flourish. Bacteria and fungi in the womb 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 C-section tend to have different gut bacteria, which has been linked to a slightly higher risk of asthma and eczema, although these differences largely disappear by the time babies are between 6 and 9 months.

A greater influence comes from breastfeeding, because breast milk contains sugar-like compounds that promote the growth of Bifidobacterium which is not present in the formula. If we still think of our microbiome as a garden, these bacteria close the gate and prevent more harmful bacteria from entering.

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

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

The affliction, as any parent knows, is that toddlers are famously picky eaters. “Food before one is just for fun,” says pediatrician Nancy Bostock of The Croft Child and Family Unit in Cambridge, UK, reminding us that toddlers don’t actually need to eat large 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 really enjoy it.

Eating whole foods doesn’t have to be expensive either, says Amati: “canned lentils, frozen raspberries, those are all good options”.

The benefits of dirt

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

Kinross says that healthy soils—those that haven’t been degraded by excessive agriculture or chemicals—are teeming with microbial life that produces more nutritious foods that feed our microbiome. “We are completely co-dependent on the health of the soil. The microbiome of the soil shapes the food we eat, which shapes our health every single day.”

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

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

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

Getting dirty should not be confused with the “hygiene hypothesis,” the outdated view that blames clean homes for inflammatory diseases. In fact, the exposure we need is not to childhood infections, which house cleaning and hand washing help avoid, but to beneficial microbes.

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

Eat well for children’s mental health

Even after the crucial first 1000 days, the microbiome remains adaptable. That is why we need to promote a love of healthy food in children, says Amati.

Bostock, who specializes in treating children with mental disorders, including eating disorders, warns against limiting certain foods. “Over and over I see parents say their child can’t have pudding until they’ve eaten this or that.” This predominance of “good” and “bad” foods increases the likelihood of eating disorders and obesity, she says.

Instead, she recommends continuing to offer a variety of foods, eating together around the table, and celebrating what each food does—whether it’s giving you a quick burst of energy or making your bones stronger.

And don’t forget to teach children about these mistakes, says Amati. “Tell them what their microbiome is doing—they love it! They love feeding their good bugs.”