The Microbiome of Kids: Why Early Gut Health Matters

I often return to the idea that “everything is connected,” and nowhere is that more evident than in the early years of life. In the garden of the gut, the seeds we plant in childhood grow into the terrain we carry into adulthood. And just as a healthy field yields a robust harvest, so too does a nurtured microbiome in children lay the foundation for lifelong wellness.

A Delicate Beginning: The Early Childhood Microbiome

There’s a great deal of research today about how early in life the human microbiome is established—and why that matters so much for long-term health.

Back in 2015, when I was just starting The BioCollective, I had the opportunity to meet Dr. Martin Blaser, Dr. Rob Knight and Dr. Gloria Dominguez-Bello, key researchers in the microbiome. Gloria’s husband, Dr. Martin Blaser, had written Missing Microbes, a book that opened my eyes to what we were losing—microbes that had co-evolved with us for thousands of years and played critical roles in immune training, metabolism, and inflammation regulation. It was the first time I fully grasped the generational consequences of our antibiotic use and the industrialized shift in how we birth, feed, and raise children

At birth, a child’s gut is a blank slate. During vaginal delivery, they receive their first dose of maternal microbes—an invisible but vital inheritance. These early colonizers begin training the immune system, teaching it to distinguish friend from foe. But in industrialized nations like the United States, that microbial bequeathment has become compromised. C-sections, antibiotics, and formula feeding, while often necessary, can shift this delicate process.

Groundbreaking research by scientists like Dr. Rob Knight showed that a child’s core gut bacteria are established by around age 3.  Dr. Gloria Dominguez-Bello has mapped how Western practices are eroding microbial diversity in infants. One strain of bacteria that’s especially important for babies is called Bifidobacterium infantis—or B. infantis for short. It’s still found in babies born into traditional, indigenous communities, but it’s mostly disappeared in babies born in Western countries like the U.S.

Why does that matter?

Because breast milk contains special sugars called HMOs that babies themselves can’t digest. These sugars are actually there to feed B. infantis. When that microbe is present, it turns those sugars into helpful compounds that lower the gut’s pH, support the gut lining, and help teach the immune system how to respond appropriately.

But if B. infantis isn’t there, those same sugars aren’t used in the same way. The gut doesn’t get the full benefit, and the immune system misses out on important early training. It’s not that harmful bacteria take over immediately—it’s more that the baby’s system doesn’t get the strong start it was designed to have.

This isn’t about blaming parents or choices. Many of the factors that shape a baby’s microbiome—birth method, feeding, antibiotic use—are sometimes out of our hands. But understanding what’s missing helps us figure out how to support our kids more effectively.

The same idea applies as a child grows up. Certain types of foods—like resistant starches found in things like green bananas, cooked-and-cooled potatoes, legumes, and oats—aren’t really digested by your child directly. These starches are there to feed their microbiome.

That might sound strange at first—feeding bacteria instead of the child—but it’s one of the most important things we can do. When those beneficial microbes eat resistant starches, they produce all kinds of “goodies”: short-chain fatty acids, vitamins like B12 and K, and even building blocks for hormones that support brain function, immune balance, and metabolic health.

So while it might look like just a scoop of lentils or a spoonful of overnight oats, what you’re really doing is feeding the system that helps your child thrive from the inside out.

What Are We Feeding Our Children?

In the United States, many children are raised on a diet of convenience. Walk down a typical grocery store aisle and you’ll see an entire wall dedicated to cereals—many of them engineered for taste, convenience, and shelf life, not nourishment. Pop-Tarts. Sugary yogurts with barely any live cultures. Chicken nuggets molded into shapes. Lunchables stacked in plastic trays. These are not real foods. They are food facsimiles—manufactured from isolated components, stripped of the very microbes and fibers that make whole foods healing.

Our children’s gut health—just like their palates—are shaped by what we feed them. And the more we rely on processed food, the more we steer them away from microbial diversity and digestive resilience.

Processed foods don’t just lack fiber and probiotics for kids. Many are made with glyphosate-treated ingredients, emulsifiers, and additives that disrupt the gut lining and microbial integrity. These disruptions don’t only affect digestion. The gut is home to 70% of the immune system and is the primary site of communication with the brain. A disrupted gut is a disrupted child.

Real Food, Real Intention

So what can we do? We can return to real food for children. That means meals prepared with fresh, whole ingredients—vegetables pulled from the earth, grains that still resemble their source, clean proteins, fermented foods with living cultures. Food made in the home, not a factory.

But there’s something deeper than ingredients. It’s the intention behind the meal. Even though I was a busy working mom I understood that the meals I made were more than nourishment, they were also a symbol of my love. Preparing a meal with care, sitting down without distractions, and enjoying each other’s company was important.  One of the more important aspects supporting healthy digestion is sitting down and being mindful of the meal and the connection, reminding us that food is relational. It’s not only about what we put into the body, but how we receive it.

As parents, grandparents, and caregivers, we’re not just shaping our children’s health. We’re shaping their story of what nourishment means. That story begins early—and it matters more than we know.

A Microbial Legacy That Begins Today

It’s never too late to make changes. But the earlier we begin, the more resilient the terrain will be. The first three years of life are important in establishing a healthy core  for  immune development, brain wiring, and metabolic calibration but you can make changes to support better outcomes at anytime. You will be amazed to see the changes a healthy, real food diet can make.  

When we choose real food, we’re not being idealistic, we’re being protective. When we prioritize fermented vegetables, bone broths, fresh fruits, and foods rich in prebiotic fiber, we’re giving our children more than nutrients. We’re giving them a microbial inheritance that can carry them through life with strength and grace.

Let’s prepare their food with love. Let’s protect their terrain. And let’s honor the innate intelligence of the body—starting from the very first bite.