Illustration by Jordan Kay
The gut is often called our second brain—and for good reason. We all know the sensation of an unsettled tummy when feeling anxious, or having a “gut feeling” about something before we can articulate it. Increasingly, science is revealing the physical and biochemical underpinnings of the link between the brain and the gut—and what they mean for neurodevelopment, digestion, immunity, and mental health.
It’s a topic of growing urgency, thanks to rising rates of pediatric neurodevelopmental disorders such as attention-deficit/hyperactivity disorder (ADHD) and autism; mental health troubles such as anxiety and depression; and autoimmune conditions ranging from Crohn’s disease to eczema and food allergies.
As researchers uncover more about the gut-brain connection, it’s becoming clear that the gut microbiome (the ecosystem of microbes in our intestines) plays a pivotal role in childhood development, behavior, immune health, and emotional regulation. For families, this means supporting gut health isn’t just about digestion—it could be a key to nurturing a child’s overall well-being.
Understanding the Gut-Brain Axis
“If you’ve ever been nervous and felt butterflies in your stomach, you’re experiencing the connection between the gut and the brain,” says Dr. Elizabeth Placzek, a pediatrician at Children’s Minnesota. “Our brain is an amazing, complicated system of neurons and chemicals that for so long we thought only existed in that part of our body. Now, we’re finding those same neurons and chemicals exist quite strongly in our gut.”
These shared neurons and chemicals make up part of what’s known as the gut-brain axis—the bidirectional communication network between the digestive system and the brain. Dr. Jara Rice, a functional medicine pediatrician at Allina Health, compares this axis to an eight-lane highway during rush hour, when traffic is skewed in one direction: “About 80% of the messages travel from the gut to the brain, and 20% come down from the brain to the gut,” says Rice.
This superhighway is mostly powered by the vagus nerve, which sends and receives signals between the gut and the brain. Some of these signals involve neurotransmitters—such as dopamine and norepinephrine—that are produced and/or influenced by bacteria in the digestive tract. According to 2022 research in Scientific Reports, as much as 90% of the body’s serotonin is made in the gut.
“Serotonin is extremely important for emotional processing, social interaction, learning, and other brain functions. Because so much of the body’s supply comes from the intestinal microbiome, changes to gut health can really influence [these things],” Rice explains.
About 80% of the messages travel from the gut to the brain,
and 20% come down from the brain to the gut.–Dr. Jara Rice, Allina Health
The immune system, too, is largely rooted in the gut, with roughly 70-80% of the body’s immune cells located there. This means the gut isn’t just digesting food. It’s processing information, regulating mood, and training the immune system, making it one of the body’s most influential—and often overlooked—control centers.
The Gut’s Role in Neurodevelopment and Mental Health
Pediatricians are seeing rising rates of both brain and gut health concerns in children. “Data shows that 1 in 10 kids has ADHD, nearly 1 in 10 kids has behavior problems, 1 in 10 has been diagnosed with anxiety, and now 1 in 31 kids has autism. The incidences of celiac disease and inflammatory bowel disease are also on the rise. These all show up constantly in our practices,” Rice says.
Illustration by Jordan Kay
That rates of all these conditions rising together might not be a coincidence. “Researchers are studying the gut microbiome in children with ADHD and autism spectrum disorder, and they’re finding significant differences in the quality and types of bacteria in their microbiomes,” says Dr. April Lind, a functional medicine practitioner at Minnesota Personalized Medicine who is board-certified in both internal medicine and pediatrics.
Rice notes that children with autism often experience digestive symptoms such as constipation and stomach pain, further supporting a gut-based component to the condition. “There are currently phase-three clinical trials going on of fecal microbial transplants for children with autism that look rather promising,” she says. While this is a nascent area of research, and experts stress that there’s likely no single cause underlying autism, a 2019 study by researchers at Arizona State University found that boosting microbial diversity via fecal transplants dramatically reduced autism symptoms in the long term.
Because of the bidirectional nature of the gut-brain axis, gut symptoms can also be fueled by the brain. “Estimates are that as many as 25% of kids have chronic abdominal pain for which we really struggle to identify a cause. One cause could be this interaction between the gut and the brain,” notes Placzek. In many cases, children experience a feedback loop: Emotional stress leads to gut discomfort, and persistent gut issues heighten emotional dysregulation.
“Those butterflies in your stomach—that’s your brain’s anxiety chemicals having a direct effect on your stomach,” Placzek says. This cycle can be particularly difficult to untangle, which is why providers often recommend a multi-pronged approach that supports both gut health and emotional resilience.
Signs of Imbalance in the Gut-Brain Axis
Because the gut-brain connection plays a role in so many of the body’s systems, signs of imbalance can show up in unexpected ways. Caregivers may be looking for digestive complaints, but the clues are often more subtle or behavioral.
“Depending on age, kids with [gut] imbalances are going to show up in a lot of different presentations,” says Rice. For infants, that might include reflux, colic, poor sleep, frequent illness, feeding difficulties, or eczema. Toddlers may show signs such as picky eating, sugar cravings, constipation, food intolerances, or unusual behaviors like bracing their bellies against furniture. Even behavior that looks like defiance or distraction may have roots in physical discomfort.
As children grow, the clues can become more complex. Elementary-age kids may struggle with mood regulation, speech or social development, frequent illness, or a poor appetite. Adolescents may present with depression, anxiety, chronic fatigue, headaches, painful periods, or hormone imbalances.
Illustration by Jordan Kay
Even without classic gastrointestinal symptoms, the gut may still be a key factor. “I’ve seen kids with chronic coughs that are probably intolerant of dairy, and if you take dairy out of their diet, their cough gets better,” Lind says. She says she keeps in mind Hippocrates’ famous observation that “all disease begins in the gut.”
That’s a particularly useful reminder for kids who have been told by providers that “everything looks normal”—yet parents know something isn’t right. “Usually after you’ve been told everything’s fine and yet you’re still not fine, that’s where I’m going to start thinking of first,” Lind said. “You can’t fix anything else until you fix the gut.”
In one case (not from Lind’s practice), a 10-year-old girl in southern Minnesota struggled for months with stomach pain, cramping, and constipation. “We felt very helpless,” says the child’s mother, Amanda Sullivan. “She cried a lot in our arms. She stopped wanting to go places, including school, because she felt like she would have to go to the bathroom there and would get embarrassed.” Over the course of about a year filled with doctor visits and blood samples, all her test results came back “normal.” It wasn’t until Sullivan pushed for food sensitivity and allergy testing that they discovered the underlying gut issue.
“I felt like our last resort was the allergy testing,” Sullivan recalls. “When the doctor told me insurance didn’t cover it, and it would be about $300, I didn’t even hesitate. No amount of money was going to be a concern to find out what was going on.” After removing gluten, soy, and dairy from the child’s diet, her symptoms improved dramatically, and she has since had little to no gastrointestinal issues.
How Caregivers Can Support Kids’ Microbiomes
Supporting a healthy gut microbiome in children doesn’t have to involve extreme measures. In fact, the most effective strategies are often the simplest—centered on food, environment, and emotional well-being.
First and foremost, experts recommend focusing on a diverse, fiber-rich diet full of fruits, vegetables, and whole grains. Rice emphasizes the “three Fs”: fiber (which serves as a prebiotic, or food for good bacteria), phytonutrients (plant compounds that help good bacteria thrive), and fermented foods (which contain helpful microbes, also known as probiotics). “It’s a complete package when we get prebiotics and probiotics from food,” says Rice.
Fiber-rich foods include fruits, vegetables, legumes, and whole grains. Phytonutrients—natural plant compounds that support immunity, reduce inflammation, and nourish the microbiome—are found in colorful plant foods (hence the popular advice to “eat the rainbow”). Beneficial fermented foods include unsweetened yogurt, kefir, sauerkraut, kimchi, miso, tempeh, and fermented pickles.
As many as 25% of kids have chronic abdominal pain for which
we really struggle to identify a cause.–Dr. Elizabeth Placzek, Children’s Minnesota
This advice seems simple enough, but anyone with a toddler might scoff at the idea of them happily downing a spoonful of sauerkraut. One trick Rice suggests is starting small, such as adding a single drop of sauerkraut juice to a familiar condiment such as mustard or ketchup, then gradually increasing the amount over time, so kids develop a taste for the flavor.
Lind stresses the importance of modeling healthy eating behaviors for kids, even if they’re not ready to participate in them. “Put all the colors they should see on the plate in front of them. They might pick the broccoli up and throw it on the floor, but it’s still visually imprinting on them—this is what a normal meal is,” she explains.
Lind also suggests getting kids involved in growing food, even if it’s just a pot of herbs on a balcony. Or going on a produce aisle “treasure hunt” to pick out a cool-looking food like dragon fruit, then researching where it comes from and how to prepare and eat it.
Fostering excitement about whole foods is especially important in light of emerging evidence on the harms of ultra-processed foods. A 2023 study by Food Research International found that ultra-processed foods may negatively impact brain health by altering gut microbiota and triggering intestinal inflammation, disrupting the microbiota-gut-brain axis. Rice notes that food additives like dyes and preservatives are seen by the immune system as foreign invaders, disrupting cellular communication pathways. “If a parent notices, ‘Hey, my kid doesn’t react well when they have ultra-processed foods,’ there’s actually a lot of biochemistry to back that up,” says Rice.
In addition to focusing on whole foods, many parents wonder whether probiotic supplements can help support their child’s gut health. While probiotic supplements can be helpful during—and following—a bout of antibiotics, our experts stress that food is still the optimal source for supporting the microbiome. Research on which specific microbial strains are best suited for any given individual is still in its infancy, and finding a product that doesn’t produce unwanted digestive effects can take some trial and error. On the other hand, it’s hard to go wrong with foods that we know support overall microbial health and diversity.
Illustration by Jordan Kay
There are also upsides to letting kids get dirty. Ample research has shown that playing outside and not over-sanitizing are associated with healthier microbiomes in kids. A 2020 study in Nature found that a 10-week, outdoor, nature-based program for preschoolers led to significant changes in gut microbiota, alongside boosted serotonin levels and reduced stress. Another 2020 study by researchers at Washington State University found that toddlers and preschoolers with higher blood and urine levels of semi-volatile organic compounds (SVOCs)—common in many cleaning products—had reduced diversity in their gut bacteria.
On the flip side, studies in infants and young children have shown that early life exposure to household furry pets increases richness and diversity of the gut microbiome. To help families make more microbiome-friendly choices, Rice recommends checking the Environmental Working Group’s website for guidance on safer cleaning and personal care products.
Strengthening the Gut-Brain Feedback Loop
Because the gut and brain are in constant conversation through the vagus nerve, strengthening this feedback loop means supporting both sides of the relationship: the gut itself and the mind that influences it.
It’s not just what kids eat but also how they eat that matters. A low-stress, screen-free, and positive mealtime environment encourages a state of relaxation known as “rest and digest,” where the vagus nerve is active and digestion is optimized.
“There are things we can do to stimulate the vagus nerve around mealtime to optimize nutrition [absorption], digestion, and elimination patterns,” Rice says. “We can take two deep breaths, or go around the table and say one thing we’re grateful for. That starts to change our brain chemistry right away and helps to activate the parasympathetic nervous system.”
Lind offers another vagus nerve-stimulating trick: Pretend you’re filling your belly like an air balloon by taking a big breath, and then slowly blow it out like you’re spinning a pinwheel with a stream of air.
Helping children develop healthy coping skills away from the table also strengthens the gut-brain feedback loop. Simple strategies like belly breathing, outdoor play, reading, and minimizing excessive screen time can all activate the parasympathetic nervous system and support gut-brain harmony. Lind points to what she calls the 5-4-3-2-1-0 rule: Each day, a kid should ideally have five fruits and vegetables, four glasses of water, 30 minutes of reading, two hours or less of screen time, one hour or more of outside play time, and zero sugary drinks.
Still, the reality is that balance—not perfection—is the goal. All three pediatric experts emphasized the importance of creating a generally supportive environment without stressing over every meal or moment. Placzek reassures parents, “Even if your kid doesn’t eat broccoli every day, their microbiome can still be healthy.”
Recognizing the [gut-brain] connection can help avoid unnecessary
treatments and lead to more holistic care.–Dr. Sundeep Arora, MNGI Digestive Health
Building a resilient gut-brain connection is about making consistent, nourishing choices most of the time while allowing for flexibility, joy, and real life. In the long run, a relaxed, positive approach to food, play, and connection may do as much for a child’s health as any specific nutrient ever could.
When issues do arise, parents should trust their instincts, says Lind. If signs point to an imbalance in the gut-brain axis, it can be very helpful to work with a functional or integrative practitioner to get to the root cause. These providers can help assess not just symptoms, but the whole ecosystem of a child’s health—nutrition, environment, stress, and lifestyle—to create a plan that supports both gut and brain resilience.
In a field where science is still evolving, the basics remain powerful: a colorful plate, a calm table, time outside, room to play, and plenty of grace for the imperfect but loving work of raising healthy kids.
Gut Check: Clues from the Brain
Courtesy of MNGI Digestive Health
Dr. Sundeep Arora, M.D.—pediatric gastroenterologist at MNGI Digestive Health—shares insights on how a child’s gut health plays a critical role in their overall well-being—starting as early as infancy.
Q: When does the gut-brain connection begin to influence a child’s health?
A: It starts very early—within weeks of birth. Even colicky babies may show early signs of nerve pathways between the gut and brain being sensitized.
Q: Have you seen gut issues linked to mental health conditions like anxiety or ADHD?
A: While research is still evolving, we see it clinically. For instance, kids with undiagnosed celiac disease often show anxiety or ADHD symptoms, which sometimes improve once gluten is removed from their diet.
Q: What are signs a child’s digestive health might be affecting their mood or behavior?
A: Watch for bloating, changes in bowel habits, poor growth, reflux, or new food sensitivities. These symptoms may signal underlying gut issues.
Q: Are there key foods to include for better gut-brain balance?
A: Yogurt with live cultures, whole grains, and plenty of fruits and vegetables. These help maintain a healthy gut microbiome and provide essential fiber.
Q: Are gut-brain disorders often misunderstood?
A: People often assume gut issues are purely physical. But in many cases, it’s about how the brain and gut interact. Recognizing this connection can help avoid unnecessary treatments and lead to more holistic care. –Alesha Taylor
Illustration by Jordan Kay
Second Brain, Real Symptoms
Courtesy of M Health Fairview
Dr. Catherine Larson-Nath—a gastroenterologist with M Health Fairview and the U of M Medical School—explains how the gut-brain connection shapes kids’ health and why parents shouldn’t dismiss tummy troubles as “all in their heads.”
Q: What exactly is the gut-brain connection?
A: Your intestines have their own nervous system—sometimes called the ‘second brain’—with over 100 million neurons. It communicates constantly with the brain, which explains why emotions and stress can physically affect digestion and vice versa.
Q: What signs should parents look for?
A: Physical symptoms like constipation, diarrhea, or nausea are common. But for younger kids especially, mood or behavior changes—like irritability, trouble sleeping, or withdrawing from activities—can also signal gut discomfort.
Q: Can stress cause digestive issues in kids?
A: Absolutely. Think of how a child might feel nauseated before a performance or trip. That’s the brain-gut connection in action. Stress—good or bad—can trigger physical symptoms.
Q: Why do some kids have food sensitivities while others don’t?
A: There are many possible triggers of abdominal symptoms for kids. Foods are just one possibility; other things that might cause symptoms include being tired, stress, constipation, and changes in the microbiome. When thinking about diet changes for a child, it is important to use systematic elimination, guided by a dietitian or doctor to assure a child’s nutritional needs are being met.
Q: Any misconceptions?
A: One of the biggest is that it’s ‘all in your head.’ It’s not. These are real symptoms. Kids aren’t imagining their pain—they just need support in calming that overactive gut-brain signal, not dismissal. –Alesha Taylor
