The microbiome isn’t just about digestion — it’s a cornerstone of nervous system regulation and mental health. And yet, it's often overlooked. Healing the gut can be a catalyst for emotional balance, focus, and behavioral improvements.
This episode is filled with powerful insights as I am joined by Dr. Aaron Hartman, a trusted expert and triple board-certified physician, to explore how gut health is deeply connected to children's emotional and behavioral well-being. Together, we dive into why microbiome imbalances can be a hidden root cause of issues like ADHD, autism, anxiety, and more — and how calming the brain through addressing the gut can open the door to real, lasting healing.
Historical Context and Importance of Gut Microbiome
The gut microbiome has been seen as vital to health for thousands of years, with ancient healers and Hippocrates emphasizing its role. In 1908, Eli Metchnikoff earned a Nobel Prize for his research, and today, modern science is finally catching up.
Dr. Hartman explains that the gut is not only essential for digestion but also central to immune function, neurotransmitter production, detoxification, and brain health. About 70% of the immune system surrounds the gut, and the gut produces the majority of calming and focusing neurotransmitters like serotonin and dopamine — which directly affect emotional regulation, focus, and behaviors tied to conditions like ADHD, OCD, autism, and PANS/PANDAS.
The gut is also a key driver of inflammation regulation through its interaction with the vagus nerve and the brain's immune system which we’re only beginning to fully understand. Research now shows the brain has its own lymphatic and immune systems, and the gut acts as a powerful lever to influence them.
As Dr. Hartman emphasizes, when we support the gut microbiome, we support the whole child physically, emotionally, and neurologically, giving us a powerful tool to promote healing and calm the brain first.
Neuroinflammation and Gut Health
Chronic neuroinflammation is increasingly widespread among children, especially those battling behavioral challenges, mental health conditions, and persistent physical issues. Brain mapping often uncovers significant inflammation across regions, rarely missing in kids with long-term struggles.
Gut health, once dismissed as a fad, remains a critical piece alongside detoxification problems and nervous system dysregulation that block deep, lasting healing. Endotoxins, toxic byproducts from gut bacteria like E. coli, cross weakened gut linings, strain liver defenses, and ignite widespread inflammation that often reaches the brain.
A leaky gut usually leads to a leaky brain, letting toxins trigger neuroinflammation seen in conditions like autism, mold toxicity, and concussions. Fortunately, healthy bacteria produce butyrate from fiber-rich foods, acting as a natural antidote to this damage.
When butyrate drops too low, brain inflammation can spiral, but supports like methoxy curcumin from turmeric, omega-3s, SPMs, activated charcoal, and low-dose naltrexone work together to calm microglia and open real paths toward deeper, lasting healing.
Brain inflammation rarely stands alone. It threads through OCD, ADHD, autism, and various forms of neurodivergence and mental health struggles. Research, including post-mortem studies on autism, shows brain inflammation is not rare at all. Understanding this offers a hopeful path forward: a chance to support natural healing rather than relying only on heavy medications burdened with side effects.
Leaky Gut and Its Impact on Health
Many still dismiss “leaky gut” as crunchy nonsense, but it's a real, measurable condition—technically called increased gastrointestinal permeability—where damage to the gut lining allows toxins and bacteria to leak into the body, triggering systemic inflammation.
Gut issues rarely stay local; they can fuel brain inflammation and play a key role in conditions like PANS/PANDAS, early Parkinson’s, and Alzheimer’s, where healing the gut is often the first step toward recovery.
When the gut’s in trouble, the brain feels it too. What many dismiss as “leaky gut” is actually increased intestinal permeability, a real issue that can trigger inflammation throughout the body, including the brain, and it can begin as early as infancy.
Everyday stress, infections, toxins, and processed foods packed with dyes and emulsifiers can break down the gut lining. Over time, this kind of dysfunction can lead to migraines, autoimmune flares, mood struggles, and even behavior issues in kids. Sometimes it shows up in subtle ways, especially in picky eaters.
Many don’t realize that inflammation from poor gut health can lead to brain fog, ADHD-like symptoms, or mood issues. And while food changes help, the real key is calming the nervous system first — making change easier and cravings weaker. Small steps like switching oils or choosing better bread matter. But healing behavior also requires re-teaching kids, not just fixing biology.
Don’t assume “this doesn’t apply to me.” If there's any immune dysfunction or neuroinflammation, gut health is part of the picture — and often the best place to begin.
Mast Cell Activation Syndrome (MCAS) keeps the body on high alert, often triggered by stress, poor sleep, or chronic illness. Commonly linked to Lyme, mold, and PANS/PANDAS, it causes overactive mast cells to release inflammation, leading to symptoms like rashes, gut issues, mood changes, and food sensitivities. Healing requires retraining the brain, calming the nervous system, and breaking this reactive cycle.
While medications like antihistamines and supplements can help manage MCAS, the focus should also be on identifying the root causes, triggers, and ongoing mediators, such as environmental factors like mold. Foods also play a big role; highly processed foods, gluten, dairy, soy, and sugar can all worsen gut and neurological health. These foods, especially in their genetically modified forms, cause inflammation and contribute to leaky gut.
The key is to focus on real, whole foods, avoid processed foods and inflammatory oils, and reduce exposure to chemicals and GMOs. Simple, clean nutrition supports both gut health and overall recovery. Healing involves not only addressing the physical aspects of the body but also nurturing mental and emotional health.
The way we process stress, our sleep patterns, and how we care for ourselves play critical roles in managing MCAS and other inflammatory conditions. Calming the nervous system through strategies like bodywork, stress management, and identifying specific triggers can make a significant difference in recovery.
Understanding the connection between food, stress, and inflammation helps promote lasting health. If your child has restrictive eating habits, start by co-regulating and gradually replacing unhealthy, processed foods that cause sugar highs and crashes.
Changing eating habits takes time. For Dr. Hartman and his wife, they took two years to transform their diet. So his advice is to be patient, focus on small changes like cooking from scratch, and remember: progress is key, not perfection.
Early Signs of Gut Issues in Children
Early signs of gut issues in children often appear as mood changes, inconsolable crying, rashes, eczema, respiratory infections, foul-smelling stool, constipation, and trouble sleeping. As kids grow, problems like asthma, eczema, behavior changes, and more restricted eating habits can emerge.
Poor diet, chronic infections, and harmful fats gradually break down gut health and impact the brain. Many parents aren't aware that common treatments like MiraLAX can disrupt the microbiome and cause long-term issues.
Children’s health can improve dramatically when the root causes are addressed. Supporting nervous system regulation, removing harmful oils, improving nutrition, and being mindful of environmental stressors can lead to quick and lasting changes.
Since kids today are showing signs of gut dysfunction at younger ages, it’s important for parents to trust their instincts, look beyond surface symptoms, and prioritize true healing rather than quick fixes.
Practical Tips for Improving Gut Health
To truly support children's gut health, it helps to begin even before conception by strengthening the mother's nutrient intake with clean proteins, healthy fats, and rare earth minerals such as strontium, silica, and lithium. In some traditional cultures, women were intentionally nourished months in advance with nutrient-dense foods like organ meats to prepare their bodies for healthy pregnancy.
Today, these essential minerals are often missing from modern diets, but one practical way to bring them back is by making bone broth. Using organic bones, filtered water, a splash of apple cider vinegar, and basic vegetables, you can prepare a mineral-rich broth at home. For convenience, an Instant Pot works well to extract nutrients in just three hours instead of the usual twelve.
In addition to diet, daily nervous system regulation plays a key role in supporting gut health. Just ten minutes a day of calming activities like deep breathing, meditation, or gentle stretching can reduce stress and improve gut function. This is especially important for those with autism, OCD, or PANS/PANDAS.
Supporting gut health is more than just taking probiotics. Some people, especially kids with SIBO, may react poorly, making spore-based probiotics or fermented foods better options. Real foods like homemade sauerkraut deliver prebiotics, probiotics, and postbiotics together, while colorful fruits and vegetables feed good gut bacteria and lower inflammation.
Using food as medicine remains the foundation for improving gut health. Homemade alternatives, such as brain-friendly mayonnaise made with pasture-raised eggs, healthy oils, and fresh ingredients, replace harmful, inflammatory processed foods.
Additionally, diets like GAPS, though restrictive, can help identify food triggers in sensitive individuals by focusing on simple, nourishing meals. Real, colorful, and fermented foods, combined with nutrient-dense homemade staples, create an environment where the gut and brain can heal and thrive naturally.
The Role of Mitochondrial Toxicity in Gut Health
Many psychiatric medications and antibiotics, commonly used to treat conditions like ADHD, can harm gut health and damage mitochondria over time.
Around 30% of pharmaceuticals are known to be mitochondrial toxicants, causing nutrient deficiencies and setting the stage for worsening health problems years down the line. While medications may offer short-term benefits, they often create long-term gut and brain dysfunction, leading to a cycle of adding more medications to manage new symptoms. Mitochondrial toxicity, therefore, plays a major role in the gradual breakdown of both gut function and overall health.
True healing requires addressing root causes, not just managing symptoms with pills. Sustainable improvement comes from making steady changes in diet, environment, and lifestyle.
Instead of looking for quick fixes, the focus should be on small, consistent actions that support mitochondrial and gut health. Over time, these changes can lead to meaningful improvements in behavior, energy, and resilience.
Whether it’s cleaning up your environment, reducing processed foods, or looking into mitochondrial-safe supplements, every step counts. Remember—gut healing isn't about perfection; it’s about progress.
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