The Experience Miracles Podcast

You’re Not Just Anxious—Your Gut Is Too

Mar 4, 2025

Anxiety, Gut Health, and the Nervous System

Episode 83 — Experience Miracles Podcast | Host: Dr. Tony Ebel, DC, CACCP — Pediatric Chiropractor & Founder of PX Docs | Published: March 4, 2024 | Duration: 57 min

Guest: Dr. Meg Mill, PharmD — Functional Medicine Practitioner & Host of the A Little Bit Healthier Podcast

Key Takeaways

  • Chronic gut issues and anxiety in children are not separate problems. They are driven by the same underlying cause: nervous system dysregulation that keeps the body locked in sympathetic dominance, shutting down the digestive cascade before it can start.
  • Stress — not just food choices — is what disrupts the microbiome. When a child is stuck in fight-or-flight, the body stops producing stomach acid, bile, and digestive enzymes, which leads directly to dysbiosis, leaky gut, and eventually neuroinflammation.
  • 90% of serotonin being in the gut is commonly misunderstood. Dr. Meg Mill clarifies that this serotonin primarily controls digestive motility, not mood — making nervous system regulation, not serotonin supplementation, the correct target for anxiety.
  • The blood-brain barrier is most permeable at the brainstem level, near the vagus nerve — the exact area most affected by birth trauma and spinal subluxation, creating a direct pathway from gut permeability to brain inflammation.
  • Dr. Meg Mill’s 3R Protocol — Regulate, Repair, Rewire — is a sequenced approach that brings the body’s physiology back into balance before attempting to address higher-level symptoms like anxiety, mood, or behavior.

Why Your Child’s Anxiety and Gut Issues Are the Same Problem

Anxiety and gut problems in children share a single root cause: a nervous system that cannot shift out of fight-or-flight. When the autonomic nervous system is stuck in sympathetic dominance, the body treats every moment as a threat — and digestion shuts down as a result. No stomach acid. No bile release. No digestive enzymes. Food reaches the small intestine incompletely broken down, feeding opportunistic bacteria, triggering dysbiosis, and eventually driving intestinal permeability (leaky gut). Particles that escape into the bloodstream signal the immune system, which creates more biological stress — and the cycle deepens.

Dr. Meg Mill, a functional medicine practitioner with a doctorate in pharmacy, calls this the anxiety-digestion loop: anxiety drives gut dysfunction, and gut dysfunction drives anxiety. The vagus nerve is the physical highway connecting these two systems, running signals bidirectionally between the gut and the brain. When vagal tone is poor — often due to birth trauma, chronic stress, or spinal subluxation at the brainstem — those signals become distorted, amplifying both the digestive and mental-emotional symptoms families are trying to treat.

The practical implication for parents: dietary changes and supplements address real problems, but they work on a system that is already compromised at the foundation. Until the nervous system is regulated, the gut cannot absorb nutrients efficiently, the blood-brain barrier remains permeable, and healing stays partial. Both Dr. Ebel and Dr. Mill have independently found that addressing nervous system regulation first — then layering in nutrition, supplementation, and targeted therapies — produces results that diet alone cannot.

How Dr. Meg Mill Found the Nervous System Before Anyone Was Talking About It [00:00:00 – 00:09:00]

Dr. Tony Ebel, DC, CACCP: Parents, if your child struggles with gut issues, constipation, reflux, food sensitivities, and at the same time deals with anxiety, emotional outbursts, or trouble focusing — you are not imagining things. The gut and the brain are in constant communication, and if one is struggling, the other is too.

Most doctors treat these issues entirely separately, and they miss the bigger picture. That’s why so many families feel stuck in an endless cycle of diet changes, supplements, and medications that never fully work on either the gut issues or the mental-emotional challenges. Today we’re bringing in Dr. Meg Mill — a functional medicine expert who knows how crucial it is to address the nervous system foundationally for full healing of the gut and everything connected to the gut-brain connection.

Dr. Meg Mill: My journey into the nervous system actually started with my own health. My background is a PharmD — a doctorate in pharmacy. I was a clinical pharmacist. I knew protocols, I knew drugs, I knew why we were prescribing them. And yet I was jumping from specialist to specialist saying, something is wrong with me. I had terrible gut issues, terrible anxiety, difficulty sleeping. And everyone kept telling me I was fine.

It got to the point where I was having panic attacks. That’s when I decided I had to make a change. I started doing my own research. I eventually went back and got trained in functional medicine, was able to put all the pieces of my own health together — and then I decided I had to change my career and help others do the same.

Dr. Tony: And what a weapon for good you are now. That’s the transformative journey for so many of us as practitioners — you have the very traditional training, the contrast and clarity that brings, and then your own personal journey as the bridge. It fosters so much more trust with patients, because you’ve run into the same dead ends they have.

So walk me through your healing sequence. You mentioned nervous system first, then microbiome, then the vagus nerve came back into focus. Did you tap into the nervous system before diet and nutrition?

Dr. Meg Mill: Yes. I would say I was working on the nervous system first. I started by asking, what can I do to regulate my nervous system? I had to shift into the parasympathetic nervous system more. I worked on limbic retraining — neuroplasticity, vagal nerve toning, somatic work. And then I got into the microbiome and healing my gut. The vagus nerve connection came after that. It was a progression — each piece rolling into the next.

Dr. Tony: That’s actually better than if you’d remembered the paper. What you just described was your healing sequence. And what’s fascinating is that in 2024, when our patients arrive to us, they’ve typically gone in the opposite order: first they’ve exhausted conventional medicine, then they’ve gone deep into nutrition and supplementation, and the nervous system is the last thing they discover. 15 years ago, patients hadn’t even gotten to the nutrition conversation. Now they’ve been there for years and they’re still not better — because no one’s had the nervous system conversation with them.

“Until the nervous system is regulated, the body stays in a stress cycle that no supplement or diet can override. Nervous system first, nutrition second — that’s the sequence that actually produces healing.” — Dr. Tony Ebel, DC, CACCP

Why Stress Breaks Digestion Before Food Even Enters the Picture [00:09:00 – 00:25:00]

Dr. Meg Mill: I want to start with the autonomic nervous system because everything connects back to it. We have our rest-and-digest system — the parasympathetic nervous system — and our fight-or-flight system — the sympathetic nervous system. Ideally, we live mostly in the parasympathetic. We should jump into sympathetic for real stressors and then come back down. The problem is most of us — and most kids with chronic health challenges — are living in sympathetic dominance most of the time.

When you’re in sympathetic dominance and you go to eat, your body is still signaling: run from a lion right now. So it doesn’t release stomach acid. It doesn’t release bile from the gallbladder. It doesn’t release digestive enzymes from the pancreas. Digestion requires all three of those things happening in sequence. When they don’t, food reaches the small intestine in larger particles than normal, and opportunistic bacteria feed on those particles. You get dysbiosis. Dysbiosis drives intestinal permeability — leaky gut. And once things start getting through the gut lining into the bloodstream, that signals the immune system, which creates more biological stress. Stress begets stress. It’s its own perfect storm.

Dr. Tony: That’s exactly right — and this is what perplexes so many parents. They come into the holistic functional world, they change the diet, add supplements, maybe even do some targeted detox protocols, and they wait for the anxiety and the gut problems to resolve. But even on a perfect clean diet, if the sympathetic nervous system is still running the show, the body cannot digest, absorb, or assimilate what they’re eating. The deepest layer is the neurological stress cycle, not the diet.

Dr. Meg Mill: Exactly. And I always tell people: we work simultaneously on testing, on lifestyle, on diet — and on the nervous system. Because if you’re just living in a stress response all the time, you’re perpetuating the situation regardless of how clean your plate is.

Dr. Tony: Every single teen I see struggling with anxiety and depression — their gut and digestion has been a mess their entire life. It’s not a coincidence. When you really understand the neurology of why this happens, you can start to see the blueprint for how to actually heal it.

“Even on a perfect clean diet, if the sympathetic nervous system is still running the show, the body cannot absorb or assimilate what you’re eating. The deepest layer is the neurological stress cycle — not the food.” — Dr. Tony Ebel, DC, CACCP

The Anxiety-Digestion Loop: How Gut Bacteria Signal Your Brain [00:25:00 – 00:38:00]

Dr. Meg Mill: The vagus nerve is the key here. It’s connecting the gut and the brain — running from the brainstem down into the gut, sending signals in both directions. Those signals are called afferent and efferent. The vagus nerve is telling your gut to digest, and your gut is telling your brain how it feels. That’s the biological basis of butterflies in your stomach. It’s real, bidirectional crosstalk.

When we have dysbiosis — opportunistic bacteria overgrowth in the gut — those bacteria signal things we don’t want to happen. They release compounds like lipopolysaccharides into the bloodstream, which trigger an immune response. That immune response is a stress signal. Then, because the gut lining is permeable, these compounds can cross into the blood and eventually cross the blood-brain barrier — causing neuroinflammation. So what starts in the gut, through this chain of events, is now affecting the brain.

One more piece that often gets misunderstood: 90 percent of the body’s serotonin is in the gut. But that serotonin is primarily driving digestive motility — how food moves through the gut — not mood. So when a gastroenterologist prescribes an SSRI for gut pain, the patient thinks, I’m not here for depression. But the doctor is responding to this gut-brain crosstalk. The problem is the SSRI doesn’t address the root. What actually needs to happen is creating the ability to self-regulate the nervous system and restore proper communication so the body can digest, so dysbiosis resolves, so leaky gut closes.

Dr. Tony: That serotonin clarification is so important, and very few people are making it. They’re telling parents the right fact — 90 percent of serotonin is in the gut — but without explaining that it’s serving the digestive system, not your child’s emotional state. Parents walk away thinking the gut is the source of their child’s mood problems, and they miss the nervous system piece that connects it all.

And here’s what we see clinically: when we start with neurologically-focused chiropractic and target the autonomic pathways first, the very first thing we see improve is digestion. Constipation resolves. Motility comes back online. That’s the body responding to nervous system regulation before we’ve even addressed the higher-level challenges.

Dr. Meg Mill: Yes. And when we support nervous system regulation — whether through vagal nerve toning, somatic work, or neurologically-focused chiropractic — digestive motility does start to improve early. It’s one of the more measurable and immediate changes we see.

The Blood-Brain Barrier, Subluxation, and Why Chiropractic Gets to the Root [00:38:00 – 00:46:00]

Dr. Tony: One thing that’s often overlooked in the gut-brain conversation is the blood-brain barrier. And here’s something most people don’t know: the blood-brain barrier is most permeable at the brainstem level — right around where the vagus nerve originates.

So when we have gut permeability and dysbiosis, the chain of events I described earlier — compounds crossing into blood, then crossing into the brain — happens most easily at the brainstem. And when there is subluxation at that level, particularly from birth trauma, there’s often physical stress to the tissues in that area. Even by design, the blood-brain barrier near the vagus nerve is already slightly more permeable than elsewhere. Add mechanical stress from subluxation and you’ve added another layer. That’s why restoring normal brainstem function through specific chiropractic adjustments has such a direct effect on neuroinflammation and immune responses that seem completely unrelated to the spine.

Dr. Meg Mill: When I look at blood-brain barrier integrity with a patient, I’m looking at inflammation and immune response as the primary levers. I approach each person as a whole — nervous system, gastrointestinal system, hormones, immune system — and I’m asking, what is going on with this specific person? Why is their body out of balance? The approach is individualized because the why behind it differs. Cookie-cutter protocols often fail exactly because the underlying cause varies between people.

Dr. Tony: And that individualization is a non-negotiable for us too. Healing is a dance between the practitioner and the patient, not a protocol applied uniformly. What we’ve found is that for most of our patients — especially teens with anxiety — the number one complaint is gut issues and sleep issues. So we’ve designed our adjusting protocols to target neurodigestion, sleep, and respiration first. When we get those systems moving in the right direction, it builds trust and makes the higher-level work — the anxiety, the behavior, the emotional regulation — much more accessible.

“The blood-brain barrier is most permeable at the brainstem level — right where the vagus nerve originates. Subluxation and birth trauma at that location creates a direct pathway from gut inflammation to neuroinflammation.” — Dr. Tony Ebel, DC, CACCP

Dr. Meg Mill’s 3R Protocol: Regulate, Repair, Rewire [00:46:00 – 00:57:00]

Dr. Tony: All right, I have to have you walk us through the 3R protocol. Because the terms you use — Regulate, Repair, Rewire — are something I’ve seen very few people put together this clearly. Take us through it.

Dr. Meg Mill: The first R is Regulate. We need to bring your body back into balance — your immune system, your digestive system, your hormones. If your body is out of balance, it can’t absorb the nutrients you’re eating or respond to the therapies you’re doing. So we regulate everything that needs to come back into a state where it’s working optimally.

The second R is Repair. There’s often damage that needs to be addressed. We repair the gut lining. We repair the blood-brain barrier. We address the imbalances that have accumulated — whether that’s dysbiosis, intestinal permeability, or chronic inflammation.

The third R is Rewire. This is what needs to happen at the nervous system level. I use a three-pronged approach: neuroplasticity work, including limbic retraining and thought reframing; vagal nerve toning to directly strengthen vagus nerve function; and somatic work to help the body release stored stress patterns. We need to build new neural pathways and help the nervous system find its way back to parasympathetic regulation.

Dr. Tony: And I’d add one thing to that Rewire phase that we see in clinical practice. When subluxation is stuck at the brainstem and throughout the spinal transition zones — particularly where the neck and shoulders meet, where the upper thoracic meets the esophagus, where the thoracolumbar junction affects the adrenals and intestines — patients often can’t fully access the rewiring work. They try deep breathing and can’t do it. They try neurofeedback or somatic exercises and they can’t go deep enough. They’re breathing through their neck and shoulders instead of their diaphragm.

Once we get 30, 60, 90 days of foundational neurologically-focused chiropractic to release that stuck subluxation and restore normal autonomic signaling, families tell us: now the therapy is working. Now I can actually breathe deeply. Now my kids can access the tools. The 3R protocol can go to the moon when the central conduit — the spine and brainstem — is cleared first.

Dr. Meg Mill: That makes complete sense. And I think it’s wonderful that you’re explaining what you’re doing and why to patients. They need to understand the reason behind the sequence. That’s what builds trust and keeps them in care long enough to see real healing.

Dr. Tony: Exactly. And that’s been chiropractic’s biggest challenge. We’ve allowed ourselves to be put in this mechanical, musculoskeletal box. Early in my career, a neuropsychologist who was running one of the first Dr. Amen clinics told me: every chiropractor on earth massively impacts and changes the nervous system and the brain. And then he paused and said, problem is, only about 20 percent of them know that’s actually happening.

You cannot work with the neck and the central conduit and not change neurology. The nervous system conversation is the one the world is desperate to hear. And that’s why having you on here, Meg — talking about microbiome, digestion, and functional medicine through the lens of a nervous system — is something families need.

“Once we get 30 to 90 days of foundational chiropractic to release stuck subluxation, families tell us: now the therapy works. Now I can actually breathe. The 3R protocol goes to the moon when the central conduit is cleared first.” — Dr. Tony Ebel, DC, CACCP

Frequently Asked Questions

Why does my child have both gut problems and anxiety at the same time?

Gut problems and anxiety in children almost always share the same root cause: nervous system dysregulation. When the body is stuck in sympathetic dominance (fight-or-flight), it shuts down the digestive system — stopping stomach acid, bile, and enzyme production. This creates dysbiosis, leaky gut, and eventually neuroinflammation that worsens anxiety. The gut and brain communicate constantly through the vagus nerve, so dysfunction in one directly worsens the other.

Can stress cause constipation and digestive issues even with a clean diet?

Yes. Dr. Meg Mill explains that stress shuts down the entire digestive cascade before food is even absorbed. Without stomach acid, bile, and digestive enzymes functioning properly, food is incompletely broken down. This feeds opportunistic bacteria, disrupts the microbiome, and can cause constipation, bloating, and reflux — regardless of how clean the diet is. Addressing nervous system regulation is required before dietary changes can fully take effect.

What is the gut-brain axis and how does it affect anxiety?

The gut-brain axis refers to the bidirectional communication network between the gut and the brain, primarily run through the vagus nerve. The gut sends signals to the brain, and the brain sends signals to the gut — constantly and simultaneously. When gut bacteria (the microbiome) become imbalanced, opportunistic bacteria release compounds that trigger immune responses, cross into the bloodstream, and can even breach the blood-brain barrier, causing neuroinflammation that drives anxiety, mood instability, and behavioral challenges.

What is Dr. Meg Mill’s 3R Protocol?

Dr. Meg Mill’s 3R Protocol is a sequenced approach to healing chronic gut and nervous system issues: Regulate (bring the immune, digestive, and hormonal systems back into balance), Repair (heal the gut lining, blood-brain barrier, and damaged tissues), and Rewire (rebuild nervous system function through neuroplasticity, limbic retraining, vagal nerve toning, and somatic work). The sequence matters — attempting to rewire without first regulating and repairing produces limited results.

Why isn’t an SSRI the right answer for gut-related anxiety?

While 90% of the body’s serotonin is produced in the gut, that serotonin primarily controls digestive motility — not mood. Prescribing an SSRI addresses a symptom of the gut-brain communication breakdown without fixing the root cause: a dysregulated nervous system that can’t shift out of fight-or-flight. As Dr. Mill explains, the actual need is to restore the nervous system’s ability to self-regulate so the body can digest properly, resolve dysbiosis, close intestinal permeability, and stop the cascade that is driving both the gut symptoms and the anxiety.

How do I find a PX Docs practitioner who addresses the nervous system and gut health together?

Visit the PX Docs Directory to find a Neurologically-Focused Chiropractor near you. PX Docs practitioners are trained to assess and address the autonomic nervous system using INSiGHT Scans and neurologically-focused adjusting protocols — targeting the specific spinal regions that affect digestion, sleep, respiration, and immune function before moving to higher-level brain-based challenges.

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