Gut-Brain Axis: How Nervous System Dysregulation Fuels SIBO Symptoms
Ever feel like your gut just didn't get the memo?
You're eating clean, avoiding gluten and dairy like the plague, and popping the "right" supplements… you even went through an elimination protocol, but you're still bloated, gassy, or running to the bathroom (or worse—not going at all).
Maybe you've been diagnosed with SIBO (Small Intestinal Bacterial Overgrowth) or IBS (Irritable Bowel Syndrome). Maybe your food sensitivities are multiplying faster than you can say "elimination diet."
Here's the truth no one talks about enough:
It's not just about what you eat. It's about how your body and your nervous system feel when you eat.
That's right. The state of your nervous system could be the reason your gut hasn't fully healed, no matter how many gut protocols, probiotics, or low-FODMAP recipes you've tried.
In this blog post, I'm going to dive deep into the gut-brain connection, how nervous system dysregulation fuels gut dysfunction, and the often-overlooked role of the vagus nerve in digestive health. Most importantly, you'll learn what you can do about it—starting today.
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The gut-brain axis
Imagine your gut and brain as two best friends texting each other all day long. That constant stream of messages—about hunger, stress, emotions, and immune responses—is called the gut-brain axis. And the phone line they use? That would be your vagus nerve.
The vagus nerve is like your body's internal Wi-Fi network—an information superhighway that connects your brainstem to your heart, lungs, and digestive tract. It tells your stomach to release acid, your intestines to move food along, and your immune system to stay calm.
Here's the kicker: This communication is bi-directional. That means…
- A stressed-out brain can send danger signals to the gut, slowing digestion and triggering inflammation.
- And a troubled gut—say, with dysbiosis (imbalance between the beneficial and pathogenic gut flora), SIBO, or leaky gut—can send distress signals back to the brain, contributing to anxiety, brain fog, and mood swings.
This is why you can't "out-supplement" or "out-diet" chronic gut issues if your nervous system is stuck in fight-or-flight mode. Healing your gut starts with helping your body feel safe.
What really happens when you're stuck in survival mode
Let's take a moment to talk about stress, not just the obvious kind like deadlines or family drama, but the sneaky, chronic type your body may have normalized over the years.
- Emotional stress (e.g., work pressure, grief)
- Past trauma (e.g., violence, accidents)
- Chronic illness (e.g., autoimmune diseases, infections)
- Physiological stress (e.g., nutrient deficiencies, over-exercising, undereating, physical injury)
- Environmental stress (e.g., noise, pollution, mold exposure)
They all keep your body in a sympathetic state, or "fight or flight." When you're in that mode, digestion is the last thing your body wants to deal with.
Think about it: if a lion is chasing you, your body doesn't care about digesting your kale salad—it wants to run.
Here's what stress does to your digestion
Slows gut motility:
When you're calm and relaxed, your digestive system creates rhythmic contractions called the migrating motor complex (MMC) that get activated between meals in a fasted state. Think of it like a gentle wave that sweeps through your intestines, keeping things moving and clean.
But under chronic stress, these contractions slow down—or stop altogether. Food lingers too long in the small intestine, giving bacteria time to ferment it and multiply where they shouldn't be. That's how Small Intestinal Bacterial Overgrowth (SIBO) starts.
Lowers stomach acid & digestive enzyme output:
Stress diverts your body's energy to muscles (for fighting or fleeing), not digestion. One of the first casualties? Stomach acid and digestive enzymes.
Without enough stomach acid:
- Food doesn't break down properly.
- Proteins ferment instead of digesting—leading to bloating, gas, and discomfort.
- You can't absorb essential nutrients like vitamin B12, iron, magnesium, and zinc.
- And you lose your body's natural first line of defense against harmful microbes.
Low enzymes = poor breakdown of carbs, fats, and proteins → indigestion and malabsorption. And guess who loves leftover, undigested food? Yep, bad gut bugs.
Weakens the gut lining:
Your gut lining is like a finely tuned security system, only allowing in nutrients and keeping out unwanted intruders. But when you're in a constant state of stress, the tight junctions in your gut wall loosen. This condition is known as intestinal permeability or leaky gut.
What slips through? Undigested food particles, toxins, and pathogens. Your immune system sees these as threats and mounts an inflammatory response, leading to:
- Food sensitivities
- Chronic inflammation
- Autoimmune flares
- Histamine reactions
This is the reason why people under stress suddenly "react" to foods they've eaten for years.
Disrupts the gut microbiome:
Your microbiome—the trillions of bacteria living in your gut—is incredibly sensitive to stress. Under normal conditions, beneficial bacteria help regulate digestion, mood, and immunity.
But stress is like a natural disaster in the gut:
- It kills off beneficial strains of Lactobacillus and Bifidobacteria
- It allows opportunistic pathogens (like Candida, H. pylori, or certain Clostridium species) to take over
- It increases gut pH, which changes the environment and allows the "bad gut bugs" to thrive
The result? More bloating, poor nutrient absorption, and increased inflammation. Plus, an imbalanced microbiome means your gut can't support hormone detox or healthy neurotransmitter production.
Dysregulates neurotransmitters:
You've probably heard that your gut is your "second brain"—and it's true. Your gut bacteria help produce critical neurotransmitters, like:
- Serotonin (mood stabilizer and feel-good hormone—90% is made in the gut!)
- Dopamine (motivation and reward)
- GABA (calm, anti-anxiety)
When your gut is inflamed or out of balance, the production of these chemical messengers drops. That's why so many people with digestive issues also struggle with:
- Anxiety
- Depression
- Brain fog
- Sleep issues
- Emotional ups and downs
It's not "just in your head"—it's happening in your gut-brain axis.
The Vagus nerve: your digestive system's on/off switch
Think of your vagus nerve as the thermostat of your nervous system. It helps you shift from fight-or-flight (sympathetic) into rest-and-digest (parasympathetic). If your vagus nerve isn't working properly—what we call low vagal tone—you'll struggle to stay in that rest-and-digest state long enough for healing to happen.
Low vagal tone can lead to:
- Bloating and gas
- Constipation or diarrhea
- Slow gastric emptying
- SIBO relapses
- GERD or acid reflux
- Anxiety, brain fog, and insomnia
- Histamine intolerance or MCAS symptoms
- Poor heart rate variability (HRV)
- Trouble swallowing or shallow breathing
If you've ever felt like your body is "stuck in high alert," or you can't relax no matter how tired you are, chances are your vagus nerve needs support.
Nervous system dysregulation and SIBO
SIBO (Small Intestinal Bacterial Overgrowth) happens when bacteria that should stay in the large intestine start growing in the small intestine. Since the small intestine is designed for nutrient absorption—not fermentation—this overgrowth can cause major digestive issues.
Common SIBO symptoms:
- Bloating (especially after eating)
- Gas and distension
- Diarrhea, constipation, or both
- Nutrient deficiencies (B12, iron, fat-soluble vitamins)
- Abdominal pain and discomfort
- Brain fog and fatigue
- Muscle and joint pain
- Skin issues (eczema, rosacea, acne)
SIBO isn't just about bacteria. It's about what allowed those bacteria to overgrow in the first place.
And one of the biggest root causes? Impaired gut motility, which is often driven by a dysregulated nervous system.
When you're stuck in sympathetic dominance:
- Your migrating motor complex (MMC)—the "housekeeping wave" that cleans your small intestine—doesn't work properly.
- Your body underproduces digestive juices, leading to poorly digested food that ferments and feeds the wrong bugs.
- You lose natural antibacterial defenses like stomach acid and bile.
So, yes—herbs, antimicrobials, antibiotics, and diets can help temporarily. But if you want lasting SIBO relief? You have to support your nervous system and vagal tone.
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How to heal the nervous system-gut axis naturally
The best part? You don't need a fancy device or endless supplements to start improving your nervous system health.
Here's what I recommend to my gut clients:
Vagus nerve activation techniques
These help shift your body into parasympathetic mode (rest-and-digest):
- Deep belly breathing (especially 4-7-8 breathing before meals)
- Gargling or humming—stimulates throat muscles linked to the vagus nerve
- Cold exposure (like splashing your face with cold water)
- Singing or chanting (yes, it works!)
- Meditation and loving-kindness practices
- Yoga and tai chi—especially poses like legs up the wall
Somatic & mind-body healing
You can't "think" your way out of chronic stress. You have to feel your way out. These help discharge stored stress from the body:
- Somatic tracking and interoception (noticing internal sensations)
- EFT tapping (Emotional Freedom Techniques)
- TRE (tension and trauma release exercises)
- Grounding and time in nature
- Co-regulation with others (safe connection is healing)
Brain retraining & nervous system programs
If your symptoms are deeply entrenched, consider working with structured programs like:
- Nerva App – a gut-directed hypnotherapy program clinically proven for IBS/SIBO relief
- The Gupta Program – rewires limbic and vagus nerve dysfunction
- Primal Trust™ – blends somatics, trauma work, and nervous system education for deep healing
I am currently participating in the Primal Trust program, learning to regulate my nervous system better, process and release stored emotions, and ultimately cultivate a sense of peace and resilience in my life. This is also something I regularly recommend to my clients.
Primal Trust Academy offers a comprehensive approach to help individuals release stuck emotions and regulate their nervous systems. This can be particularly beneficial for those dealing with the long-term effects of trauma.
Here's how the academy can support you:
- Somatic practices: Techniques that focus on body awareness and movement to release stored tension and emotions.
- Mind-body integration: Programs that integrate mindfulness, meditation, and breathing exercises to calm the nervous system.
- Emotional processing: Guided exercises to help recognize, process, and release trapped emotions.
- Community support: Access to a supportive community where you can share experiences and gain insights from others on a similar journey.
Nervous system-supporting eating tips
- Eat in a calm, seated environment. No phones, no rushing.
- Take 3–5 deep breaths before each meal.
- Chew your food thoroughly (20–30 times per bite!).
- Don't eat in fight-or-flight—go for a quick walk or breathwork break if needed.
- Don't under-eat—undereating = a major stressor for the nervous system.
You're not broken—your body's just trying to protect you
Let me remind you of something important:
If your body is stuck in stress mode, it's not because you've failed.
It's because your body is trying to protect you.
Maybe from trauma. Maybe from overexertion. Maybe from years of ignoring symptoms because life demanded it.
But guess what? You can teach it something new. You can help it feel safe. You can restore trust between your brain and your gut.
Healing your gut means healing all of you.
If you're tired of the food fears, bloating, and constant worry over what's going to trigger your next flare, know this:
Healing your gut isn't just about food. It's about feeling safe in your body.
Healing starts with the nervous system.
So next time you're tempted to add another supplement or cut another food, pause and ask yourself:
- Am I actually feeling safe and calm when I eat?
- Is my nervous system supported in this healing process?
Because once your body feels safe, everything else—digestion, hormones, energy, mood—starts to fall into place.
Disclaimer:
The information provided on this site is for educational purposes only, is not intended as medical advice, and does not claim to diagnose, heal, treat, or cure any conditions Always consult with a healthcare professional before starting any dietary regimen, supplement, or lifestyle changes, especially if you have underlying health conditions or are taking medication.
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