Gut Dysbiosis and Strategies for Healing the Gut

This is the fourth post in a series on gut dysbiosis. This post covers gut dysbiosis and strategies for healing the gut.

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Who is Betsy Leighton?

I’m a writer, blogger, and healer dedicated to helping individuals reconnect with their innate peace and wholeness by healing nervous system dysregulation. My personal experience with chronic illness called Mast Cell Activation Syndrome (MCAS) shapes my work, and my content offers tools to empower those with chronic illness to improve their well-being and take charge of their health.

I created the Sacred Self-Healing Method and am a trained and certified Safe and Sound Protocol provider, an author, blogger, and A Course in Miracles Teacher. I hold a Master of Divinity in Spiritual Counseling and am a trained spiritual mentor, with certificates in sound healing, aromatherapy, nutrition, and Sacred Deathcare. I offer a self-study certificate program in the Sacred Self-Healing Method, provide spiritual counseling and coaching, courses, and supported subscriptions for the Safe and Sound Protocol.

What is MCAS?

Mast Cell Activation Syndrome (MCAS) is a chronic condition that affects all organ systems. It can cause severe, disabling symptoms every day, including potentially fatal anaphylaxis.

The common triggers for MCAS are infections, toxic exposures including mold exposure and EMFs, trauma, concussions, and stress.

MCAS often occurs with other chronic conditions like Ehlers-Danlos Syndrome (EDS) and Postural Orthostatic Tachycardia Syndrome (POTS). Managing MCAS is challenging because many healthcare providers are unaware of it, and diagnostic tests can be unreliable. Treatments include antihistamines and mast cell stabilizers in the form of medications and supplements, along with avoiding triggers. Check out this post on managing MCAS.

What is gut dysbiosis?

Gut dysbiosis is an imbalance in the community of microorganisms that live in the digestive tract, where harmful or inflammatory microbes become too dominant and beneficial microbes decline. In a healthy gut, diverse bacteria help digest food, support the immune system, maintain the gut lining, and produce important compounds like vitamins and short-chain fatty acids. When this balance is disrupted—due to factors like antibiotics, chronic stress, infections, poor diet, or toxin exposure—the gut becomes more prone to inflammation, reduced digestive efficiency, and increased permeability (“leaky gut”). This imbalance can contribute to digestive symptoms, immune dysregulation, and a variety of chronic health conditions.

Healing the Gut

Another piece of the puzzle in healing the gut dysbiosis that was exacerbating my MCAS was that an unhealed gut, or a leaky gut, was a site of constant mast cell activation. Within your abdomen lies an expansive intestinal lining, covering an area of over 4,000 square feet. When functioning optimally, this lining acts as a protective barrier, regulating the absorption of substances into the bloodstream. However, an unhealthy gut lining can develop cracks or holes, allowing partially digested food, toxins, and microbes to infiltrate the underlying tissues. A compromised gut lining can trigger changes in gut flora (normal bacteria) and inflammation, potentially leading to various digestive issues and systemic health problems.

Leaky gut

We all have some degree of leaky gut, as this barrier isn’t completely impermeable (and isn’t supposed to be!). Some of us may have a genetic predisposition and may be more sensitive to changes in the digestive system. Emerging evidence suggests that the standard American diet, which is low in fiber and high in sugar and saturated fats, may contribute to the development of leaky gut. Heavy alcohol use and stress also seem to disrupt this balance.

Supergut diet

My osteopathic doctor recommended that I try following the Supergut diet in March of 2024 to begin healing my gut. The Super Gut Diet focuses on gut health and includes a four-week plan to reprogram the microbiome, restore health, and stabilize weight. The Super Gut diet is based on Dr. William Davis’ book of the Same Name, which advocates using healing foods to restore the balance of gut microbes, such as homemade probiotic-rich yogurt and fermented foods like sauerkraut.

Yogurt offers several advantages over supplements for introducing probiotics into your gut. Firstly, yogurt aids in the survival of bacteria throughout the stomach and small intestine, ensuring their viability longer. Secondly, probiotic capsules can be costly, whereas culturing yogurt from probiotic supplements allows for the growth of significantly more probiotic units as they multiply within the yogurt culture. You can make months (or years!) worth of probiotic-rich yogurt from one bottle of 30 capsules that would be used up in a month. Additionally, research suggests that consuming probiotics in yogurt form can be more effective than solely relying on supplements.

Homemade probiotic yogurt

After researching different strains of probiotics, I began making a type of yogurt from a strain known to help crowd out gut parasites (everyone has them). This yogurt was a game-changer for my health. My sleep, gut health, mental health, and even my libido improved once I started eating this yogurt.

I’d had significant struggles with intestinal parasites, and I know that parasite infections play a role in MCAS. In early 2024, I underwent a month-long parasite treatment, hoping to knock back the parasite colonization of my gut. But as always, I noticed the uncomfortable signs of parasites returning after a few weeks.

My osteopath wondered if Davis’ probiotic yogurt might help my MCAS, and I found the notion of healing the gut with probiotic yogurt intriguing, so I began experimenting with different probiotic strains. I first tried the three probiotic strains Davis suggests for getting SIBO under control, and I had some moderate improvement in symptoms.

Beneficial microbes

I found evidence that specific strains of probiotics, including Bacillus sp. and Enterococcus faecium, have the potential to help eliminate parasite infections while simultaneously strengthening the immune system’s response to them. I read studies on the complex relationship among diet, gut bacteria, and parasitic infections.

Probiotics, particularly Bacillus sp. and Enterococcus faecium, have various inborn mechanisms to eliminate parasitic infections and help maintain intestinal health.

I found a brand of probiotic called AOR Probiotic-3, which contains both Bacillus sp. TO-A and Enterococcus faecium T-110 probiotics, as well as Clostridium butyricum TO-A. Clostridium butyricum helps the body to make butyrate, also known as Butyric acid. I’ve mentioned before that Butyrate helps with the sulfur cycle, too.

Many people with MCAS can’t tolerate dairy, especially yogurt, because it is fermented, so I needed to start very slowly and experiment until I could tell I was tolerating it. I’ve found that the long culture time for homemade probiotic yogurt denatures the milk, so I don’t have a problem with it. Using A2 milk is also helpful because it contains a form of protein that is easier to digest.

Digestive enzymes

Yet another piece of my gut-health puzzle was digestive enzymes, and once I added one capsule of Healthy Gut Holozyme, my body was able to digest my food better, and I reacted less to MCAS food triggers.

Nervous system retraining

The vagus nerve is the longest in the human body, running from the cranium, around the digestive system, and to the lungs. It passes through the neck via the vocal cords and around the major organs: the liver, spleen, pancreas, heart, and lungs.

The vagus nerve is an integral part of the parasympathetic nervous system, which is key to our capacity to rest, digest, calm, and soothe. Having a healthy vagus nerve enables you to adapt to stressful situations, helps regulate cortisol and blood sugar levels, and is associated with feeling more relaxed. A healthy vagus nerve indicates a higher vagal tone, whereas a low vagal tone is associated with many maladies, including heart disease, diabetes, mood disorders, inflammatory conditions, and autoimmune dysfunction.

The vagus nerve is central to addressing MCAS. Eighty percent of the vagus nerve is sensory, meaning it senses what is going on in your body, and it sends information back to the brain about what it finds. And twenty percent of its function is as a motor nerve.

Vagus nerve injury can occur from actual injury to the nerve (such as with a concussion or other physical injury), from contracting an infection (such as Epstein-Barr), or from exposure to mold or other toxic environmental agents. The vagus nerve is surrounded by mast cells and is constantly in communication with them via its receptors, collecting information about the body’s safety.

Feedback loop

If the vagus nerve sustains an injury, it signals to the brain that the body is not safe. And as long as it senses the effects of injury, infection, inflammation, or exposure, it will continue to send signals to the brain that the body is not safe. If the injury to the vagus nerve goes untreated, it will continue to send a signal that the body is in danger. The mast cells respond to the threat by activating wherever it is perceived — whether in the gut, tissues, or elsewhere — further signaling the vagus nerve that the body is not safe. And on and on.

So you can see how there is a feedback loop via the vagus nerve: when it senses an attack on the body, it signals the brain that a problem exists. At the same time, mast cells compound the problem by overreacting and releasing mediators that further inflame the body, further notifying the vagus nerve that the body is not safe.

The vagus nerve has branches to all major organ systems, and it is meant to balance the nervous system. When you have this chronic perceived threat to the body at the neurological level, it can contribute to dysautonomia, postural orthostatic tachycardia syndrome (POTS), slowed intestinal motility, heart palpitations, dysregulation of blood pressure and temperature, neuropathy, paresthesias, and many other conditions.

So, how do you heal your vagus nerve?

There are many easy ways to increase vagal tone, including:

Mindful breathing techniques. Just five minutes a day stimulates the vagus nerve.
Alternate nostril breathing.
Chanting, humming, singing, laughing, and talking.
Gargling.
Loving-kindness meditation.
Washing your face with cold water.

However, for someone with extreme MCAS, these measures may not be enough to heal the vagus nerve. My favorite strategy for healing the vagus nerve is the Safe and Sound Protocol.

Healing the vagus nerve

One of my favorite tools for vagus nerve healing is the Safe and Sound Protocol. It’s an app on your phone that you use alongside a trained therapist.

These treatments help retrain the brain through the principle of neural plasticity. You can actually change the way your brain functions by developing new ways of thinking about stressful triggers, and these techniques teach you how to do that.

MCAS practitioners will tell you that the more ways you can gently address vagal and limbic system dysfunction at once, the better. However, because MCAS patients are so sensitive, you may need to start slowly and often adjust the program(s) to suit your particular sensitivities.

Gut dysbiosis and non-native EMFs

The relationship between gut dysbiosis and non-native EMFs (electromagnetic fields from devices like Wi-Fi routers, cell phones, Bluetooth, and smart meters) centers on how EMFs can influence the body’s stress response, immune activity, and microbial environment. Although research is still emerging, several studies suggest that non-native EMFs may create low-level biological stress by increasing oxidative stress and altering cellular signaling. Because the gut microbiome is highly sensitive to changes in the body’s internal environment, this stress can make it harder for beneficial bacteria to thrive while giving more resilient, potentially harmful microbes an advantage.

Non-native EMFs may also affect gut health indirectly through their impact on the nervous system. The enteric nervous system mainly controls the gut and communicates closely with the vagus nerve. EMFs appear to influence autonomic nervous system balance by shifting the body toward sympathetic dominance (“fight-or-flight”). When this happens, digestion slows, stomach acid production can drop, and motility becomes irregular—all factors that encourage dysbiosis. A stressed nervous system can also weaken the gut barrier, increasing permeability and destabilizing the microbiome.

Additionally, EMFs can alter immune regulation, and because 70% of the immune system is located in the gut, even small shifts can influence microbial balance. An overactivated immune system may trigger inflammation in the gut lining, disrupt microbial communities, and worsen existing dysbiosis. This becomes especially relevant in chronic illnesses like MCAS, where the gut and immune system are already more reactive. While EMFs are not typically the sole cause of dysbiosis, they can act as an additional stressor, lowering microbial resilience and making gut imbalances more pronounced. Reducing unnecessary EMF exposure—especially during sleep—may help support a healthier, more stable gut environment.

Red light therapy heals the gut

Use Red Light Therapy — Red light therapy can be helpful for MCAS because it supports cellular healing and reduces inflammation in a gentle, non-triggering way. The wavelengths used in red and near-infrared light help stabilize mitochondria, improve energy production, and calm overactive immune responses—all of which can reduce the baseline reactivity that drives mast cell symptoms. Red light also enhances microcirculation and tissue repair, which may ease pain, skin issues, and gut irritation common in MCAS. Because it acts through cellular and nervous system regulation rather than chemical ingredients, many people with sensitivities find it a soothing, well-tolerated, supportive therapy.

Butyrate

Taking supplements that aid in healing concussions, such as turmeric or curcumin, and Tributyrin-X, my diverticulitis pain immediately resolved. I read that many types of butyric acid on the market don’t reach the colon, where it is needed, because it’s absorbed earlier in the gut. Tributyrin-X is specially formulated so that it is not absorbed until it reaches the colon. And I learned that, in addition to healing and sealing the colon’s walls, Tribut yrin-X is also helpful for a host of other issues.

Low-dose naltrexone

Naltrexone is a drug that was developed to help people get off opioid drugs. Therapeutic dosages for naltrexone are around 50 mg or more, and are administered several times a day. In contrast, Low Dose Naltrexone (LDN) is a tiny dose of Naltrexone, often between 0.1 and 14 mg, and it is usually used once per day. Low Dose Naltrexone, which has been shown to:

Support healthy weight management.
Heal leaky gut & tight junction support
Regulate gut speed (motility)
Promote microbiome diversity
Help healthy mucosal layers
Support proper immune system activity
Support healthy mast cells and histamine levels

Factors in healing gut biosis

I’ve written a five-part series on the factors at work in healing gut dysbiosis, including:

Concussions
SIBO
Circadian health
Sulfur Cycle Dysfunction

Check out those linked posts for more information.

The bucket theory

The bucket theory simplifies understanding symptom reactions with MCAS. Imagine your body as an empty bucket you don’t want to overflow. Reactions to various stimuli fill the histamine bucket at different rates, forming the total histamine level (how full your bucket is). More histamine means more symptoms. By managing triggers, reducing exposures, and taking medications and supplements, you can control your bucket’s level.

Know your typical symptom progression

Understanding your symptom progression during a flare is key to developing your rescue plan. This post discusses how to recognize symptom progression so you can be prepared to address them.

Get my free ebook, symptom log, and meal plan!

Want a tool to easily track your symptoms?

Check out these circadian health tools!

I’m an affiliate with Bon Charge, a company that makes tools for circadian health, and you can receive 15% off your order with my coupon code BETSYL.

Bon Charge offers tools such as yellow– and red-tone blue-blocking glasses, red light therapy devices, PEMF mats, infrared saunas, and EMF-blocking products.

Sign up for the SSP!

I’ve found the Safe and Sound Protocol (SSP) to be the most helpful bottom-up healing strategy if your nervous system has been overloaded with toxic exposures, including mold or non-native EMFs, chronic infections, concussions, stress, or trauma. The SSP is a passive listening therapy that helps heal nervous system dysregulation. Many people with MCAS and other chronic conditions have nervous system dysregulation stemming from infections, toxic exposures, concussions, and trauma. The SSP is an easy-to-use app that lets you listen to specially filtered music for 30 minutes each day as part of a 5-hour cycle. Studies show the SSP has a profound effect on mental health and chronic conditions. Here’s a short podcast describing the Safe and Sound Protocol.

You can sign up for the SSP here!

Heal your mind!

While the SSP is a bottom-up, somatic therapy for healing the nervous system, the Sacred Self-Healing Method I offer is a top-down nervous system-healing modality that focuses on cognition, attention, perception, and emotion, using the mind’s higher functions. The SSP and the Sacred Self-Healing Method complement each other and together produce lasting results. Here’s a short podcast on my self-healing practice.

I provide one-on-one in-person and remote chronic illness and caregiver coaching, as well as Sacred Self-Healing Sessions based on the Sacred Self-Healing Method, a proven, novel co-creative healing modality detailed in my Books.

Order my books!

Here’s a short podcast highlighting my five books.

My latest book, Living In The Light: Healing with Forgiveness, Sound, and Light, is all about the tools that have been most helpful for me to heal: forgiveness, sound, through nervous system retraining using the Safe and Sound Protocol, and light, through entraining my circadian rhythm with the energy of the sun. Living In The Light is available here!

Rocks and Roots chronicles my solo backpacking journey on the Superior Hiking Trail and my efforts to overcome nervous system dysregulation, gut dysbiosis, and Mast Cell Activation Syndrome symptoms to complete the 328-mile hike successfully.

The Sacred Self-Healing Method ebook is available here and in most ebook retailers!

The Sacred Self-Healing Workbook is available for purchase here!

Betsy’s first book, Sacred Self-Healing: Finding Peace Through Forgiveness, is available here

Companion Recordings

The companion audio recordings of chants, guided meditations, and sound healing demonstrations that accompany the Sacred Self-Healing Method are available for free on my YouTube channel here

What do you think?

I’d love to have your reply below!

Disclaimer

The preceding material does not constitute medical advice. This information is for information purposes only and is not intended to be a substitute for professional medical advice, diagnosis, cure, or treatment.