CIRS and Gut Health: Why Mycotoxins Often Trigger Digestive Issues

If you’ve been living with chronic gut issues — bloating, diarrhea, constipation, SIBO that keeps coming back, food reactions, abdominal pain — you’re not alone. Many of the patients I work with have tried multiple gut protocols, yet the symptoms return the moment they stop antimicrobials or antifungals.

Here’s the part most people never get told:

For many, the gut isn’t the root problem.

CIRS is.

Chronic Inflammatory Response Syndrome (CIRS) — triggered by exposure to molds, mycotoxins, or other biotoxins — can profoundly disrupt gut integrity, microbiome balance, detoxification, and motility. And unless the underlyingbiotoxin-driven inflammation is addressed, gut protocols rarely stick.

This is why, in my clinical experience, restoring CIRS physiology often leads to spontaneous gut improvement — especially when we raise MSH (Melanocyte-Stimulating Hormone) levels using the Shoemaker Protocol.

In this guide, I’ll walk you through:

• how mycotoxins damage the gut

• why CIRS often triggers SIBO, SIFO, parasites, and infections

• why treating CIRS first leads to better outcomes

• how MSH drives gut integrity — and why restoring it heals digestion

• what the research shows

• a clear roadmap for healing

As always:

This is educational, not medical advice. Always work with a qualified practitioner.

Mycotoxins Disrupt Gut Health at Multiple Levels

Mycotoxins from water-damaged buildings are not passive irritants — they are biologically active compounds that affect nearly every layer of digestive function.

Mycotoxins damage the gut lining

Research shows that common mycotoxins (like ochratoxin, aflatoxin, trichothecenes):

• break down tight junctions

• increase intestinal permeability (“leaky gut”)

• damage epithelial cells

• disrupt mucosal immunity

🧬 Evidence:

• Mycotoxins impair epithelial integrity and increase permeability.

• They also cause shifts in gut microbiota and inflammatory signaling.

This alone can trigger symptoms like:

• gas and bloating

• diarrhea or alternating bowel patterns

• abdominal pain

• food reactions

• fatigue after meals

Mycotoxins create microbiome chaos

Mycotoxins reduce beneficial species and support opportunistic microbes, creating:

• dysbiosis

• decreased diversity

• impaired nutrient absorption

• disrupted detox signaling

This is where SIBO, SIFO, fungal overgrowth, parasites, and bacterial infections often enter the picture.

Why CIRS Often Looks Like SIBO, SIFO, or Chronic Gut Infection

Gut symptoms are often misdiagnosed as “IBS,” or treated as standalone infections.

But with CIRS, the deeper issue is the immune and neuroendocrine dysregulation that makes the gut unable to defend itself.

CIRS drives the perfect conditions for overgrowth:

1. Slowed motility → encourages SIBO/SIFO

2. Weak mucosal immunity → encourages parasites + bacterial colonization

3. Low bile flow → reduces antimicrobial defense

4. High inflammation → impairs digestion + absorption

Clinical pattern I see constantly:

Someone has:

• SIBO

• then SIFO

• then parasites

• then another SIBO recurrence

They treat each one…

But nothing holds.

That’s because the underlying biotoxin inflammation hasn’t been addressed.

When we correct the CIRS physiology — especially restoring MSH — the gut finally stabilizes.

Why I Recommend Treating CIRS Before Gut-Only Protocols

Trying to fix the gut before fixing CIRS is like…

Trying to paint a wall while water is still pouring through the ceiling.

Here’s why treating CIRS first works better:

You must stop the source of ongoing inflammation

The biotoxin pathway is still active until CIRS is treated.

This means:

• gut protocols only give temporary symptom relief
• antimicrobial/antifungal protocols don’t “stick”
• inflammation keeps the microbiome in chaos

Low MSH prevents gut healing — no matter the diet or protocol

Low MSH is one of the biochemical hallmarks of CIRS.

And MSH is critical for gut integrity. We’ll explore that in depth below.

3.3. Treating CIRS reduces “herx” and reactions

CIRS patients often react severely to gut treatments:

• nausea
• diarrhea
• anxiety
• bloating
• fatigue
• worsening brain fog

Once inflammation and MSH normalize, these treatment reactions soften dramatically.

3.4. The Shoemaker Protocol repairs the foundation

 

CIRS affects multiple systems:

 

immune

hormonal

neurological

metabolic

detoxification

microbiome

mitochondrial

 

Gut protocols can’t fix all of that.

CIRS treatment does.

If you’re new to how CIRS works, you can revisit our foundational blogs:

 

What Is CIRS?

Symptoms of CIRS

Causes of CIRS

How to Treat CIRS

The Role of MSH: The Missing Link Between CIRS and Gut Health

Of all the hormones disrupted in CIRS, MSH (melanocyte-stimulating hormone) may be the most overlooked — and the most important — for gut healing.

MSH is a regulatory hormone produced from POMC (Proopiomelanocortin).

It is crucial for:

• gut barrier integrity
• immune balance
• microbiome regulation
• appetite + motility
• sleep
• pain regulation
• inflammation control

Low MSH = inflamed gut, unstable microbiome, chronic symptoms

This is why people with CIRS often experience:

• severe bloating
• food intolerances
• alternating constipation/diarrhea
• SIBO/SIFO recurrences
• intestinal permeability
• systemic inflammation after meals

🔬 Evidence for MSH’s impact on gut health

Research shows:

POMC cells in the small intestine release α-MSH, which supports mucosal integrity and gut homeostasis.

α-MSH directly influences gut motility and colonic secretion.

Mycotoxin-induced dysbiosis affects MSH-related pathways, reinforcing the inflammation cycle.

Low MSH is strongly associated with CIRS, and restoring it improves multi-system symptoms — including gut symptoms.

Mold/mycotoxins directly disrupt the gut lining and microbiome.

This is why CIRS treatment often restores gut health — even before gut protocols begin.

When MSH rises:

• tight junctions heal
• motility normalizes
• microbiome stabilizes
• inflammation drops
• food sensitivities soften
• infections become easier to treat
• SIBO/SIFO relapse rates drop significantly

This is the physiology patients feel as:

“For the first time in years, my gut feels calm.”

Why the Shoemaker Protocol Often Resolves GI Issues Naturally

The Shoemaker Protocol doesn’t directly “treat the gut.”

But it removes the source of inflammation and restores neuroendocrine balance — especially MSH — which allows the gut to heal.

As MSH and cytokine patterns normalize:

• gut permeability decreases
• immune tolerance improves
• microbiome diversity increases
• digestive enzymes normalize
• bile flow improves
• motility stabilizes
• mucosal immunity strengthens

This is one of the reasons patients with “IBS,” “SIBO,” or “candida overgrowth” often find genuine, lasting relief.

Real Clinical Patterns I See Over and Over

Here’s the typical progression:

Before CIRS treatment:

• SIBO relapse
• SIFO/yeast overgrowth
• parasites
• bloating
• gut protocols don’t hold
• food list shrinks
• reactions to everything increase

After proper CIRS treatment:

• digestion settles
• motility normalizes
• fewer food reactions
• better tolerance for probiotics or antimicrobials
• gut protocols become optional rather than urgent
• deeper infections finally clear
• energy increases
• brain fog fades

The gut is one of the most responsive systems after CIRS physiology stabilizes.

A Practical Roadmap: How to Approach Gut Healing If You Suspect CIRS

Here’s the order I recommend for most people:

Step 1 — Evaluate for CIRS

Use:

• symptom clusters
• exposure history
• VCS testing
• laboratory markers (with a trained provider)

Step 2 — Treat CIRS First

Follow a structured protocol like Shoemaker:

• remove exposure
• binding biotoxins
• correcting biomarkers
• restoring neuroimmune balance
• raising MSH

Step 3 — Reassess Gut Health

Once inflammation drops and MSH stabilizes, most gut symptoms naturally improve.

Then we can identify what still needs attention:

• SIBO
• SIFO
• parasitic infections
• lingering dysbiosis

But now your body can actually handle treatment.

Step 4 — Gentle Gut Support

This may include:

• probiotics (when tolerated)
• enzyme support
• motility support
• mucosal repair nutrients
• antifungals or antimicrobials if truly needed

Step 5 — Long-term Gut and Immune Resilience

• avoid re-exposure
• maintain circadian rhythm
• nourish microbiome diversity
• support mitochondrial health

Final Thoughts: Healing the Gut by Healing the Root

If you’ve been treating the gut over and over with minimal progress — it’s not your fault.

Your body hasn’t been failing.

It’s been overwhelmed.

CIRS-driven inflammation, low MSH, disrupted microbiome, and impaired gut-brain signaling create a perfect storm for chronic digestive symptoms.

When we treat the root cause, not just the gut, people finally get their lives back.

You deserve a gut that feels calm, trustworthy, and resilient again.