CIRS and GI issues: How Mycotoxins affect gut health

Expert Recap: CIRS and GI issues

Your intestinal wall is not a simple barrier. It’s a layered system; a combination of physical, chemical, immunological, and microbial systems all working together to let nutrients in and keep harmful things out. Mycotoxins compromise every layer of that system, causing measurable structural and functional changes to your intestinal architecture.

Treating CIRS properly through the Shoemaker Protocol often leads to spontaneous gut improvement. Especially when we raise MSH (Melanocyte-Stimulating Hormone) levels. This is because MSH directly affects intestinal permeability, gut motility and the stability of the gut microbiome.

Why Mycotoxins Often Trigger Digestive Issues

*Note: this blog was written by me, Mark Volmer. All spelling mistakes, misquotes, errors, and omissions are my own doing. It is not AI generated.*

If you’ve been living with chronic gut issues like bloating, diarrhea, constipation, IBS, 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.

Every functional medicine doc says that all issues start in the gut. But CIRS is a different beast. I often tell patients that CIRS is like the upside down world. Things that make sense in the non-CIRS world don’t work in the CIRS-world. If you have CIRS, your gut is one of those areas where conventional wisdom doesn’t work.

I’ll start this blog with a bold statement:

Your gut isn’t the root problem. CIRS is.

More specifically, low levels of MSH are likely driving a lot of your GI symptoms. More on this later.

Chronic Inflammatory Response Syndrome (CIRS), which you likely know is triggered by exposure to molds, mycotoxins, or other biotoxins, can profoundly disrupt gut integrity, microbiome balance, detoxification, and motility. And unless the underlying biotoxin-driven inflammation is addressed, gut protocols don’t work.

This is why, in my clinical experience, treating CIRS properly through the Shoemaker Protocol often leads to spontaneous gut improvement. Especially when we raise MSH (Melanocyte-Stimulating Hormone) levels.

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.

What Mycotoxins Do to your Gut Lining

The research here is fairly clear. A 2020 review published in Toxins documented the specific mechanisms through which common mycotoxins (including deoxynivalenol, aflatoxins, and ochratoxin A) damage the gut. They:

degrade epithelial cells,
reduce the expression of tight junction proteins,
thin the mucosal layer, and
trigger inflammation that destabilizes intestinal immunity. (Source)

Tight junctions are the protein “clasps” that hold intestinal cells together and regulate what moves through the wall. When mycotoxins break those down, the result is increased intestinal permeability. Something you probably know as leaky gut. Once the barrier is compromised, partially digested food particles, bacteria, and more mycotoxins can travel into other body systems, driving inflammation well beyond the gut itself.

If you’ve ever done an IgG food sensitivity panel and had reactivity to just about every food listed, it’s not a food issue. It’s a compromised gut barrier.

A related review in the International Journal of Molecular Sciences confirmed this across multiple mycotoxin types and multiple species models, concluding that mycotoxin-induced barrier disruption results in both bacterial translocation and activation of systemic and local immune responses. (Source)

This is not a subtle effect. These are measurable structural and functional changes to your intestinal architecture. And these changes don’t resolve simply by leaving a moldy building or taking a binder. Nor is it as simple as supplementing gluatamine and cod liver oil.

Mycotoxins Disrupt your Microbiome

Gut dysbiosis is not just about eating too much sugar or taking antibiotics. Mycotoxin exposure is a significant and under-recognized driver of microbiome disruption.

A comprehensive review in Toxins (2020) examined the bidirectional relationship between mycotoxins and gut microbiota. The conclusion is important: mycotoxin exposure depletes beneficial species and creates conditions where opportunistic bacteria and fungi can expand. The review notes this disruption is linked to bacterial translocation and the onset of chronic inflammatory disease. (Source)

A 2018 review in Frontiers in Microbiology reinforced this, summarizing evidence that mycotoxins produce measurable alterations in the intestinal epithelium and microbiota. This includes reduced biodiversity and increased susceptibility to pathogenic colonization. (Source)

The result is a gut that can’t defend itself. Beneficial species like Lactobacillus and Bifidobacterium decline. Short-chain fatty acid production drops, which affects the intestinal lining and the regulation of inflammation. Opportunistic organisms move in to fill the gap.

This is where SIBO, SIFO, fungal overgrowth, and recurrent parasitic infections enter the picture. Not as separate bad luck, but as predictable consequences of a gut that has lost its microbial defence.

Remember, these “infections” are caused by a lack of beneficial bacterial species and a decline of SCFA (short-chain fatty acids). More anti-microbial protocols ARE NOT the answer. Antimicrobials will destroy even more of the Lactobacillus and Bifidobacterium species in your gut, which then perpetuates your GI issues.

To be clear, I’m not opposed to using antimicrobials. In fact, I often think them to be necessary. But like most things with CIRS, proper sequencing is essential.

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

I see this pattern every week in the clinic. A new patient who has already treated SIBO two or three times. Then they develop SIFO. Then a parasitic infection clears, but SIBO comes back. Each treatment works temporarily, then unravels.

The reason isn’t bad luck, poor compliance, or improper treatment. It’s that the underlying conditions driving those overgrowths were never corrected. Remember, sequencing is essential in CIRS treatment. The right intervention at the wrong time doesn’t work.

In CIRS, the biotoxin inflammatory pathway creates near-perfect conditions for gut dysfunction:

Motility slows, which encourages bacterial buildup in the small intestine.

Mucosal immunity weakens, reducing the gut’s ability to resist colonization by pathogens.

Bile flow and antimicrobial defenses are impaired. Chronic inflammation disrupts digestion and absorption at every level.

A 2023 review in Microorganisms examining the relationship between gut dysbiosis and conditions like SIBO, SIFO, and intestinal methanogen overgrowth found that increased intestinal permeability and LPS-driven inflammation are consistently tied to microbial overgrowth. (Source)

Treating each overgrowth without addressing the root cause is like draining a flooded room without turning off the tap.

Ready to start real recovery?
Book a consult with our team today.

The MSH Connection: The Missing Piece Most Clinicians Overlook

MSH is the most important hormone you and your functional medicine doctor have never heard of. Of all the biomarkers disrupted in CIRS, MSH (melanocyte-stimulating hormone) is the one most directly tied to gut health.

MSH is a neuropeptide derived from POMC (proopiomelanocortin). It regulates immune balance, gut motility, mucosal integrity, appetite, pain regulation, sleep, and inflammation control. Research shows that low MSH is a defining feature of CIRS. A review published in PMC in 2024 confirmed that reduced MSH consistently appears in patients with chronic biotoxin-related illness, and that it functions as a master controller within the neuroimmune regulatory network. (Source)

What does low MSH mean for the gut?

A 2017 study in PLOS ONE tested this directly. Using human Caco-2 intestinal epithelial monolayers, researchers found that alpha-MSH protects the intestinal barrier against cytokine-induced damage, preserving tight junction protein expression (ZO-1 and claudin-4), reducing intestinal permeability, and suppressing NF-kB activation and downstream inflammatory cytokine production.

Basically, when MSH is present, the intestinal barrier can fight inflammation. Without MSH, the intestinal barrier breaks down. (Source)

Research has also established MSH’s role in gut motility. A review in the Journal of the Chinese Medical Association documented that alpha-MSH influences small intestinal transit and colonic motility through central melanocortin receptor signaling.

Meaning that low MSH in CIRS impairs the gut’s ability to move contents through at a normal rate. Slowed motility is one of the primary drivers of SIBO. (Source)

The clinical implication is significant. Without adequate MSH:

The gut lining is more vulnerable,
Motility is impaired,
The microbiome is harder to stabilize.

No amount of probiotics, antimicrobials, or dietary interventions can fully compensate for a depleted neuroimmune regulatory signal.

Why I Recommend Treating CIRS Before Gut-Only Protocols

The analogy I use with patients: trying to heal the gut before treating CIRS is like painting a wall while water is still pouring through the ceiling. The work won’t hold.

Here’s the science behind that.

The biotoxin inflammatory pathway in CIRS remains active until CIRS is treated. That means inflammation keeps the microbiome destabilized. Antimicrobial and antifungal protocols produce temporary results because the conditions that allow overgrowth are never resolved. Low MSH means the gut lining cannot repair itself regardless of diet, binders, or supplements.

CIRS patients also commonly react severely to gut protocols: nausea, increased bloating, worsening brain fog, fatigue, anxiety. These reactions soften significantly once the underlying inflammatory cascade is addressed and MSH begins to normalize.

The Shoemaker Protocol, the only treatment for CIRS with documented clinical efficacy in the peer-reviewed literature, addresses CIRS systematically:

Removes biotoxin exposure,
Clears biotoxins,
Corrects inflammatory biomarkers, and
Restores neuroendocrine balance including MSH.

A 2024 literature review confirmed that across 13 identified treatment studies, the Shoemaker Protocol was the only approach with evidence of reversing the underlying physiological dysregulation of CIRS. (Source)

As MSH and cytokine patterns normalize through this process, what I observe clinically is:

Gut permeability decreases.
Motility normalizes.
Microbiome diversity increases.
Bile flow and digestive enzyme function improve.
Food sensitivities soften.
SIBO and SIFO relapse rates drop considerably.

The gut becomes a system that can actually respond to treatment.

A Practical Roadmap

Here’s the sequence I recommend for patients who present with both CIRS and significant GI issues.

Step 1: Evaluate for CIRS. Use symptom cluster analysis, exposure history, VCS testing, and laboratory biomarkers through a trained provider. Don’t skip this step. Treating chronic gut symptoms as a standalone problem without ruling out CIRS is one of the most common reasons patients cycle through protocols without resolution.

Step 2: Treat CIRS first. Follow the Shoemaker Protocol in sequence: remove exposure, bind biotoxins, correct biomarkers, restore neuroimmune balance. MSH restoration is particularly critical for gut outcomes.

Step 3: Reassess gut function. Once inflammation has dropped and MSH has stabilized, many gut symptoms resolve without additional intervention. Reassess what actually remains before layering in new protocols.

Step 4: Targeted gut support where needed. This may include probiotics (when tolerated), digestive enzyme support, mucosal repair nutrients, motility agents, and antimicrobials if truly necessary. The difference at this stage: your body can actually tolerate and respond to these interventions.

Step 5: Long-term maintenance. Ongoing exposure avoidance, supporting circadian rhythm, nourishing microbiome diversity, and mitochondrial health support are the foundation of sustained recovery.

Ready to start real recovery?
Book a consult with our team today.

Final Thoughts

If you’ve been treating your gut over and over without lasting results, the missing variable may not be the protocol. It may be that the system driving the problem was never addressed.

CIRS-driven inflammation, low MSH, disrupted mucosal immunity, and impaired motility create a setup for chronic digestive symptoms that gut treatments alone cannot resolve. When you treat the root cause (low MSH levels) the gut often heals in ways that years of GI protocols couldn’t produce.

That’s not guesswork. That’s what the physiology predicts, and what I see in the clinic.

If this is your first introduction to CIRS, be sure to check out my other posts to further your CIRS knowledge:

Mark Volmer has attained the highest level of Shoemaker Protocol certification, and is one of only two of Canada’s Shoemaker Protocol practitioners. The Shoemaker Protocol is the only scientifically proven method of treating CIRS.