Mold series · The mechanism

Mold & mycotoxins: how they affect the body

Mold illness isn’t an allergy — it’s an inflammatory cascade. Here’s how mycotoxins move through Dr. Shoemaker’s Biotoxin Pathway, why the immune system never stands down, and what the most common indoor molds actually do.

Key takeaways
Mold illness is CIRS — in genetically susceptible people (HLA-DR), mycotoxins aren’t cleared, so inflammation flares and never resolves.
Mycotoxins bind cell receptors and trigger inflammatory markers (TGF-β1, MMP-9, IL-1B, PAI-1) that can damage tissue in every organ system.
Low MSH is a hallmark — driving poor sleep, chronic pain, gut malabsorption, recurrent infection, and thirst/ADH issues.
Four common indoor molds — Fusarium, Aspergillus, Penicillium, and Stachybotrys (black mold) — carry distinct mycotoxins and risks.
In this article
1. Moving through the Biotoxin Pathway
2. Their impact on the body
3. Harm everywhere & immune dysregulation
4. Specific molds & their mycotoxins

If you read our earlier piece on mold illness, you may remember that it’s also called CIRS (Chronic Inflammatory Response Syndrome) — a condition that occurs when someone susceptible to mold has had significant exposure. A significant exposure can mean a large exposure over a short time, or small exposures over a longer period. Those who are genetically susceptible — carrying HLA-DR genes — are most affected.

With mold exposure comes exposure to mycotoxins — the toxic chemicals present on mold spores and fragments of mold or fungus. They can travel through the air and be inhaled, be ingested in mold-contaminated food, or enter through skin contact with contaminated surfaces. Dr. Ritchie Shoemaker, a research pioneer in biotoxin-related illness, described the process the bodies of CIRS patients go through: the Biotoxin Pathway.

1. Moving through the Biotoxin Pathway

All cells have a surface receptor, which binds to other molecules and communicates to the cell what to do. When a person has significant mycotoxin exposure, the mycotoxins begin to bind to surface receptors of nearly every kind of cell in the body. This sets off multiple inflammatory pathways, including the production of pro-inflammatory cytokines and markers like TGF Beta-1, MMP-9, IL-1B, and PAI-1.

These inflammatory pathways have an important role — addressing and healing insults to the body — and ideally they do their job and then calm down to restore homeostasis. In mold illness, the immune system flares up but never calms down. Over time, that persistent inflammation can begin to cause tissue damage.

The cascade, step by step
01
Exposure. Mycotoxins enter by inhalation, ingestion, or skin contact.
02
Receptor binding. Mycotoxins bind surface receptors on nearly every cell type.
03
Inflammatory cascade. Cytokines and markers (TGF-β1, MMP-9, IL-1B, PAI-1) surge.
04
No off-switch. In susceptible people, inflammation never resolves — and tissue damage follows.

2. Their impact on the body

This consistent inflammation can do the following:

  • Cytokines bind cell receptors, which can increase clot formation and arterial blockage and affect the hypothalamus — producing headaches, muscle aches, unstable temperature, and difficulty concentrating.
  • Elevated cytokines attract white blood cells that restrict blood flow and reduce tissue oxygen. Vascular endothelial growth factor (VEGF), which normally builds blood vessels, drops — causing fatigue, shortness of breath, and muscle cramps.
  • People with HLA genotypes may develop other inappropriate immune responses — antibodies that lead to gluten sensitivity, ulcerative colitis, blood-clotting conditions, and more — continually re-activating inflammation.

The low-MSH cascade

The body also suffers from low production of MSH (melanocyte-stimulating hormone), a group of hormones made by the pituitary gland, hypothalamus, and skin cells. Low MSH can cause:

  • Low melatonin — and the sleep problems that follow
  • Reduced endorphin production — leading to chronic, sometimes unusual, pain
  • Gut malabsorption, which further weakens the immune system

White blood cells can also lose regulation of the cytokine response, resulting in more infections and slower recovery. Reduced MSH lets staph bacteria persist in the biofilms of mucous membranes — and that bacteria further lowers MSH, creating a vicious cycle of poorer sleep, chronic pain, gut malabsorption, and more infections. Low MSH can also decrease pituitary production of antidiuretic hormone (ADH), leading to thirst, frequent urination, low blood pressure, low blood volume, and static-electricity shocks.

3. Harm everywhere & immune dysregulation

Mycotoxins don’t discriminate against any one part of the body. They can target all organ systems — nervous, cardiovascular, respiratory, digestive, urinary, immune, endocrine, reproductive, and integumentary (skin, hair, nails).1 And because the inflammatory process can become cyclical — from repeated exposure, or because mycotoxins aren’t cleared in those with the HLA genotype — the immune system becomes dysregulated. That dysregulation can create:

  • Lack of tolerance to the environment — multiple chemical sensitivities, and increasing reactions to foods (food sensitivities)
  • Lack of self-tolerance — leading to autoimmunity (destruction of self tissues)
  • Hormonal disturbances — blood-sugar dysregulation, altered thyroid patterns, and a host of other imbalances

4. Specific molds & their mycotoxins

As you learn about mold, it helps to know the major categories, what they look like, and where they’re found. This isn’t exhaustive, but these are some of the more prolific.

Fusarium

A large genus of fungi — many species are harmless decomposers, but some are pathogens and serious agricultural threats. Indoors, Fusarium can grow quickly, cause structural damage, and make you sick; it often appears black. It enters or grows on humans via inhalation, contact with contaminated surfaces, or contaminated food. Some cause superficial or local infections treatable with an antifungal; others cause disseminated infections that travel from their origin (respiratory tract, GI tract, skin) to other parts of the body — more serious, and more likely in those with a compromised immune system.2

Aspergillus

Found on dead leaves, compost, grains, and other foods — often black on the surface and whitish or yellow underneath. An estimated 25% of the world’s agriculture is contaminated with mycotoxins, often from Aspergillus molds.3 Its most common mycotoxins are aflatoxins; much exposure traces back to diet (corn, peanuts, certain tree nuts), though there’s mounting evidence that inhalation of Aspergillus and its mycotoxins contributes to symptoms and disease,4 and its spores can be carried inside and grow indoors.5

For those with chronic lung problems or weak immune systems, aspergillosis is a concern. There are three types — pulmonary, allergic bronchopulmonary, and invasive:6

  • Pulmonary aspergillosis — often no early symptoms; later, coughing (sometimes with mucus or blood), wheezing, fever, chest pain, and difficulty breathing.
  • Allergic bronchopulmonary — an allergic reaction inflaming the lungs and airways; more common with asthma, cystic fibrosis, or bronchiectasis.
  • Invasive aspergillosis — the most severe; the infection travels from the lungs into the bloodstream to organs like the kidneys, liver, skin, or brain. Most likely in weakened immune systems, and if untreated can be fatal.

Penicillium

Found in air, soil, and homes, with over 300 species — usually recognized by green, blue-green, or gray-green color (sometimes white, yellow, or pinkish). Penicillium gave us the antibiotic penicillin. Inhaling its spores can cause respiratory issues (coughing, shortness of breath, chronic sinusitis, sneezing, runny nose); people may also experience rashes, hives, or throat swelling, and mycotoxins from some species can damage internal organs.7

Stachybotrys chartarum

Known as black mold or toxic black mold. Occasionally found in soil or grain, but most often indoors in water-damaged buildings — it grows easily on high-cellulose material like fiberboard, gypsum board, and paper. It requires constant moisture, which is a major reason to check for structural leaks and keep humidity at 50% or below. Though causation is hard to prove, many symptoms have been associated with high exposure:8

Nasal irritation, burning, congestion
Cough & wheezing
Chest tightness & dyspnea
Headache & lightheadedness
Irritability
Sleeping difficulty
Concentration problems & mental fatigue
Alopecia & rashes
Eye irritation

While these descriptions cover some of the better-known conditions, the mycotoxins from any of these molds can set off the inflammatory cascade above — especially in susceptible individuals with the HLA gene. Those are the people who end up with mold illness after exposure.

When to seek medical care
Aspergillosis and invasive fungal infections can become serious, particularly for those with chronic lung disease or a weakened immune system. If you have persistent cough with blood, high fever, chest pain, or difficulty breathing, seek medical care promptly — don’t wait to rule out mold first.
What this may mean
If mold illness or another mold-associated condition sounds like your experience, you are not alone — and this inflammatory cascade is exactly what a proper work-up looks for. Understanding the mechanism is the first step; the next is removing the exposure and calming the pathway. See how CIRS is diagnosed and how to address mold at home.

Common questions

What is the Biotoxin Pathway?
Described by Dr. Ritchie Shoemaker, the Biotoxin Pathway is the process the body of a CIRS patient goes through after mycotoxin exposure. Mycotoxins bind to cell surface receptors and set off multiple inflammatory pathways — producing cytokines and markers like TGF Beta-1, MMP-9, IL-1B, and PAI-1. Normally inflammation resolves; in mold illness it flares and never calms, leading to tissue damage.
Why do only some people get mold illness?
People who are genetically susceptible — carrying certain HLA-DR genes — can't clear mycotoxins efficiently, so the inflammatory process becomes cyclical and the immune system stays dysregulated. Others exposed to the same mold may clear it and recover; the genetically susceptible develop chronic mold illness (CIRS).
What is MSH and why does it matter in mold illness?
MSH (melanocyte-stimulating hormone) is made by the pituitary, hypothalamus, and skin. In mold illness MSH drops, which lowers melatonin (poor sleep), reduces endorphins (chronic pain), and causes gut malabsorption. Low MSH also lets staph persist in mucous-membrane biofilms — further lowering MSH in a vicious cycle — and can reduce ADH, causing thirst, frequent urination, and low blood pressure.
Which molds are most dangerous indoors?
Four common categories are Fusarium, Aspergillus, Penicillium, and Stachybotrys chartarum (black mold). Stachybotrys grows on water-damaged, high-cellulose materials and needs constant moisture; Aspergillus can cause aspergillosis in vulnerable people. All can carry mycotoxins that trigger inflammation in genetically susceptible individuals.
References (8) ▾
  1. Occupational Safety and Health Administration (OSHA). Preventing mold-related problems in the indoor workplace. https://www.osha.gov/sites/default/files/publications/preventing_mold.pdf
  2. Nucci M, Anaissie E. Fusarium infections in immunocompromised patients. Front Cell Infect Microbiol. 2018;8:60. https://www.frontiersin.org/articles/10.3389/fcimb.2018.00060/full
  3. Aspergillus, aflatoxins, and the global agricultural mycotoxin burden. Clin Ther. 2018. https://www.clinicaltherapeutics.com/article/S0149-2918(18)30229-7/pdf
  4. Kwon-Chung KJ, et al. Aspergillus species in indoor environments and their possible occupational and public health hazards. PubMed Central. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490296/
  5. Post-flood occurrence of mycotoxin-producing Aspergilli in indoor environments. Int J Environ Res Public Health. 2020. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7711759/
  6. Aspergillosis and Aspergillus-associated disease. Toxins (Basel). 2013;5(4):605-617. https://www.mdpi.com/2072-6651/5/4/605
  7. Saghir SA, Bancroft J, Ansari RA. Molds and mycotoxins indoors II: toxicological perspective. Arch Clin Toxicol. 2025;7(1):8-40. https://www.probiologists.com/article/molds-and-mycotoxins-indoors-ii-toxicological-perspective
  8. Health effects associated with Stachybotrys chartarum exposure. PubMed. https://www.ncbi.nlm.nih.gov/pubmed/24946038
This article is educational and is not medical advice, diagnosis, or treatment. Mold-related illness should be evaluated with a qualified practitioner.
An immune system that won’t stand down needs a reason.

Mold illness is findable and treatable. We work up the inflammatory picture — and the exposure behind it — instead of chasing symptoms one at a time.

Request a Consultation