The Neurogenesis Issue

Mycotoxins and the Gut: What the Research ShowsThe term "leaky gut" — or more precisely, intestinal permeability — refers to a breakdown in the tight junctions between intestinal epithelial cells. When those junctions loosen, partially digested food particles, bacterial fragments, and toxins can pass into the bloodstream and trigger systemic immune responses. It's an increasingly recognized contributor to chronic inflammation, a precursor to autoimmune conditions, and a factor in a range of health issues.
Several major mycotoxin families have now been studied for their effects on intestinal barrier function. The findings are consistent: these toxins don't just pass harmlessly through the gut. They cause problems.

Aflatoxin (AFB1)
Produced primarily by Aspergillus species on corn, peanuts, tree nuts, some spices, and oilseeds. Aflatoxin is best known as a potent liver carcinogen, but its gut effects are substantial.
Aflatoxin is also immunotoxic, reducing secretory IgA (sIgA) — the front-line antibody of gut mucosal defense. This creates a compounding effect: barrier disruption plus impaired immune surveillance.

Ochratoxin A (OTA)
Produced by Aspergillus and Penicillium on cereals, coffee, dried fruits, wine, and some spices. OTA is primarily nephrotoxic, but recent reviews have shifted attention to its gut effects.
A 2025 review explicitly frames the gut as both a target and modulator of OTA toxicity: OTA disrupts epithelial barrier integrity, increases intestinal permeability, and alters microbiota composition, with downstream metabolic and immune consequences (Więckowska et al., 2025). Sub-chronic low-dose OTA exposure in mice decreases overall microbial diversity, shifts the Firmicutes/Bacteroidetes ratio, and selectively inhibits some Firmicutes — suggesting a direct antimicrobial effect on beneficial taxa (Izco et al., 2021).
Worth noting: most coffee sold in the US has acceptable levels of OTA. But some people may want products as close as possible to mold-free, which is why sourcing and testing matter (more on this below).

Deoxynivalenol (DON) and Other Trichothecenes
Produced by Fusarium on wheat, barley, oats, and other cereals. DON (also called vomitoxin) is acutely notorious for causing flu-like illness with vomiting, diarrhea, headache, and fatigue at high doses. At lower chronic doses, the gut effects are subtler but well-documented.
DON directly injures intestinal epithelial cells, increases tight-junction permeability, disrupts microvilli, and activates TLR4/MyD88/NF-κB-mediated inflammation (Guerre, 2020). Research in animal models demonstrates that gut microbiota dysbiosis induced by DON can transmit toxicity to the liver and trigger systemic inflammation — suggesting the gut is not just a local target but a propagation site for broader harm (Jin et al., 2026).

Zearalenone (ZEA)
Another Fusarium toxin found in corn, wheat, barley, and other grains. ZEA is structurally similar to estrogen and is best known for its endocrine-disrupting effects — including effects on pubertal timing, menstrual irregularities, and fertility. Its gut effects are less publicized but real.
Experimental ZEA exposure inhibits beneficial bacteria including Lactobacillus intestinalis and Clostridium leptum, driving an "unstable" flora associated with IBS (Wang et al., 2018). ZEA also induces mucosal immune activation, inflammatory cytokine production, and histologic damage to the small-intestinal mucosa, including villus injury and epithelial disruption.

Fumonisins and Patulin
Fumonisins (FB1, FB2), produced by Fusarium on corn and corn-based products, are associated with possible cardiovascular effects in animal models, though human data are less established. The practical takeaway: fresh corn is the safest type; the risk concentrates during drying and storage.
Patulin, produced by Penicillium, Aspergillus, and Byssochlamys on apples and apple-based products, causes GI irritation and nausea at higher doses and shows genotoxic and immunotoxic effects in animal studies. It is a concern in juice and applesauce, but also because many of us cut out soft spots instead of discarding the whole apple.

Which foods carry which possible mycotoxins:

• Apples, apple juice, processed fruit products → Patulin
• Cereals (wheat, barley, oats) → Ochratoxin A, DON/Trichothecenes, Zearalenone
• Coffee → Ochratoxin A
• Corn and corn-based products → Aflatoxin, Fumonisins, Zearalenone
• Dried fruits and wine → Ochratoxin A
• Peanuts → Aflatoxin
• Spices and oilseeds → Aflatoxin, Ochratoxin A
• Tree nuts → Aflatoxin

Building Mold vs. Food Mold: Can You Tell the Difference?
One of the most confusing areas for patients (and practitioners) is the interpretation of urine mycotoxin testing. A positive result does not automatically mean the person is living or working in a moldy building. It may simply reflect a diet rich in grains, nuts, spices, and dried fruit.
Functional testing labs (such as MosaicDX MycoTOX) state explicitly that ingestion of contaminated foods and inhalation in moldy buildings are equally valid routes for the same analytes — and that the test cannot separate them. Mold-testing and remediation sources summarizing CDC and academic data note that positive urine findings in otherwise healthy people are expected from normal consumption of these foods, and correlate with high consumption of grains, for example.

Suspect building-related mold exposure when you notice:

• A musty odor in the home, office, or school
• Visible mold growth on walls, ceilings, or under sinks
• History of water damage: roof, window, or plumbing leaks
• Symptoms that clearly improve when leaving the building and return upon re-entry

Before pursuing expensive environmental testing or remediation, it is worth doing a structured dietary trial to reduce mycotoxin-heavy foods and re-test.
On internal colonization: this is possible but not well-proven. Conventional physicians normally diagnose colonization when they see a fungal ball in a body cavity such as the sinuses.

A Category-by-Category Guide to Mycotoxin Risk in Food
CoffeeCoffee is a frequent concern because green coffee beans can harbor ochratoxin A during post-harvest drying, especially in humid climates with poor processing controls. However, most coffee sold in the US tests below detection limits for OTA.
If you already use an organic, small-batch, single-origin coffee from a company that tests its lots, there is no strong evidence to switch to a more heavily marketed "mold-free" brand. What matters is sourcing quality, storage conditions, and periodic verification.

Brands that publish or make available third-party mycotoxin test results:

• Holistic Roasters / Biodynamic Coffee — Demeter-certified biodynamic, USDA organic; states that every batch is third-party lab tested for mold, mycotoxins, and heavy metals.
• Fresh Roasted Coffee (lab-tested SKUs) — USDA organic; explains testing methodology in detail; emphasizes specialty-grade 100% Arabica with transparent lab verification.
• Lifeboost Coffee — single-origin, high-altitude beans; multiple independent sources report having reviewed mycotoxin documentation from the company.
• Natural Force Clean Coffee — USDA organic; publishes test results for mycotoxins, heavy metals, mold, yeast, gluten, and pesticides.
• Purity Coffee — tests all batches; their own published data found 5 of 21 commercial coffees had detectable OTA, while Purity's lots were non-detectable.

Tree Nuts
Almonds and pistachios are under rigorous aflatoxin surveillance through the Almond Board, USDA, and export certification programs. Consignments exceeding regulatory limits are blocked from market. This does not mean risk is zero — it means the commercial supply chain has meaningful checks.
Lot-to-lot variation still occurs. Practical guidance:

• Look for organic brands that state they independently test each batch for aflatoxins. Brands that openly discuss testing include Terrasoul, Burroughs Family Orchards, and Philosopher Foods.
• Nuts should be dry, crisp, and sweet-nutty — not soft, rubbery, or musty. If a familiar brand suddenly tastes off or provokes symptoms, stop that batch and switch lots.
• Store in airtight containers, cool and dark. Refrigerate or freeze bulk quantities.
• For highly symptomatic patients or those with elevated aflatoxin on urine testing: consider a 4–8 week low-nut trial, or limit intake to a single tested brand while addressing other exposures.

Storage triage for nuts and seeds:

• Highest priority for fridge/freezer: almonds and hazelnuts (higher fat, more mycotoxin scrutiny); ground flaxseed (highly unsaturated fats; rancidity confounds symptom tracking).
• Medium priority: pumpkin seeds and sesame seeds — more stable fats; fine in airtight glass in a cool pantry if turnover is good.

Spices
A 2025 review of herbs, spices, and supplements concluded that chili/paprika, ginger, and various peppers are the most heavily contaminated spice group overall, frequently carrying aflatoxins plus OTA and sometimes fumonisins (Kanabus et al., 2025).
Given this risk profile, choosing specialty brands with direct sourcing, small lots, and third-party microbial testing is a reasonable strategy. The supply chain matters: direct farm relationships and fast turnover reduce the window for mold to develop.

• Burlap & Barrel — small-lot, direct-trade sourcing with third-party microbial testing.
• Diaspora Co. — single-origin, directly sourced from small farms in India and Sri Lanka; pays farmers 4–6× commodity price.
• Curio Spice Co. — directly sourced from small and women-led farms; certified B Corp; pays up to 10× commodity rates; short supply chains.

Practical rules:

• Buy high-risk spices (paprika, chili, black pepper, nutmeg, ginger, turmeric) in small jars from brands with good turnover; avoid bulk bins and anything older than a year.
• Store cool, dark, and dry. Replace annually — or sooner if you are sensitive.
• For reactive patients: a 2–4 week trial limiting high-risk spices and substituting fresh aromatics (garlic, onion, citrus, fresh herbs) can help clarify their contribution to symptoms.

Grains
Not all grains carry equal risk. Here is a practical comparison based on available survey data:

• Lower risk: quinoa and amaranth (surveys show generally low levels; OTA often non-detectable); teff (moderate overall burden in available data).
• Moderate risk: polished white rice (zearalenone, occasional AFB1, but often below limits when well-stored); buckwheat (DON up to 580 µg/kg in some surveys — behaves more like a cereal than a pseudocereal, despite its reputation).
• Higher risk: corn (fumonisins, zearalenone, aflatoxin), wheat (DON, zearalenone), conventionally processed oats (DON).
• Gluten-free blends: a 2021 study found 95% of GF pasta samples contaminated with Fusarium mycotoxins — FB1, zearalenone, and DON were most common, reflecting the rice/maize content of most GF products. Gluten-free does not mean mycotoxin-free.

For oats specifically, purity-protocol products — which maintain strict separation from wheat and include lot-level mycotoxin testing — are worth seeking:

• Montana Gluten Free — developed the original purity protocol; submits each lot to state grain labs for mycotoxin testing; also independently tests for glyphosate.
• One Degree Organics — organic sprouted oats; glyphosate-free emphasis; comprehensive "clean grain" program.

Dried Fruit
There is no strong solution here from a mycotoxin standpoint. Raisins, currants, and sun-dried tomatoes are among the most consistently contaminated foods in survey data. Freeze-dried fruit may be a reasonable substitution if you want an alternative to fresh fruit: the process is faster and avoids the extended ambient-temperature drying that allows mold to proliferate. Once the package is opened, however, freeze-dried fruit last a short time.

Seeds
Sunflower seeds and sunflower oil warrant more caution than other seeds, with mycotoxin contamination documented in surveys. Preferred alternatives include pumpkin seeds, sesame seeds, and hemp seeds. Terrasoul explicitly states it independently tests every ingredient for mycotoxins, heavy metals, and microbials, with results available on request.

The Safest Foods for GI Symptom Management
If you are working through an active gut-healing protocol, or simply trying to reduce mycotoxin burden while addressing health issues, the following are reasonable foods to prioritize:

• Fresh meat and fish — not aged, processed, or cured
• Citrus fruits — low mold burden in most surveys
• Quinoa and amaranth — generally low mycotoxin levels in available data
• Polished white rice — well-stored, tends to carry a lighter burden than corn or wheat
• Purity-protocol oats (e.g., Montana Gluten Free) — batch-tested
• Fresh vegetables — low risk if stored correctly and consumed with good turnover; potatoes, sweet potatoes and squash are among the lowest risk vegetables. Just don’t make soup stock with celery that is past its prime.
• Tested-brand coffee (see above) — if tolerated
• Tree nuts from tested brands, stored cold

This isn't a permanent elimination diet. It's a diagnostic and therapeutic tool. A 4–8 week trial of these lower-risk staples, combined with a review of your pantry and living environment, can help clarify whether dietary mycotoxins are a meaningful contributor to your symptoms.

Practical Guidance: What Actually Moves the Needle
Buy smarter, not just "organic." USDA organic certification reduces pesticide risk but does not guarantee mycotoxin testing. What actually matters: brands that source in small lots with direct farm relationships, test each batch independently, and publish or share results on request. Organic is a reasonable starting filter; verified testing is the meaningful one.

• Store properly. Cold, dark, dry, and airtight are the four principles. Mycotoxins do not form in the freezer. Bulk nuts, seeds, and flours stored in warm pantries can accumulate mold and toxins even after purchase, regardless of original quality.
• Heed the recommendations on refrigerated vegetables and fruit. Most should be discarded after 1-2 weeks, depending on the water content.
• Trust your senses — mostly. A musty, bitter, or dusty smell in oats, nuts, or spices is a reliable signal to discard. A soft, rubbery texture in nuts is another. That said, many mycotoxin-contaminated foods look and smell completely normal, which is why sourcing and testing matter — your senses are a useful secondary filter, not a primary safeguard.
• Interpret urine tests carefully. A positive urine mycotoxin result is not a diagnosis of building-related mold illness. Food sources, building sources, and internal colonization can all contribute to the same analytes. A structured dietary trial is often the most useful first intervention — both diagnostically and therapeutically.
• Don't over-restrict. Tree nuts are nutritious and heavily regulated. Coffee from tested sources is fine for most people. The goal is informed, proportional risk reduction — not the elimination of entire food groups based on theoretical worst-case contamination. As soon as your health improves, remember to diversify your diet as much as possible.

IN CONCLUSION
What I learned through this journey is that there are so many layers to improving health. I’ve been practicing functional medicine for 16 years. I was a conventional physician 21 years before that. Yet, there are more issues to discover when we stay curious!

Why I use stool DNA tests with caution, if at all, in my practice

If you've ever sent a stool sample to one of those mail-in microbiome companies to learn about your gut health, here's something important you should know: the results depend heavily on which company you used — not just what's actually living in your gut.
A new study put this to the test in a pretty clever way.

​What researchers didScientists at a top government lab (NIST) took stool from a single healthy person and carefully divided it into identical samples. They then sent the exact same material to seven different consumer microbiome testing companies — the kind that promise to tell you about your gut bacteria and what it means for your health.
The idea was simple: if these tests are reliable, the same sample should produce roughly the same results everywhere.

What they foundIt didn't.
The companies came back with wildly different answers — different bacteria detected, different amounts reported, and different "health scores." In fact, the differences between companies were about as large as the differences you'd expect between two completely different people.
A few companies at least got consistent results when testing the same sample multiple times. Others couldn't even agree with themselves.
Perhaps most concerning: the same sample sometimes landed in different health risk categories depending on who analyzed it. "Normal" with one company could mean "at risk" with another — using the exact same stool.

Why does this happen?Each company uses its own process from start to finish — how they handle the sample, how they extract DNA, how they sequence it, and especially how their software interprets the data. There are no universal standards, and the "healthy" vs. "unhealthy" cutoffs companies use are largely made up in-house, with little scientific backing.

What this means for you

• Don't treat these results like a medical test. They are not held to the same standards as clinical diagnostics.
• Don't compare results across companies. Switching services and noticing a change likely reflects the companies' differences, not changes in your gut.
• Be skeptical of health scores and risk labels. The thresholds behind them are not standardized or clinically proven.
• Use them as a curiosity, not a guide. If something in a report concerns you, talk to your doctor and rely on conventional testing and clinical judgment.

The bottom lineConsumer microbiome testing is a fascinating window into an emerging science — but the technology isn't ready to reliably guide health decisions. Researchers are calling for standardized testing practices, more transparency from companies, and proper regulation before these tests should be used clinically.
This puts functional medicine physicians in a quandary because the article doesn't say which companies were at least consistent with themselves. If a company can reliably come up with the same answer, it might be believable that they can tell us when a person's stool is changing over time. Many clinicans may argue that "they know" because they have seen it in their practice. BUT don't get me started on the research showing how biased clinician's impressions typically are.

For now, I absolutely would use these tests with enormous caution.