While we’d all like to think of our bodies as our own, the truth is a little bit more complicated than that. You see, our bodies are cohabitated by trillions of microorganisms that collectively make up your microbiome. While it’s obvious that these microscopic organisms rely on us to survive, what’s less obvious is that we are equally reliant on them for our own survival.
Just how well this ecosystem of microbes is able to function impacts quite literally every facet of your being – from your digestion to your immune system and from your skin's appearance to your mood. And one factor that can have a significant impact on the health of your microbiome, is your exposure to a class of compounds known as mycotoxins.
Today we’re going to dive into exactly what mycotoxins are, explore the complex bi-directional relationship between these toxins and your gut microbes, and most importantly – cover what you can do to protect yourself and keep your gut in tip-top shape.
What Exactly Are Mycotoxins?
Mycotoxins are a type of metabolite or substance that’s created as a result of a chemical metabolic reaction. Mycotoxins are naturally generated by fungi – a family of organisms that includes mold, mushrooms, and yeasts.1 As the name implies, mycotoxins have a toxic effect – acting as a microscopic poison when they enter our bodies.
Because these toxic metabolites are naturally produced by countless fungal species, we inevitably come into contact with them on a regular basis either through inhaling free-floating spores, ingesting them via the food we eat, or even coming into physical contact with them.2 While we’re well-equipped to handle small amounts of these natural toxins, thanks to present-day construction practices paired with modern agricultural and food processing operations, our indoor air and food sources can have unprecedented levels of mycotoxins.
Exposure to elevated levels of mold and other mycotoxin-containing fungi for prolonged periods of time can have a major impact on just about every facet of your health. Let’s zoom in on one aspect of your health that these mycotoxins can have a particularly detrimental impact on – your gut health.
How Does Mold Affect Your Gut Health?
Mycotoxins are known to be potent disruptors of gut health thanks to their ability to:3,4
- Skyrocket inflammation: Once your body detects the presence of these toxic compounds it sounds the alarm – releasing a cascade of pro-inflammatory cytokines and immune cells in an attempt to neutralize and eliminate the threat.
- Compromise the integrity of your intestinal barrier: Mycotoxins trigger what’s known as increased intestinal permeability – the development of gaps or pores in the cells that line the inside of your intestines. When gaps develop in this crucial barrier, toxins, pathogens, and waste inadvertently leak their way into your bloodstream – further stoking inflammation and the introduction of mycotoxins to the rest of your tissues.
- Alter the balance and diversity of your gut microbiome: Mycotoxins also disrupt the delicate ecosystem of microbes that call your gut home.
Let’s dive a little deeper into the complex interaction between the microorganisms in your gut and the mycotoxins you may be exposed to.
How Your Microbiome Impacts Absorption of Mycotoxins
Because mycotoxins are often present in many foods you might consume, your gut is one of your primary lines of defense against mycotoxin toxicity and mold-related illnesses. Meaning the menagerie of microbes that make up your microbiome as well as the overall health of this fragile ecosystem can dramatically impact how you process, respond to, and eliminate mycotoxins.
Your gut microbiome influences how you respond to mycotoxin exposure by:5,6
- Modifying the toxicity of mycotoxins: The microbes in your gut secrete enzymes that chemically transform mycotoxins – forming metabolites that are less toxic.
- Activating “masked mycotoxins”: In some cases, your gut microbiome can inadvertently transform a specific type of mycotoxins dubbed masked mycotoxins into a more toxic compound. This occurs when mycotoxins have been structurally modified and bound by plants as a defense mechanism. So when modified by your gut microbiome, the mycotoxins are released and become more toxic than when they were initially ingested.
- Binding to mycotoxins: Certain microbes contain compounds on the exterior of their cell walls that allows them to bind to mycotoxins – blocking them from being absorbed and making their way into your bloodstream.
But the interplay between your microbiome and mycotoxins is a two-way street – with your gut microflora being equally impacted by exposure to mycotoxins.
How Mycotoxins Can Alter Your Microbiome and Impact Gut Health
While it’s clear that your microbiome has a significant impact on how you’re able to process and break down mycotoxins, there is a bi-directional relationship between the two – meaning these tricky toxins can also have a dramatically negative impact on your microbiome. Mycotoxins can shift the overall balance of your microbiome in the following ways:5,6
- Antimicrobial effects of mycotoxins: Some mycotoxins have potent antimicrobial properties which can damage or even kill off any gut microbes they come into contact with.
- Damage to epithelial cells: Mycotoxins can harm the epithelial cells that form the barrier that lines your gut. This damage elicits an immune response and the launch of immune cells to the site of the threat. These immune cells can launch an attack against any microbes it encounters – meaning they can attack mycotoxins and beneficial gut microbes alike.
- Release of antimicrobial peptides: In response to damage, immune activation, and rising inflammation, your epithelial cells and immune cells release compounds known as antimicrobial peptides – molecules designed to target and terminate any microorganisms they come into contact with.
- Alteration of amount and composition of essential fatty acids: The microbes within your microbiome assist in the breakdown of nutrients while creating secondary by-products like fatty acids that we rely on for gut health, immune function, and much more. As the composition of your gut microbiome shifts, the production of these crucial compounds begins to shift as well – creating a vicious cycle that further contributes to declining gut health.
While a healthy, thriving gut microbiome can certainly be an excellent line of defense against exposure to ingested mycotoxins, the truth is, even the healthiest microbiome can be negatively impacted by elevated or prolonged exposure to mycotoxins. So what can you do if your gut microbiome has been damaged from exposure to these toxic compounds?
How Do I Repair My Gut After Mold Exposure?
If your gut health and microbiome have been compromised due to exposure to mycotoxins, healing any damage and restoring balance requires a big-picture approach and a little patience. Here’s what I recommend:
Minimize Exposure:
While it’s impossible to completely avoid mycotoxins (mold, fungi, and their toxic metabolites are a normal part of our natural world) you can certainly minimize your exposure by:
- Minimizing your intake of foods that tend to be higher in mycotoxins
- Following a low mold diet
- Addressing and preventing any mold growth in your home
Just a few simple tweaks can drastically reduce the amount of mycotoxins you’re exposed to on a daily basis – giving your gut and microbiome an edge in recovering.
Prioritize Gut Health:
It can be immensely helpful to ensure your gut has the support and resources it needs to bounce back as quickly as possible. Some of the most effective ways to do that are:
- Eat a healthy, well-rounded diet full of nutrient-dense whole foods. If you need help finding some fresh, healthy, and delicious recipes, head over and check out my recipe library – it’s got tons of gut-healthy and tasty ideas for you to try.
- Reinoculate your gut with a variety of gut-supporting beneficial bacteria. Diversity is key when it comes to creating a flourishing microbiome, so it can be helpful to add in different strains like those found in my Probiotic 100 Billion Plus combined with Spore Probiotic Plus IgG.
- Beef up the integrity of your gut barrier lining by incorporating things like bone broth, collagen, and Gut Shield.
The nutrients, probiotics, and healing compounds you ingest are quite literally the building blocks your gut relies on to heal and rebuild itself.
Amplify Detoxification
Supercharge your ability to detox from mold, mycotoxins, and other toxic compounds that can “clog up” your gut and detoxification pathways by:
- Adding in strategies like Infrared saunas, IV infusion therapy, and PEMF therapy which can all help your body release and process toxins.
- Incorporating detox-boosting and toxin-binding supplements to support your body in removing mycotoxins and other harmful compounds. Some of my favorites include N-acetyl cysteine (NAC), Liver Essentials, and ZeoBind Plus.
- Boosting your intake of antioxidants like Glutathione Essentials and ResveraMax to support optimal healing.
- Maximizing the function of your mitochondria (the powerhouse of your cells) to accelerate detoxification with supplements like MitoVite.
Detoxification is a crucial step that cannot be skipped when it comes to healing and recovering from exposure to mold and harmful mycotoxins. That’s why I teamed up with Dr. Shade and Quicksilver Scientific to comprehensive mold detox kit to simplify and streamline the process of detoxing from mold and mycotoxins.
This kit and easy-to-follow protocol have everything you need to complete an effective yet gentle, 30-day detoxification program that will support optimal detox and healing. Click here to learn more about my exclusive Dr. Jill’s Miracle Mold Detox Box.
A Healthy Gut and Diverse Microbiome: The Key to Preventing and Reversing Damage from Mycotoxins
We still have much to learn about mycotoxins and the impact they have on both our gut health and our overall well-being. But one thing we know for certain is that the microbes that coexist within our bodies play a pivotal role in every aspect of our health. Supporting and promoting a diverse and flourishing ecosystem of microorganisms is key when it comes to not only shielding us from the toxic effects of mycotoxins – but also creating the vibrant health and longevity we all deserve.
If you’ve been diagnosed with any kind of mold-related illness, are concerned that you may have been exposed to toxic mold, or are struggling with unexplained, ongoing symptoms, it’s crucial to evaluate and prioritize the health of your gut and microbiome. The steps outlined in this article are a good place to start, but I also encourage you to seek out the guidance of an Integrative and Functional Medicine Practitioner to help you come up with a personalized plan of action and ongoing support.
If you enjoyed this article and are looking for ways to support your healing journey, find information to help you navigate your symptoms, or simply optimize your overall health, I’ve got you covered. I’ve got loads of science-backed and easy-to-understand resources available to you on my blog, my YouTube channel, and in my weekly newsletter. Be sure to head over and take a peek and sign up for my newsletter by entering your name and email address in the form below!
Now it’s time to hear from you. Were you surprised to learn about the bi-directional relationship between mycotoxins and your microbiome? What's your favorite way to support a happy, healthy gut? Leave your questions and thoughts in the comments below!
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In Unexpected: Finding Resilience through Functional Medicine, Science, and Faith, Dr. Jill Carnahan shares her story of facing life-altering illness, fighting for her health, and overcoming sickness using both science and faith so that others can learn to live their own transformative stories.
Dr. Jill’s riveting and compassionate exploration of healing through functional medicine demonstrates how to replace darkness and fear with hope and find profound healing, unconditional love, and unexpected miracles in the process.

Resources:
- Mycotoxins (who.int)
- Mycotoxins (nih.gov)
- Mold, Mycotoxins and a Dysregulated Immune System: A Combination of Concern? (nih.gov)
- Association Between Gut Microbiota and Autism Spectrum Disorder: A Systematic Review and Meta-Analysis (nih.gov
- Mycotoxin: Its Impact on Gut Health and Microbiota (nih.gov)
- Mycotoxin and Gut Microbiota Interactions (nih.gov)
* These statements have not been evaluated by the Food and Drug Administration. The product mentioned in this article are not intended to diagnose, treat, cure, or prevent any disease. The information in this article is not intended to replace any recommendations or relationship with your physician. Please review references sited at end of article for scientific support of any claims made.
4 Comments
Thank you for writing this very informative article about mycotoxins and the microbiome! In our attempt to avoid mold in our daily lives, I am wondering if you have any thoughts about the use of allergy shots containing mold? Do you think these subcutaneous injections of mold could interact with or harm our gut microbiome? I would be very interested to hear your thoughts about this topic! Thanks so much!
Usually allergy shots or LDI are low potency and create an immune resilience so the patient is less reactive. I do not suspect these minuscule doses would be harmful under proper supervision.
Thank you so much for your reply! This is very helpful and makes me feel better about continuing my allergy shots. I really appreciate the work you are doing in this area!
Thanks for this article Dr!! I want to give my family quicksilver sensitive binder for mold and metals but it has a prop 65 on it and the company claims there is a very small amount of lead from the soil in the product. Is that okay for kids to take? Thank you!
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