New in Gut Health: Fungi’s Impact on the Body

New in Gut Health: Fungi’s Impact on the Body


The role of the gut in our overall well-being seems to grow bigger with every new study. But while attention—and research dollars—have focused on the importance of bacteria in our gut, a crucial player in digestive (and general) health has been largely overlooked by most: fungus.

The exception is scientist Mahmoud Ghannoum, Ph.D., an NIH-funded researcher since 1993, who’s spent his career studying fungi in the body (there are about 50 different species living in our gut specifically). Dr. Ghannoum is credited with uncovering the significant interplay between bacteria and fungi, which affects the critical balance of the body’s microbiome. (Much of this interaction occurs at a digestive plaque wall that Ghannoum discovered with his research team at Case Western Reserve University in 2016.) It was Ghannoum who also came up with the name that is now used by the scientific community for the body’s fungal ecosystems: the mycobiome. Most recently, Ghannoum’s research led him to develop the first probiotic (called BIOHM) designed to balance the body’s larger microbiome by addressing good and bad native fungi, as well as bacteria. Here, he shares his expertise on our fungal communities and gut health.

A Q&A with Mahmoud Ghannoum, Ph.D.


Can you explain what the mycobiome is (as opposed to the microbiome)?


When people talk about the microbiome, they’re usually referring to the entire ecosystem of organisms found in your body. The body doesn’t actually have a single microbiome, though; there are distinct communities of organisms in various parts of our bodies. For example, the microbiome in your mouth or skin is completely different than the microbiome in your gut.

Most of the published work on the microbiome has been done on the bacterial community, called the bacteriome. Interestingly, it was not until 2010, when my team of researchers identified a native fungal community in the oral cavity, that scientists started to identify the specific fungal communities in our bodies. The term I came up with—the mycobiome—has been adopted by the scientific community to describe the fungal ecosystems/communities in our bodies. There are several different mycobiomes in our bodies, including in our lungs, our guts, and even our skin.

As a result, the definition of the microbiome has now broadened beyond bacteria; it includes bacterial, fungal, and the viral communities of the body.


How did you find the digestive plaque wall in the gut? Do we all have it? How is it (or might it be) problematic?


Yes, we do all have digestive plaque. Bacteria and fungi aren’t just free-floating in our system, but tend to stick to the lining of our guts, and some of these then work together to form digestive plaque. This plaque can be bad or good:

Our team was conducting studies when we found a substance gathering against the intestine that we found to be quite curious. After analyzing the substance (with an electron microscope at 5000x magnification), we stumbled upon the fact that bad bacteria and bad fungus were working together in the intestine to form this plaque.

An important characteristic of a plaque, whether it’s on our teeth or in our gut, is that it protects microbes within itself. These microbes can cause imbalances, which can lead to oral care issues in the mouth (such as cavities and gum disease), and a host of occasional digestive issues (such as upset stomach, gas, bloating, feeling full, stomach pressure, diarrhea, bowel irritation, difficulty processing lactose), and even immunity issues, which ultimately affects more than just our digestive health.

We found, though, that not all digestive plaques are actually bad. In fact, good microbes form modest-size plaques (less robust than plaques formed by bad microbes) that do not cause digestive imbalances. To the contrary, they actually help maintain the balance of the microbiome in our gut and keep bad plaque at bay. Good digestive plaque also plays a beneficial role in our digestive system by helping break down food, so our body can efficiently use nutrients as a source of energy.

We start to see problems when homeostasis in our gut’s microbiome is disrupted, which reduces the good bacteria and fungus and increases the bad bacteria and fungus. It’s at that point that bad digestive plaque starts to take over, and the resulting imbalance creates digestive issues. That’s why it’s critical to maintain a healthy balance in our gut.


How does fungi work in concert with bacteria in the gut?


Our studies show that the microbial communities (bacteria and fungi) have developed cooperative evolutionary strategies, culminating in the development of digestive plaque, which benefits both bacteria and fungi. The fungi benefit by gaining virulence factors, meaning they have the ability to secrete enzymes that can break down our bodies’ tissues, or form more plaques. Living under the protective digestive plaque, bacteria can develop antibacterial tolerance, meaning they become increasingly hard to balance and control. This cooperation can affect our immune system, potentially weakening our bodies’ ability to protect itself, which can lead to health issues.


What causes fungi-related imbalances? How do we avoid them and keep our gut healthy?


A variety of factors can contribute to fungal imbalance. Our bodies are increasingly under pressure from: the types of food we eat; the alcohol we drink; and the stress we put ourselves under, trying to fit everything we want to do into what seems to be ever-shortening days. Genetics also makes some people more susceptible to fungal imbalance.

Diet & Alcohol

The types of food that best encourage your microbiome to flourish are prebiotic-rich foods, such as avocados, whole-grain breads, soy beans, and peas. Vegetarian diets have also been found to decrease the pH levels in our gut, which prevents the growth of different strains of bad microorganisms.

On the other hand, a diet that’s high in fat, refined sugar, and artificial ingredients can cause an imbalance between good and bad microorganisms in your gut.

Recent studies point to the fact that alcohol can tip the balance of the gut’s equilibrium and disrupt our digestive tract’s environment, which can potentially lead to a host of digestive issues. Unlike food, the research doesn’t overwhelmingly suggest that one type of alcohol can have a worse effect on our gut’s natural balance than others. With that being said, there is some evidence that suggests red wine can promote gut health, because it contains polyphenols, which in one study was found to increase some strains of good microorganisms.

While BIOHM will support total digestive balance, you can impact your gut’s health by making adjustments to your diet. The impact of particular foods on digestive balance varies person to person; same goes for alcohol: Some people are more affected by the occasional happy hour than others. If you have digestive issues, I’d follow the above guidelines; and you can of course experiment with your diet, temporarily removing any other particular foods or drinks that seem to cause you problems so you can see how your body responds. (This is best done with professional assistance, from a nutritionist or physician.)


Stress can have a substantial effect on our gut’s microbiome, by altering the balance of organisms in our digestive system, and also by changing the types and number of organisms that are found in the gut. Research indicates that when the microbiome becomes less diverse due to stress, bad organisms start to flourish, and our body’s immune response is negatively affected.

To balance your gut—this is very important—you must work to lower your stress levels because we know that stress can have a negative effect on your microbial balance, gut health, and overall health. It’s why I practice yoga and mindful breathing every single day, even if it’s just for a few minutes.


We know that our genetics can cause changes in our gut’s microbiome. A study led by Cornell University researchers found that some people with a specific set of genes had higher levels of certain good microorganisms in their gut. Other studies have even found certain microbes are inherited. Our genes influence which organisms thrive in our gut by themselves, and which organisms need a boost through adjustments to diet (including supplementing with probiotics like BIOHM), alcohol intake, and stress levels.


Why haven’t we heard much (up until this point) about fungus in the body?


For decades, the medical community thoroughly dismissed—and as a result, underestimated—just how big a role fungus plays in our health and wellness. Most scientific funding has been directed toward studying our body’s bacterial community, while very little research has been done on fungus in comparison. While that’s starting to change, in part due to the research my team has been doing with the National Institutes of Health (NIH), we’re still far behind when it comes to fungal research.

Almost seven years ago, I tried to draw attention to the issue in a letter (published in Microbe, an American Society for Microbiology Journal) recommending that the NIH’s Human Microbiome Project should investigate not just people’s bacterial inhabitants, but also our native fungal and viral communities.

Research on the human virome (the body’s viral community) has increased in recent years, but the scientific community has really not heeded our advice with regard to the fungal components of the microbiome. To put it in perspective: Before 2010, there were zero papers that addressed either the mycobiome or the virome. By 2015, there were 737 papers that analyzed the bacterial “microbiome” (94.5 percent of all research), 31 that analyzed the “virome” (3.9 percent of all research) and just 12 studies that addressed the “mycobiome” (1.5 percent of all research).


What kind of fungi lives in the gut?


Recent studies are starting to reveal that our gut contains a large number of fungal genera—approximately 50 different fungal genera. The most abundant genera in the gut are:

  • Aspergillus: Aspergillus is a group of molds that peak in the fall and winter and are commonly found in our homes. It’s considered a bad fungi for the body, but only a few types of Aspergillus can actually affect our health. Some Aspergillus species are used for interesting commercial applications—for instance, because of their ability to breakdown the starch in rice, they are used to make sake.

  • Candida: The species of Candida called Candida albicans is commonly found in the gut, where overgrowths cause problematic health imbalances.

  • Cladosporium: Cladosporium includes some of the most common molds in our environment. It rarely has a negative effect on healthy people.

  • Cryptococcus: The majority of cryptococcal species live in the soil and are not harmful to humans.

  • Fusarium: Fusarium is a very common soil fungi that can be found all over the world.

  • Mucor: Mucor is a mold commonly found in nature, and is also present in the digestive system. The vast majority of Mucor species don’t have negative health implications for humans due to their inability to grow in warm environments.

  • Penicillium: Penicillium is one of the most scientifically important types of fungus, well-known for its ability to kill and control the growth of certain types of bacteria in the body.

  • Pneumocystis: Pneumocystis is found all over the world in both humans and animals. It’s usually found in low levels in healthy humans, but can cause substantial health issues for people who are immunocompromised.

  • Saccharomyces: Overall, Saccharomyces is one of the most useful types of fungus (from food production to brewing), and in the body, Saccharomyces boulardii is considered to be the king of good fungus.


What distinguishes “good” fungi from “bad”?


A bad fungus has what we call virulence factors, including the ability to secrete enzymes that can break down our body’s tissue or form plaque (which is scientifically known as biofilm). These “bad” fungi can overrun our digestive system, especially when our gut is susceptible to imbalances due to factors like diet, alcohol consumption, stress, or our genetics. Examples of bad fungi include: Candida, Aspergillus, Fusarium.

In comparison, “good” fungi, like Saccharomyces, do not have properties that lead them to invade and overrun our bodies. In fact, they do quite the opposite, acting as a checks and balances against bad fungi that’s present in our digestive tract.


Can you talk a bit about why you developed BIOHM and how it works?


After I published the study showing that bacteria and fungus work together to create destructive digestive plaque, I had many people reach out, asking me if there was a probiotic that I thought could help with gut imbalance and overall digestive health. When I looked at what was available, I saw that no probiotic had been created to address the total nature of the gut’s microbiome. Additionally, no probiotic had been proven to break down digestive plaque, which was protecting bad bacteria and bad fungi. By ignoring fungus and digestive plaque, the probiotics on the market offered only a partial solution to digestive imbalance.

My team saw this as an opportunity to engineer the first total probiotic that would address not only good and bad bacteria, but also good and bad fungus as well. We combined 30 billion live bacteria and fungus together, and spent months selecting and studying the best probiotic strains that target bad bacteria and fungi. We infused the good bacteria and good fungus in BIOHM with an enzyme that breaks down digestive plaque.

This was only 80 percent of the solution, though. We needed to ensure that the live cultures in BIOHM would stay alive all the way into the gut because ultimately, unlike drugs, which are chemicals, probiotics are living organisms. So while they can have an incredible effect on our health and wellness, they need to be alive in order to so. (In other words, they can’t die in an overheated car, or traveling through the body down to the gut.)

We addressed this in two ways: BIOHM’s jar is made from heat-resistant resin that protects the live bacteria and fungus from fluctuations in temperature that could kill them. We applied a coating to the formulation, called an enteric coating, which protects the entire formulation from the harsh environment of the stomach, as the capsule moves down to the gut, ensuring that when BIOHM enters the digestive tract, all 30 billion cultures are still alive.


What do you see as potential future implications of your work on fungi? What’s next?


Some personal work that I’m excited about is on a drug currently going through FDA approval that seems to have an effect on Candida auris, a deadly antibiotic-resistant fungus that is starting to emerge in hospitals globally. This is very concerning because Candida auris causes infections with a very high death rate, and it is resistant to multiple drugs. Multi-drug resistance used to only be found in bacteria, but some strains of Candida auris are actually resistant to all commercially available antifungal drugs (which is why this new drug could be significant in curbing the fungus).

More generally, I believe we are only seeing the tip of the iceberg when it comes to understanding the role fungus plays in health and wellness. While bacteria and viruses (i.e. infectious diseases like influenza) have been thoroughly researched for decades, it is only recently that the NIH and scientific community have started to turn their attention to fungus. I’ve been working to shine a light on the fungal communities with the body, and more importantly, to try and understand how we can harness the power of beneficial fungus to actually improve our health and wellness. With a new appreciation for how important fungus is, I think we are going to see some amazing scientific breakthroughs in the next few years as we further unlock the complexity of fungus.

Scientist Mahmoud Ghannoum, Ph.D., an NIH-funded researcher since 1993, has spent his career studying fungi in the body, and their impact on gut—and overall—health. He is a professor and director of the Center for Medical Mycology at Case Western Reserve University and University Hospitals Cleveland Medical Center, and developed the probiotic BIOHM.

The views expressed in this article intend to highlight alternative studies and induce conversation. They are the views of the author and do not necessarily represent the views of goop, and are for informational purposes only, even if and to the extent that this article features the advice of physicians and medical practitioners. This article is not, nor is it intended to be, a substitute for professional medical advice, diagnosis, or treatment, and should never be relied upon for specific medical advice.