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Understanding the Fungus in Your Gut

Heal
Woman making a heart shape in front of her belly

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Everyone knows the importance that bacteria plays in gut health, but what about fungus? Understanding how to balance your mycobiome, or the ecosystem of fungus that lives in the gut, is crucial for maintaining good health.

While everyone has been focused on the bacteria in their guts, they’ve completely missed the fact that there is a whole ecosystem of fungi that not only lives in the gut, working intimately with bacteria to control your gut health in both positive and negative ways. Successful management of bacteria and fungus in the gut is crucial for the eradication of unwanted gut symptoms including inflammation, indigestion, and more.

Fungi are a little like the black sheep of the microbiome. They are part of the microbiome—a subcommunity—but they can cause big trouble by going against the current of what is most beneficial for the microbiome's human host. But fungi aren't all bad. Some are helpful, contributing to the complex workings of your body, and some are helpful in small amounts but harmful if they become too numerous or abundant. 

The Fungus Among Us

Let’s give your mycobiome a closer look. While bacteria may be the “majority microbe,” fungi are vying for the spotlight. They represent just 0.1 percent of your microbial species, but they compensate by being larger in size. One fungal cell is larger than 12 bacterial cells.

Fungi are all over you. They exist in your mouth, in your gastrointestinal tract, on your skin, and sometimes in your lungs. Fungi can develop between your toes, under your fingernails and toenails, in and around your genitals. When it overgrows it can cause infections in all these places—superficial skin infections such as tinea pedis (athlete’s foot), tinea corporis (ringworm, which is not caused by a worm but rather by fungus), tinea cruris (jock itch), and tinea versicolor (small pale, dark tan, or pink patches of skin), as well as thrush in the mouth (mostly in babies and the elderly), and vaginal yeast infections. Inhaling fungus can cause lung infections, and fungi can even get into your bloodstream.

Fungi have also been implicated in all sorts of gut disorders, from irritable bowel syndrome (IBS) to inflammatory bowel diseases (IBDs) like Crohn’s disease (CD) and ulcerative colitis (UC). It causes many serious infections in hospitals and in people with compromised immune systems. It can also cause plenty of trouble for healthy people, like digestive problems, blood sugar imbalance, and excessive weight gain or weight loss resistance. 

For example, studies have linked obesity to higher levels of certain fungi, such as Eurotiomycetes, while weight loss is associated with higher levels of Mucor. Fungi have been associated with increased inflammation, and at least one study clearly demonstrated that a high-sugar diet leads to excessive growth of Candida species and related infections, but that decreasing sugar and artificial sweetener intake helped to decrease this growth and re-establish balance. Studies have discovered higher numbers of Candida species in the gastrointestinal tracts of malnourished children, and theorize that vitamin and iron deficiencies may be risk factors for Candida infections. 

These are just a few examples of the many ways in which fungi can influence human health, and how what you eat is closely linked to the fungus that lives inside you.

Balancing Your Mycobiome

Fortunately, you can completely refurbish your fungi in 24 hours, just by changing your diet, which can help improve your health in numerous tangible ways. We call this the short-term diet effect, and it means that changing your diet can create swift and meaningful shifts in your mycobiome within hours, while your bacteriome slowly works to catch up. 

Once you begin changing the way you eat, you are likely to begin noticing positive changes in your energy level and gastrointestinal symptoms within the first 24 hours. As you shift your diet to modify your microbiome, you will continue to experience improvements in your energy and feelings of good health. After four weeks of eating to control your mycobiome and balance your gut, you are likely to notice significant changes in weight (if you have excess weight to lose) as well as even more profound differences in the way you feel. The longer you sustain these changes, the more lasting your microbiome shifts will be, resulting in longer-term effects like a strengthened immune system, enhanced weight regulation, rejuvenated skin, fewer allergies, less inflammation, and in many cases, the complete disappearance of gastrointestinal problems such as IBS and heartburn or acid reflux. 

Rebalancing fungi is step one—as beneficial species like Saccharomyces boulardii increase and pathogenic fungi like Candida decrease, the beneficial bacteria (such as Lactobacillus and Bifidobacterium) that regulate fungal balance and do so much to improve health have more room and a better environment for growth and reproduction. 

Fungal control is the door that can lead to a whole new world of better microbiome balance for optimal health. You’ll enjoy bolstered immunity, reduced inflammation, fewer digestive problems, easier weight loss, more energy, less fatigue, and a brightened mood.

Want more about gut health? Check out “Six Veggies (and Recipes) for Optimal Gut Health.”

Key tips that will help you achieve better gut health quickly:


  • Cut out (or drastically reduce) refined sugar. The fungi most likely to cause trouble in your gut (like Candida) love sugar, so when you feed them, they reproduce at an accelerated rate. Just one day without sugar will make a difference.
  • Eat the right carbs…and not too much at once. You can have carbs, and should, because carbohydrate-rich foods that specifically contain fiber and resistant starch feed the most beneficial bacteria in your gut. The trick, though, is to never eat too much at once, so excessive carbs don’t wind up as Candida food. Stick to one serving of whole-food carbs at every meal. 
  • Eat as many vegetables as you can. Vegetables are full of phytochemicals that specifically foster beneficial microbes and discourage inflammatory microbes. Every vegetable has a different phytochemical profile, so the more variety you get, the better. 
  • Add some berries and fermented foods. Every week, try to fit in at least 3 cups of different kinds of berries, which foster anti-inflammatory microbes, and a few servings of fermented foods, which contain probiotics (good bacteria and yeast) to improve gut balance.
  • Avoid meat and dairy high in saturated fat. Research has proven that a lot of saturated fat feeds the bacteria that increase inflammation. Opt for low-fat dairy products and lean fresh cuts of meat—or, ease into mostly plant-based eating—for the best microbiome-balancing results.
  • Get more exercise and sleep. Exercise and sleep may not seem to be directly related to your gut, but science has demonstrated the microbiome benefits of moderate-intensity exercise, and seven to nine hours of sleep per night.
  • Go outside and get dirty. Surprisingly, being less hygienic, with more outdoor time and time around animals, actually strengthens your microbiome and increases your beneficial microbes (especially during childhood). Try gardening, visiting a farm, or going on hikes through the woods. Even having a pet helps.
  • Stop worrying. Because of a direct connection between the gut and the brain (called the gut-brain axis), stress can actually cause imbalance. People who exercise less and people who are chronically stressed tend to have more microbiome imbalance, even when they eat a good diet. Take measures to reduce stress (I like yoga and meditation), and don’t worry too much.

Try this recipe for a gut-friendly "Strawberry Breakfast Bake."

Excerpted from Total Gut Balance: Fix Your Mycobiome Fast for Complete Digestive Wellness© 2020 by Dr. Ghannoum LLC. Reproduced by permission of The Countryman Press. All rights reserved.


Mahmoud Ghannoum, PhD, is the director of the Center for Medical Mycology at Case Western Reserve University and University Hospitals Cleveland Medical Center. He studies Crohn’s disease, cancer, and heart disease. He has been featured by Forbes, NPR’s Tech Nation¸ MindBodyGreenWell + GoodGoop, and other outlets.


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