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The Sneaky Reason For Your Brain Fog & Gut Issues — And How To Fix It

Christine Maren, D.O.
Doctor of Osteopathic Medicine By Christine Maren, D.O.
Doctor of Osteopathic Medicine
Christine Maren, D.O., is the founder of a high-tech, functional medical practice in Colorado, Michigan, and Texas. She received her degree from the Chicago College of Osteopathic Medicine at Midwestern University and is board-certified by the American Board of Family Medicine.
The Sneaky Reason For Your Brain Fog & Gut Issues

Did you know that one in four people with unexplained digestive symptoms may actually be suffering from small intestine fungal overgrowth, or SIFO? By now, many patients and practitioners are aware that small intestine bacterial overgrowth, or SIBO, is a common underlying cause of irritable bowel syndrome (IBS). However, there's another condition emerging in the literature that is a largely unrecognized issue. SIFO occurs when there is an overgrowth of yeast in the small intestine and shares many of the same symptoms of SIBO, such as abdominal pain, bloating, nausea, diarrhea, and gas. Like most chronic digestive issues, diet and nutrition are a cornerstone of getting better.

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The predominant thought in conventional medicine is that we all have yeast in the gut and that fungal infections of the gastrointestinal tract become a problem only in people with severe immune dysfunction. However, recent scientific literature now supports the belief that the alternative and functional medicine community has held for decades: Fungal overgrowth can be a cause of unexplained GI symptoms in immunocompetent patients as well. This is best studied in people with motility disorders and in those who take acid-blocking medications like proton pump inhibitors (PPIs). But anything that upsets the balance of organisms in the gut can lead to SIFO. Clinically, we should have heightened concern for fungal overgrowth in the following populations:

  • Motility disorders such as gastroparesis
  • Other disorders that can cause dysmotility, including celiac disease, endometriosis, and radiation therapy
  • Thyroid disorders including hypothyroidism and Hashimoto's
  • Long-term use of acid-blocking medications like proton pump inhibitors (PPIs)
  • Hypochlorhydria or low stomach acid
  • Frequent or broad-spectrum use of antibiotics
  • Hormone replacement like birth control pills
  • Chronic stress
  • Exposure to environmental toxins, including mercury, and mold or mycotoxins
  • Long-term use of prednisone or immunosuppressant medications
  • Anyone with a compromised immune system, including autoimmune disease, diabetes, food sensitivities, alcoholism, pregnancy, and any chronic debilitating disease

Signs that you have small intestine fungal overgrowth.

Many of the signs and symptoms of SIFO are nonspecific and can mimic or overlie other gastrointestinal issues, so diagnosis can be tricky, and proper testing with a functional medicine doctor is important. In my functional medicine practice, I use a variety of testing methods including urine organic acids, stool tests, and breath tests to help diagnose and differentiate chronic gastrointestinal complaints. These would be indicated if you suspect excess yeast based on the risk factors mentioned above, and/or suffer from many of the symptoms listed below.

Some common gastrointestinal symptoms associated with SIFO include:

  • gas
  • belching
  • bloating
  • diarrhea
  • nausea
  • indigestion
  • anal itching
  • thrush or a white coating on the tongue

More systemically, fungal overgrowth may lead to:

  • carbohydrate and sugar cravings
  • recurrent vaginal yeast infections
  • brain fog
  • fatigue
  • anxiety or depression
  • headaches
  • sleep disturbance
  • alcohol intolerance
  • skin rashes
  • toenail fungus
  • chemical sensitivities

What to eat when you have SIFO.

I often treat SIFO with a combination of probiotics, herbs, and sometimes prescription antifungal medications, but the critical element to making these interventions successful is diet. I recommend that most people follow a low-carb, paleo-style diet that is high in fiber and healthy fats. The focus should be on whole, organic, non-GMO foods, including:

Nonstarchy vegetables

Focus on greens and cruciferous vegetables like cauliflower, broccoli, kale, Brussels sprouts, and arugula.


Low-glycemic fruits

Stick to blackberries, blueberries, cranberries, raspberries, and strawberries. Green apples, pomegranate seeds, grapefruit, lemons, and limes are decent options as well.

Healthy fats

Use minimally refined, cold-pressed oils like avocado, coconut, extra-virgin olive, and sesame oils. Coconut and olive oils can be especially therapeutic, as they possess antifungal properties. You can also include whole avocados, coconut manna, full-fat coconut milk, olives, and vegan pesto.


Nuts and seeds

Eat raw, unsweetened almonds, brazil nuts, flaxseeds, hazelnuts, pecans, pine nuts, pumpkin seeds, sunflower seeds, tahini, and walnuts. These are best stored in the refrigerator to maintain freshness and prevent mold.

Nondairy nut milks and yogurt

Stick to unsweetened almonds, cashews, coconut, flaxseed, hazelnuts, and hemp. Look for products that are free of sweeteners and additives like carrageenan.


High-quality, lean protein

For those who consume animal products, this includes pastured eggs, chicken, grass-fed beef, buffalo, and lamb. Look for wild-caught, low-mercury fish like anchovies, clams, salmon, sardines, scallops, sole, and trout. Pure, organic pea or hemp protein powder can also be used.

Herbs and spices

These can be especially therapeutic and include chili, fresh garlic, ginger, rosemary, oregano, cloves, and cinnamon. Garlic is a natural antimicrobial due to its high sulfur content. Clove also possesses powerful antifungal activity.

Unsweetened condiments

Use unsweetened condiments like fresh lemon and lime juice, Dijon mustard, apple cider vinegar, and salsa.

Unsweetened beverages

Drink plenty of filtered water, and enjoy unsweetened drinks like bone broth, vegetable broth, and fresh-pressed vegetable juices. Herbal teas like echinacea, fennel, ginger, lemongrass, and peppermint are healing for digestion. Spice up your mineral water with fresh mint and a slice of cucumber or grapefruit.

What to avoid when you have SIFO.

If you suffer from fungal overgrowth, dietary goals include elimination of sugar in its many forms, which is food for yeast. It is also best to keep carbohydrate intake low and avoid naturally occurring molds and yeasts in foods.

Sugar and sweeteners

Eliminate all sugar, natural sweeteners (maple syrup, honey, agave, etc.) and artificial sweeteners. This includes sweetened beverages like fruit juice and soda. You can substitute with small amounts of raw organic stevia. Also, steer clear of condiments with added sugar like most commercially prepared salad dressings and sauces.


Avoid most dairy, including cheese, cow's milk, goat's milk, and all flavored or sweetened yogurts. Dairy is high in lactose, which is a sugar.

Processed and smoked meats

Avoid all deli meat, lunch meat, aged meats, and processed meats.

Corn and refined grains

Avoid corn and corn products like chips, polenta, and tortillas. Also avoid all refined grains like white bread, sweetened cereals, baked goods, and yeast breads. Most people should avoid whole (intact) grains as well, but some tolerate a small serving of gluten-free grains like quinoa, jasmine, or basmati rice.

Starchy and root vegetables

You don't have to avoid these completely, but limit starchy vegetables like sweet potatoes, white potatoes, and winter squash (acorn, butternut, kabocha, etc.).


It's best to avoid edible fungi like mushrooms, morels, and truffles.

High-glycemic fruit

Limit most fruits not mentioned above, and eliminate all dried fruits and fruit juices.

Moldy foods

Avoid cashews, pistachios, and peanuts as they can be contaminated with mold. Other foods prone to mold include many listed above, such as corn, grains, and blue cheese.

Fermented foods and vinegars

I recommend avoiding kombucha, in part because of its high sugar content. I find that some people tolerate lactofermented vegetables like sauerkraut, pickles, and kimchi, which are rich in lactic acid bacteria. It's best to limit vinegar as well, with the exception of apple cider vinegar.

It certainly takes work, but you will find that as symptoms subside and bloating resolves, following these dietary restrictions becomes easier. Hang in there! I've been there, done that…and it was well worth the effort.

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