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Understanding Small Intestinal Fungal Overgrowth (SIFO)

Updated: Feb 25

In the intricate ecosystem of our bodies, various microorganisms coexist, playing essential roles in functions such as vitamin production, immune support, and nutrient absorption. However, when this balance is disrupted due to factors like a compromised immune system, dietary choices, stress, or medication use, an overgrowth of certain microbes, including fungi and yeast, can occur.

One such overgrowth, often overlooked but increasingly recognized, is Small Intestinal Fungal Overgrowth or SIFO. In this article, we delve into the world of SIFO, its symptoms, causes, and how to address it, drawing on insights from functional medicine.

Graphic of intestines on a women's abdomen

What is Small Intestinal Fungal Overgrowth (SIFO)?

SIFO occurs when an excessive amount of fungi or yeast proliferates in the small intestine, leading to various gastrointestinal symptoms. These symptoms can include abdominal bloating, pain, gas, belching, diarrhea, and nausea. If left untreated, SIFO may even result in malnutrition and weight loss over time.

Studies suggest that SIFO is a common underlying cause of unexplained gastrointestinal distress, affecting approximately 25% of individuals with symptoms often associated with conditions like irritable bowel syndrome (IBS). The predominant culprit behind SIFO is an overgrowth of Candida species, which are typically present in small quantities in the mouth, skin, and intestines but can cause issues when they multiply excessively.

Candida albicans fungus on agar dish

The Candida Connection

Candida species, primarily Candida albicans, make up a substantial portion of the fungi linked to SIFO, accounting for around 97% of cases. These yeasts or fungi naturally inhabit various parts of our body, such as the skin, mouth, throat, gut, and vagina. When Candida populations are balanced, they contribute to a healthy microbial environment. However, when these fungi overgrow in the small intestine, they disrupt the microbial equilibrium and trigger problems like SIFO.

Symptoms of SIFO

The symptoms of SIFO closely resemble those associated with Small Intestinal Bacterial Overgrowth (SIBO) and often overlap with those of IBS. Common symptoms include:

  • Belching

  • Bloating

  • Gas

  • Indigestion

  • Fullness in the upper abdomen

  • Reflux / Heartburn

  • Nausea

  • Diarrhea and/or Constipation

Furthermore, SIFO can extend its impact beyond the gastrointestinal tract, leading to additional signs like:

  • Chronic skin yeast infections or rashes in areas where skin meets skin (e.g., armpits, under the breasts)

  • Vaginal yeast infections

  • Itching behind the ears

  • Toenail fungus

  • Thrush (a white coating on the tongue)

  • Urinary tract infections

If left unaddressed, SIFO can contribute to inflammation throughout the body, as well as malnutrition and weight loss.

Contributing Factors to SIFO

Several factors increase the likelihood of fungal overgrowth in the small intestine or other body sites. To maintain a healthy balance of gut bacteria and fungi, factors such as proper immune function, stomach acid, and bowel motility are crucial.

  • Immunocompromise: People with weakened immune systems, including the very young, elderly, and those taking immunosuppressant drugs, are more susceptible to fungal overgrowth.

  • Low Stomach Acid: Inadequate stomach acid can heighten the risk of fungal overgrowth since stomach acid plays a pivotal role in neutralizing bacteria and fungi before they reach the small intestine.

  • Antibiotic Use: The use of antibiotics can disrupt the balance of healthy gut bacteria and create an environment conducive to fungal (or certain bacterial) overgrowth.

  • Slow Motility: Impaired movement of food through the small intestine, due to conditions like diabetes, hypothyroidism or sedentary behavior, increases the risk of bacterial and fungal overgrowth.

  • Lifestyle Factors: Dietary choices, such as high consumption of refined carbs or sugars, excessive alcohol intake, and chronic stress, can contribute to dysbiosis and SIFO.

Diagnosing SIFO

Diagnosing SIFO can be challenging, but several tests and approaches can help pinpoint the issue:

  • Comprehensive Stool Testing: A comprehensive stool test provides valuable insights into the overall health and balance of the digestive tract by measuring various microbes and intestinal health markers. It can uncover Candida albicans overgrowth and investigate underlying reasons for the overgrowth, such as dysbiosis.

  • SIBO Breath Test: Since SIBO and SIFO share similar symptoms and often co-occur, evaluating for bacterial overgrowth in the small intestine through a breath test is essential when SIFO is suspected.

  • Small Bowel Aspirate Test: The gold standard for diagnosing SIFO involves a small bowel aspirate, a procedure that collects fluid from the small intestine during an upper endoscopy. This fluid is then analyzed for the presence of abnormal fungi and/or bacteria.

female microbiologist in sterile clothing dropping reagent in petri dish

Addressing SIFO through Functional Medicine

Functional medicine takes a holistic approach to address SIFO, considering individual factors and tailoring treatment to the patient's specific needs. Here are some key strategies:

  • Dietary Approaches: Customized dietary strategies designed to deprive fungi of their primary fuel source are crucial. Practitioners utilize various diets, including the Anti-Candida Diet, Keto diet, Low Carb diet, anti-inflammatory Mediterranean diet, and elemental diet. Nonetheless, the fundamental step in curbing fungal overgrowth and reinstating gut equilibrium is the avoidance of sugar, alcohol, high-carb, and heavily processed foods.

  • Rebalance the Gut Microbiome: Emphasizing a Mediterranean diet, rich in citrus fruits, vegetables, legumes, and complex carbohydrates, can help balance inflammation and promote gut health. Probiotic-rich foods like kimchi and sauerkraut, as well as prebiotic-rich foods like artichokes and garlic, support healthy bacteria.

  • Herbal Medicine: Herbal antimicrobials such as caprylic acid, oregano oil, garlic, and berberine may be employed to inhibit fungal growth. These herbs can confer both antibacterial and antifungal properties.

  • Probiotics: These beneficial bacteria, when introduced in adequate quantities, help restore microbial balance in the digestive tract. In the context of SIFO, probiotics contribute to creating a slightly acidic environment in the gut, which is less hospitable to Candida and other harmful fungi. By doing so, probiotics help inhibit the overgrowth of these pathogenic organisms. Additionally, probiotics support immune function and strengthen the intestinal barrier, aiding in the prevention of further fungal infiltration into the bloodstream.

  • Supporting Digestion: Strategies to improve stomach acid and motility, such as the use of zinc, B vitamins, betaine HCl, enzymes like papain or bromelain, and bitters, can be integrated.

  • Herbal Prokinetics: Natural supplements such as ginger, 5-HTP, bitter candytuft, angelica root, chamomile, and caraway can aid in restoring proper stomach and intestinal muscle function and motility.


Small Intestinal Fungal Overgrowth (SIFO) is an increasingly recognized issue that can significantly impact health and well-being. Recognizing the signs, addressing contributing factors, and adopting personalized approaches through functional medicine can provide effective solutions to restore balance to the gut microbiome and alleviate symptoms. If you suspect SIFO, don't hesitate to seek help and prioritize your health.


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