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Intestinal Yeast Overgrowth – Driver of Multiple Symptoms

Jonathan Vellinga, MD -

Intestinal Yeast Overgrowth

There are many different types of yeast, including yeasts that help create bread and beer! They are types of fungi that mostly live in harmonious, mutually beneficial relationships with bacteria, plants, and humans (1). Yeasts, along with bacteria, viruses, and parasites, are part of the millions of microscopic organisms that humans host. Yeasts are a subcategory of fungus along with mushrooms and molds, and if someone is not being specific may use the terms “yeast” and “fungus” interchangeably. There are about 1,500 species of yeast, and they can have unique characteristics depending on their species. Some species of yeast, such as Candida, can create health problems by overgrowing in the human body.

The idea of yeast creating health problems has not always been accepted or popular. It’s been known for a long time that yeast dwells in and on humans, but it was thought that its presence was always benign. Then, in 1984, William G. Crook, M.D., wrote the book “The Yeast Connection,” outlining the symptoms of yeast overgrowth, bringing the condition to the public’s attention. It has remained a classic read for a good foundational knowledge of the condition, with new editions and cookbooks added over the years.

Candida albicans (C. albicans) – Yeast Species of Interest

Candida albicans is a species of yeast that is often the culprit in an overgrowth situation. It is a single-celled fungus that thrives in the human body and is often simply called “yeast” or “candida.” C. albicans lives on our skin and within us, mostly living in the linings of our gastrointestinal tract (mouth, throat, esophagus, stomach, small and large intestines, rectum), but also dwelling in the reproductive tracts (2). It is estimated that roughly half of adults have C. albicans in them without having negative symptoms. They divide easily, but the cell walls of yeast are very tough and difficult to penetrate, making them very hardy and resistant to medications. Oddly, C. albicans is known to produce a toxin that can damage the host’s cells (3).

Double Trouble – This Yeast Can Take Two Forms

Not only can C. albicans take the form of a cell, but they can also grow filamentous cells, tendrils that can grow out like a vine. These tendrils, called “hyphae,” can grow through groups of cells that form a tissue, such as intestinal linings. In the lab, they can grow through tissues as fast as 22 hours (4). Not surprisingly, the hyphae form of the yeast is considered “pathogenic,” meaning it can cause a health issue or disease. In severe (but rare) cases, C. albicans pierces the walls of the large intestine with the hyphae, causing an acute health crisis (5).

C. albicans can also become part of a biofilm or help create one. A biofilm is a tight mat of microorganisms that form together as a form of protection, which can be beneficial or pathogenic, as not all biofilms are dangerous to humans. In the intestine, C. albicans can help form a biofilm with their hyphae, which overlap like a basket weave and form a structure to which other microorganisms can also join. This biofilm is very difficult to eradicate once grown, as the microorganisms combine their protective capabilities, making it difficult for medications to penetrate the mass (6). This sets the yeast up to live a long time, creating a chronic condition of gut flora imbalance. They can clog up the large intestine, making water reclamation from the wastes more difficult.


The overgrowth of any of the Candida family of yeasts is called “candidiasis.” The symptoms may vary depending on where the overgrowth occurs. It is always our goal to find the root cause of illness, and we find that the overgrowth of Candida in the intestines is often the root cause of a wide variety of symptoms. If the underlying Candida overgrowth is not addressed, the symptoms can persist and worsen over time until the patient is seriously ill. The longer the condition persists, the harder it becomes to eradicate.

Yeast Overgrowth in the Small Intestines (SIFO - Small Intestine Fungal Overgrowth)

Many people are already familiar with SIBO – Small Intestine Bacterial Overgrowth. However, bacteria are not the only thing that can negatively impact the small intestine and disrupt the digestive tract. Normally the small intestine resists being populated by microorganisms. The small intestine naturally has an environment that discourages microorganisms from growing in there. However, there are a variety of conditions that make it more likely for funguses such as Candida yeasts to not only survive but thrive in the small intestine and start causing problems. The mere presence of GI symptoms can be an indication of an issue. There have been a few studies that showed that about 25% of people with “unexplained GI symptoms” actually had SIFO (7).

Common Symptoms of SIFO (7):

  • belching

  • indigestion

  • nausea

  • bloating

  • gas

  • diarrhea or constipation

Factors that increase risks of SIFO (8, 9):

  • weak stomach acid

  • food poisoning

  • frequent or prolonged use of antibiotics

  • lack of motility (muscle contractions that push substances through the digestive tract)

  • being immunocompromised

  • prolonged use of proton pump inhibitors (PPIs)

  • prolonged use of birth control pills

Diagnosis of SIFO:

Diagnosis of SIFO is tricky, unlike SIBO, which can be diagnosed by breath testing because bacteria can ferment a sugary substance given before the test. Yeasts don’t do any fermenting, so there is no convenient breath test to diagnose SIFO. The most reliable test for SIFO is getting a sample from the small intestine during an endoscopy procedure by a gastroenterologist. However, this is invasive, and few clinics perform this test.

Some strategic blood tests can show if there are antibodies to Candida, but these won’t determine if there is a current infection. Other blood tests can hint at an infection, such as low secretory IgA results. (Secretory IgA helps remove Candida but gets “used up” in the process.) Increased Beta-alanine in the blood can be a sign of SIFO because it’s a breakdown product of Candida.

Stool tests can pick up Candida strains, but the test cannot say if the Candida came from the small or the large intestine. Just because Candida can pathogenically thrive in the small intestine does not mean it has also conquered the large intestine. A negative stool test could just mean the Candida has not taken over the large intestine, but it could still be alive and well in the small intestine. So, most doctors will treat SIFO simply based on symptoms.


Typically, a prescription antifungal or plant-based antifungal supplement course will be suggested. An “anti-candida” diet may be suggested in addition to the antifungals. There is a much better chance of addressing yeast overgrowth if the diet is done in addition to the treatments. A pilot study found that adhering to the diet during and after the treatment resulted in much less Candida in the stool three months after the antifungal treatment, and subjects were considered cured (10).

If a patient has already been diagnosed with SIBO, often doctors will tag on treatment for fungal infection as well, since the conditions that allow SIBO will also allow SIFO.

Herbal or other plant-based antifungals perform remarkably well when compared to prescription antifungals. Typically, plant antifungals take a little longer, but they are less harsh on the whole system and anecdotally have a slightly better rate of preventing future overgrowth. Unfortunately, recurrence can happen after a course of either type of antifungal treatment. Sticking to the treatment plan, repopulating the gut flora with good bacteria post-treatment, and cutting out the foods that foster Candida overgrowth are key to addressing yeast overgrowth.