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Intestinal Yeast Overgrowth – Driver of Multiple Symptoms

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.

The diet:

The anti-candida diet is essentially a whole food (but low sugar) diet. (Note, it’s sometimes called “the Candida diet,” but it involves reducing foods that contribute to Candida growth.) The foods that Candida thrives on are often pleasurable to eat or drink, such as sugary desserts, sodas, beer, and wine. Unfortunately, carbohydrates, especially from sugar and grains, greatly contribute to Candida growth. It may be difficult at first to stay away from pasta, bread, muffins, and cookies washed down with a glass of wine or a cold brew. However, if you can stick with the diet, Candida will begin to die off when they don’t have as many of their favorite foods. In other words, they can be starved down to a smaller population size, allowing the gut flora to rebalance. After a potentially harsh withdrawal period, people generally feel so much better that they continue to leave many foods out of their diet even after the Candida is dealt with.


1) Getting it right the first time you do treatment will save numerous headaches (literally) in the future because what does not get killed off in the first treatment may be able to resist future treatments. Also, it’s a catch-22, as doing repeated Candida treatments back-to-back can harm the natural balance of gut flora.

2) The anti-candida diet can be difficult for the first 3 days. Candida will begin to die off when deprived of their favorite foods. This can result in a “Herxheimer reaction,” which is a normal and natural reaction to the toxins released when Candida and other microorganisms die. The reaction to the die-off can cause headaches and body aches, but these are usually fairly mild, allowing people to continue activities and go about their day.

3) IV ozone therapy may be a game-changer for those who get recurring SIFO infections. Recurring infections could indicate a rare kind of invasive Candida infection that enters the bloodstream, called candidemia (11). The closed-loop system of IV ozone therapy takes your own blood out of your body, uses ozone to kill microorganisms, and puts the cleansed blood back in your body. Ultraviolet (UV) light can be added to this treatment, which extends the cleansing power to eradicate microorganisms in the blood.

Yeast Overgrowth in the Large Intestines

Yeast overgrowth can also occur in the large intestines, but this infection can be independent of SIFO, which is in the small intestine. In other words, it’s not a given that a SIFO infection will cause an infection in the large intestine. Likewise, a diagnosis of fungal overgrowth in the large intestine does not necessarily mean an infection in the small intestine. Both the small and large intestines can have an overgrowth of yeast at the same time! Luckily, however, if the small intestine is targeted for a SIFO treatment, the treatment can and does reduce the number of yeast in the large intestine, which is lower in the GI tract. The symptoms are overlapping with SIFO, but there are a few symptoms that are distinct to yeast overgrowth in the large intestine, largely due to the tight relationship of the gut with the brain.

Increases Risk of Yeast Overgrowth in the Large Intestine (12):

  • all of the risks listed above for SIFO in the small intestine

  • diabetes

  • high sugar diet

  • already have a disease of the GI tract (Crohn’s, ulcerative colitis, ulcers)

Symptoms of Yeast Overgrowth in the Large Intestine:

  • bloating

  • diarrhea

  • constipation

  • gas

  • abdominal cramping

  • fatigue

  • depression

  • allergies

  • recurrent vaginal yeast infections

  • headaches

  • recurrent jock itch or nail fungus (toe or finger)

  • aching joints

  • brain fog

  • anal itching, especially after a sugary meal or alcohol *this is a very common symptom

Diagnosis of Yeast Overgrowth in the Large Intestine:

The go-to test for yeast overgrowth in the large intestine is a stool test. There are some drawbacks to stool testing, though, especially if only testing for the presence of Candida. Newer, more advanced tests include DNA tests on the microorganisms collected from the stool to positively identify particular species and also give the amount found in the sample. This can greatly aid diagnosis. Some stool tests include a microscopy portion to identify microorganisms visually as a double-check. Questionnaires can also be fairly accurate for picking up cases of Candida overgrowth. The blood tests mentioned for SIFO also apply.

Testing the blood for blood sugar levels (glucose and A1C) at this time is also helpful, as the high sugar diet that creates a welcoming environment for Candida can also push the body towards a diabetic state. Many cases of pre-diabetes and diabetes are caught in this manner.

Treatment of Yeast Overgrowth in the Large Intestine

It’s usually the symptom of anal itching that finally drives patients to seek treatment. An overgrowth of yeast in the large intestine can cause yeast to grow on the surface of the body where stool exits the body- the anus. This can create a strong urge to itch, one that cannot be ignored. Topical treatments are sometimes prescribed to kill the yeast there and reduce itching, while prescription medications or plant antifungals are suggested to address Candida from the inside. The dosage and makeup of the prescription or plant antifungals may be slightly different than the treatment for SIFO, however, pairing them with the anti-candida diet for efficacy still applies. Post-treatment use of probiotics may be required to seed the large intestine with beneficial bacteria and rebalance gut flora.

As complementary therapies, colon hydrotherapy or IV ozone therapy may be suggested. Colon hydrotherapy could be helpful in cases of extreme yeast overgrowth in the large intestine, as it would help expel large colonies and biofilms from the colon. IV ozone therapy could help reduce the overall burden on the body and catch any Candida that has made it into the blood.

Addressing yeast overgrowth can be daunting but can be made much easier with the guidance of an experienced health practitioner. If you suspect you have an underlying yeast issue, make an appointment with TCIM for an evaluation. Addressing yeast overgrowth early in the process will make it much easier to eradicate. You’ll feel so much better, you’ll wonder why you waited so long!


Jonathan Vellinga, M.D.

Jonathan Vellinga, MD is an Internal Medicine practitioner with a broad interest in medicine. He graduated Summa cum laude from Weber State University in Clinical Laboratory Sciences and completed his medical degree from the Medical College of Wisconsin.​

Upon graduation from medical school, he completed his Internal Medicine residency at the University of Michigan. Dr. Vellinga is board-certified with the American Board of Internal Medicine and a member of the Institute for Functional Medicine.




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