Could Small Intestinal Fungal Overgrowth Be The Mysterious Cause of Your GI Troubles?

Stephanie Eckelkamp
Medically Reviewed
April 12, 2021

SIFO stands for small intestinal fungal overgrowth—and it’s responsible for a range of seriously unpleasant gastrointestinal symptoms like bloating , abdominal pain, and diarrhea. Often, it can get mixed up with SIBO (small intestinal bacterial overgrowth), but there are key differences and they don’t necessarily respond to the same treatments. Keep reading to get the rundown on SIFO, which could be the underlying cause of your GI symptoms.

What is SIFO?

“SIFO is essentially fungal overgrowth in the small bowel (or small intestines), as opposed to the bacterial overgrowth that occurs in SIBO ,” says Sarah Steinberg, MDPhD , a double-board certified internal medicine and gastroenterology physician at Parsley Health.

Research has found that 97 percent of the fungi associated with SIFO is some form of Candida , such as Candida albicans. Candida is a member of the fungal family, but is typically referred to as a yeast, and it’s actually supposed to be in your gut. In fact, Candida normally lives on the skin and inside the body, in places like the mouth, throat, gut, and vagina, without causing problems.

“But, like anything else in the gut, when [Candida] gets really out of balance, that’s when it becomes an issue,” says Dr. Steinberg. A variety of factors, from lack of movement to low stomach acid to certain medications, may contribute to fungal overgrowth in the gut.

(Candida overgrowth can take place in other areas of the body, too—learn how it can affect the health of your skin and nails, vagina, mood, and more.)

What are common SIFO symptoms?

In one study , around 25 percent of people with unexplained GI issues were found to have SIFO, and their most common symptoms were belching, bloating, indigestion, nausea, diarrhea, and gas .

“The most common symptoms of SIFO are really the same as those for SIBO ,” says Dr. Steinberg. “But my red flags for SIFO go up when I see other signs of fungal overgrowth such as chronic yeast infections or rashes in areas where skin meets skin, like armpits or under the breasts. Some patients also experience itching behind the ears.”

Toenail fungus, anal itching, and thrush (a white coating on the tongue) may also be indicators that you have some sort of systemic fungal overgrowth occurring. While these non-GI symptoms aren’t always present in people with SIFO, they do prompt Dr. Steinberg and others at Parsley Health to investigate further. “If there is fungal overgrowth in other places, it makes me think there may be fungal overgrowth in your gut as well,” she says.

What are the major SIFO risk factors?

While SIFO may be causing your GI symptoms, there are deeper root causes that lead to unhealthy proliferation of fungi in the first place. So, what are the major factors? According to Dr. Steinberg, these are some of the most common:

You’re immunocompromised.

Overgrowth of fungi is often more common in people with weakened immune systems , research has shown . This includes very young children, the elderly, and people taking immunosuppressant drugs like steroids, such as patients with certain autoimmune diseases and cancers.

You’ve used proton pump inhibitors (PPIs).

Proton pump inhibitors (PPIs) are medications commonly prescribed for acid reflux. They work by inhibiting certain stomach cells from “pumping” acid into the stomach. However, a certain level of stomach acid is needed not only for digesting food but for killing potentially harmful microbes (including bacteria and fungi) before they reach the intestines. With PPI use, this can’t happen, and long-term use of these medications has been implicated in both SIFO and SIBO.

If you have low stomach acid levels.

In addition to long-term PPI use, a variety of factors such as age, nutrient deficiencies , and high stress levels can contribute to the low stomach acid levels that would make you more likely to experience SIFO. Some signs and symptoms include bloating, undigested food in the stool, nausea while taking supplements , hair loss, and brittle fingernails. (Parsley Health practitioners often use a baking soda test, described here , to test stomach acid levels.)

You’ve recently taken antibiotics.

If you’ve been on a lot of conventional antibiotics like doxycycline recently—say, you were treated for Lyme disease—you may experience GI symptoms that could be fungal related (or fungal and bacterial). “Just the way you can get a yeast infection after taking antibiotics, you can get fungal overgrowth in your gut, too,” says Dr. Steinberg.

If you do need to go on antibiotics, Dr. Steinberg recommends taking a probiotic containing the beneficial yeast Saccharomyces boulardii to help prevent SIFO.

Something’s slowing your gut motility.

Anything that slows movement of food through your small bowel is also a significant risk factor for both SIFO and SIBO. These include things like diabetes, Ehlers-Danlos syndrome, or if you’ve had a colectomy. Sedentary behavior can also be a big one, says Dr. Steinberg, because it impairs blood flow to the digestive tract. Anytime food sits in the small intestines longer, bacteria and fungi can take up residence (and grow in numbers) where they shouldn’t.

How is SIFO diagnosed?

Sometimes a clinical diagnosis is made if your GI symptoms fit the SIFO profile and you have other signs of fungal overgrowth, such as recurrent yeast infections or worsening GI symptoms in response to consuming sugary, probiotic-rich, or vinegary foods and beverages.

But the “gold standard” of determining if someone has SIFO is with a duodenal aspirate (or a small bowel aspirate), says Dr. Steinberg. This is performed during an upper endoscopy—a procedure in which a tubular instrument is passed through your esophagus and stomach and into a portion of the small intestines called the duodenum. From there, fluid can be collected and analyzed for the presence of abnormal fungi. This is also a way to test for SIBO.

Only a gastroenterologist can perform an upper endoscopy and duodenal aspirate. But, based on your results, doctors at Parsley Health can work in conjunction with your gastroenterologist to determine your best course of SIFO treatment.

How is SIFO treated?

SIFO treatment often requires a multipronged approach involving conventional or herbal antifungals, and dietary and lifestyle changes. Each individual’s specific SIFO treatment will depend on the severity of their case and their personal risk factors, but may include these:

  1. Conventional or herbal antifungals

At Parsley Health, doctors often treat SIFO with conventional antifungal medications such as fluconazole, which, Dr. Steinberg explains, are pretty benign and don’t have much risk. They may also use herbal treatments containing naturally antifungal and antimicrobial ingredients such as olive leaf extract, grapefruit seed extract, and tea tree oil.

  1. An anti-candida diet

There are strategic dietary changes that can help limit fungal growth, too. Research has shown that cultured Candida cells flourish when glucose is added, so scaling back on sugar and refined carbs may curb SIFO symptoms. Additionally, Dr. Steinberg advises some patients to temporarily eliminate refined carbs and sugars, most fruits, grains, and foods or drinks containing yeast (e.g., alcohol, vinegar, sauerkraut, kombucha).

You probably won’t need to eliminate these foods forever, though. This is meant to be a short-term strategy that gets your small bowel back to homeostasis, at which point you can eat a more balanced diet, explains Dr. Steinberg.

  1. Movement and meal spacing

If low gastrointestinal motility is contributing to your SIFO, two big things can help improve it. According to Dr. Steinberg, the number one way we can support healthy motility is through frequent movement throughout the day—frequent walks (especially after meals), taking Sun Salutation breaks throughout your work day, doing a few squat jumps and pushups, or anything that gets your blood flowing.

Another way to improve motility: Space out your meals by 3-5 hours, and don’t eat within 3 hours of going to bed. You don’t always want to be noshing on something. Constantly having food in your stomach can impair one of your body’s key digestive mechanisms called the migrating motor complex (MMC)—a cyclic, recurring wave of movement that clears food out of the small bowel. It occurs every 90 minutes or so, but only when your stomach is empty.

  1. Addressing low stomach acid

If your clinician determines you have low stomach acid levels, they may recommend a hydrochloric acid (HCL) supplement. HCL can help to bring stomach acid levels back to normal so you can adequately digest food, absorb nutrients, and kill off unwanted fungi and bacteria.

Working with a qualified care team can help prevent SIFO recurrences.

Similar to SIBO , treating and preventing SIFO requires a multifaceted approach, and it can often recur if you’re not addressing the underlying symptoms that contributed to it in the first place, like low stomach acid and low motility. To make things more complicated, you could have SIFO and SIBO simultaneously, which will require a slightly different approach. Bottom line: SIFO is tricky, which is why enlisting the help of a care team, like the clinicians and health coaches at Parsley Health , can be so smart. They can aid in diagnosis, come up with a tailored treatment plan, and provide the necessary long-term support that will keep your SIFO risk factors in check.

Stephanie Eckelkamp

Stephanie Eckelkamp is a writer and certified health coach based in Allentown, PA. She received her B.S. in journalism from Syracuse University with a minor in nutrition. Her work has appeared in Martha Stewart Living, mindbodygreen, Greatist, Women's Health, Men's Health, Prevention, and Good Housekeeping. When she's not writing or nerding out on the latest health news, she's most likely on a walk with her pup Lucy Goose or trying to convince her boyfriend to eat more broccoli.

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