Small intestinal bacterial overgrowth can lead to bloating, diarrhea, constipation, and more.
Credit: Prasit photo

Having bacteria in your gut is a good thing–as long as it’s the right bacteria in the right place.

But people with a condition called small intestinal bacterial overgrowth or SIBO have bacteria that are supposed to live in the colon (aka the large intestine) trapped in the small intestine.

“It’s normal to have bacteria in your small intestine, but in SIBO two things happen,” explains Eamonn Quigley, MD, chief of gastroenterology and hepatology and professor of medicine at Houston Methodist Hospital. “You have more bacteria and you have bacteria that would normally be found in the colon. The small intestine begins to function a lot like a colon.”

That leads to symptoms much like those of irritable bowel syndrome or IBS, namely bloating, diarrhea or constipation, flatulence, and distention, though typically not vomiting. The exact symptoms depend on what kind of bacteria are running rampant in the small intestine, says Ali Rezaie, MD, director of the GI Motility Program at Cedars-Sinai Medical Center in Los Angeles.

IBS and SIBO, though, are not the same. “Not every IBS patient has SIBO and not every SIBO patient has IBS, but there’s a big overlap,” says Dr. Rezaie. Here’s what you need to know about SIBO–and how to tell if it’s causing your tummy trouble.

What causes SIBO?

SIBO is usually caused by a movement problem in the small intestine. “Every two hours, your small bowel initiates something called a ‘housekeeper wave,’ which sweeps through the small bowel and dumps everything, including excessive amounts of bacteria, residual food, digestive enzymes, and bowel secretions,” explains Dr. Rezaie.

But if something impairs the wave, the small intestine can’t expel the bacteria.

This can happen when the autoimmune disease scleroderma damages the muscle of the small intestine. “The small intestine becomes like a stagnant pool, an ideal environment for bacteria to thrive and reproduce,” says Dr. Quigley. Nerve damage in the gut, say, from diabetes, can also lead to SIBO.

Diverticulitis of the small intestine (a rare condition, not to be confused with the more common diverticulitis of the colon) may also cause SIBO, as can some surgeries or a fistula (a kind of abnormal “tunnel” connecting two parts of the body) between the colon and the small intestine.

Any bowel obstruction can also cause SIBO, making Crohn’s disease a possible culprit if the obstruction lasts long enough.

SIBO can also result from conditions that reduce naturally occurring stomach acid, which normally kills bacteria. SIBO is also more common as we age.

The use of some painkillers or excessive amounts of alcohol may play a role in SIBO; the condition is more common in alcoholics, says Dr. Quigley. There’s no evidence that your diet or drinking normal amounts of alcohol increase your risk.

You can even get SIBO after a bout of food poisoning, says Dr. Rezaie. “The symptoms of food poisoning should not last beyond two weeks,” he says. After that, lingering GI issues could be SIBO-related.

SIBO symptoms

In addition to the bloating, diarrhea, abdominal pain, and farts, SIBO can also bring symptoms that have nothing to do with the gastrointestinal tract, Dr. Rezaie says, such as brain fog and fatigue.

Severe SIBO can cause malnutrition. “The bacteria can consume some of the nutrients you should be getting, so you [become] deficient,” says Dr. Quigley. “One of the classic examples is vitamin B12 deficiency, which can have serious neurological consequences.”

If you have SIBO, you may also be low in iron, thiamine, niacin, and fat-soluble vitamins like A and K.

SIBO treatment

Doctors diagnosis SIBO with a breath test. The test measures how much hydrogen or methane gas–both byproducts of bacteria breaking down sugar in your gut–ends up in your breath. There are no blood or stool tests for SIBO.

If the breath test indicates SIBO, doctors often first look to address any underlying issue that’s causing the problem. For example, if narcotic painkillers are causing the backup, stopping the medication is often a good step to resolving the issue.

Clearing up the overgrowth usually requires antibiotics, however. And because recurrences are common, you may need repeat courses of the meds.

Any nutritional deficiencies caused by SIBO also need to be treated, usually with supplements.

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Two to three weeks of a liquid diet can "reset" the bacteria in your small intestine, and a diet low in fermentable foods can help prevent the bacteria from growing back, says Dr. Rezaie. That means cutting back on fiber and carbs (including sugars) and amping up the protein. However, “that’s not necessarily a heart-healthy diet,” adds Dr. Rezaie. “We need other remission strategies,” which may include medications to help keep the housekeeper waves stable.

Probiotics will likely make SIBO worse, says Dr. Rezaie. “SIBO is not about ‘good’ bacteria or ‘bad’ bacteria.” Rather, it’s about bacteria that are usually in your colon living in the small intestine. “Topping it off with a blast of bacteria from probiotics is not going to help anything,” he says.