SIBO: Definition, Causes, & Treatment

By Nathalie Boutros, Ph.D.
​Reviewed by Tchiki Davis, M.A., Ph.D.
Learn what SIBO is, how to tell if you have SIBO, some of the potential causes of SIBO, and how you may be able to treat SIBO.
*This page may include affiliate links; that means we earn from qualifying purchases of products.
By some estimates, the human body contains as many bacterial cells as it does human cells (Sender et al., 2016). You’re just as much bacteria as you are human! Many of these bacteria live in the digestive system. The bacteria that live in our guts play a part in breaking down the foods that we eat into the nutrients that power our bodies, help to protect us from potentially harmful microorganisms, and create some of the chemical building blocks used to make our cells (Hooper et al., 2002).​
A healthy digestive system is equipped with a system of checks and balances, keeping bacteria where they ought to be and keeping their numbers at appropriate levels. However, for several reasons, things can get out of balance, and the number of bacteria in the digestive system, especially in the upper part of the digestive system, can increase to abnormally high levels. When this happens a condition called SIBO, or Small Intestinal Bacterial Overgrowth, may develop. This may lead to negative effects on health and well-being. In this article, we’ll talk about what SIBO is, how it may develop, how you may be able to tell whether you have SIBO, and potential treatments for SIBO. ​​
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What Is SIBO? (A Definition)

SIBO, or Small Intestinal Bacterial Overgrowth, describes a condition either where the total number of bacteria in the small intestine increases, or there is a change in the diversity of bacterial species in the small intestine. To qualify as SIBO, these physiological changes must be accompanied by gastrointestinal discomfort or symptoms of digestive distress (Bures et al., 2010).
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In a healthy digestive system, there are usually fewer bacteria in the upper part of the digestive tract compared to the lower part of the digestive tract. Gut bacteria are usually at their lowest concentrations in the small intestines and their highest concentrations in the colon (Stearns et al., 2011). In SIBO, this balance is altered and there are excessive bacteria in the small intestines, leading to gastrointestinal symptoms (Pimental et al 2020). Moreover, the bacteria found in the upper digestive tract of people with SIBO are from species more typically found in the lower parts of the digestive system. 

Symptoms of SIBO

Excessive bacteria in the small intestine can interfere with how nutrients like carbohydrates, proteins, lipids, and vitamins are metabolized and absorbed. Bacteria in the small intestines may metabolize the foods you eat before your body’s cells have the time to extract and absorb nutrients. The metabolites that these bacteria produce may then cause gastrointestinal discomfort. In addition, elevated levels of gut bacteria or their metabolites may “leak” out of the intestine, leading to an inflammatory immune response (Ghoshal & Ghoshal, 2017). The effects of excessive bacteria in the small intestine may lead to the gastrointestinal or nonspecific symptoms of SIBO.

The most common symptoms of SIBO are digestive discomfort and can include (Rao & Bhagatwala, 2019)
  • Diarrhea
  • Constipation
  • Abdominal pain or cramping
  • Bloating or abdominal distension
  • Flatulence
  • Belching
  • Indigestion
  • Nausea

In more severe or extreme cases, symptoms of SIBO can include:
  • Steatorrhea (fatty stool)
  • Weight loss
  • Anemia
  • Vitamin deficiencies (especially of the fat-soluble vitamins A, D, E, and K)
  • Mucosal inflammation

SIBO may also have some effects on mental processes and cognition. People with SIBO have been known to report symptoms of brain fog including mental confusion, impaired judgment, impaired short-term memory, and difficulty concentrating (Rao et al., 2018).

There is no single symptom that unambiguously points to SIBO - symptoms of SIBO can look like symptoms of irritable bowel syndrome, Celiac disease, or a range of other conditions affecting the digestive system. This may make it difficult to diagnose SIBO without laboratory testing.

Tests for SIBO

The gold standard for SIBO testing involves taking a sample from the small intestine and testing it for bacterial content (Choung et al., 2011). This is done via a medical procedure called an endoscopy in which a long tube is interested through the mouth and is guided into the intestines. This procedure is invasive, time-consuming, expensive, and requires sedation (Pimental et al., 2020). 

A simple, non-invasive, inexpensive alternative to endoscopic testing is a breath test. Breath tests rely on the fact that human cells do not produce the gases hydrogen and methane (Pimental et al., 2020). If these gases are detected in the breath, bacteria capable of producing these gases are implicated. Bacteria in the intestines metabolize the foods that you eat and produce these gases, which are then absorbed into your bloodstream and then eventually expelled through your lungs when you breathe (Gasbarrini et al., 2007).

In a SIBO breath test, you ingest a specific carbohydrate (usually glucose or lactulose). You then provide a breath sample every fifteen minutes for anywhere between 90 to 240 minutes (Resaie et al., 2017). 

You will probably receive instructions from your doctor on how to prepare for the SIBO breath test. You may need to avoid antibiotics or other medications for up to four weeks before the test. You may also be asked to avoid fermentable food like complex carbohydrates for a day and may need to avoid all food for twelve hours before the test. You probably won't be able to smoke or engage in heavy physical exertion while taking the breath test.

These breath tests may not be suitable for all people, especially those with underlying medical conditions. For example, if you have diabetes, you may not be able to tolerate glucose. Working with a doctor who is familiar with your medical history may help ensure that you get the test that is right for you. Alternative tests more appropriate for people unable to tolerate glucose or lactulose may be available (Bhagatwala et al., 2018).

What Causes SIBO?

In most healthy digestive systems, gut bacteria tend to be most highly concentrated in the lower parts of the digestive system, with comparatively fewer bacteria in the small intestines (Stearns et al., 2011). Many physiological mechanisms safeguard against bacteria migrating and overgrowing in the small intestines.

Some of these safeguards include gastric acids, pancreatic enzymes, and bile acids all with antimicrobial effects. In addition, the natural contraction patterns of the digestive system tend to push downwards, ensuring that there is very little migration up the digestive tract. The intestines are also equipped with anatomical features like one-way valves that prevent excessive bacterial migration from the colon to the small intestine (Bures et al., 2010). Lastly, mucosal immunity in the small intestine prevents excessive bacterial growth. 

When any of these safeguards become impaired, bacteria from the lower part of the digestive system may migrate to the upper part of the digestive system, leading to SIBO (Sekirov et al., 2010). Normal digestive system functioning may be disturbed by a range of different illnesses, medications, or medical interventions (Pimental et al., 2020), and sometimes no underlying cause can be found to account for SIBO.

Some of the illnesses and disorders that may lead to SIBO can include (Bures et al., 2010)
  • Diabetes
  • Irritable Bowel Syndrome. Up to 85 percent of people with IBS may have SIBO.
  • Crohn's disease. About 25 percent of people with Crohn's disease may have SIBO.
  • Celiac disease that is not responsive to a gluten-free diet.
  • Alzheimer's
  • Some cancers
  • Muscular Dystrophy
  • Parkison's
  • Chronic Renal Failure
  • Fibromyalgia 
  • Alcoholism
  • Multiple Sclerosis
  • Pancreatitis
  • Cystic Fibrosis
  • Immunodeficiency syndromes including AIDS
  • Inflammatory Bowel Disease
  • Restless Leg Syndrome
  • Coronary artery disease
  • Short-Bowel Syndrome 
  • Morbid obesity with no other symptoms. Up to 17 percent of morbidly obese people may have SIBO, compared to 2.5 percent of non-obese people

Some medications may also cause SIBO. For example opioids, antidiarrheals, or anticholinergics may reduce movement in the intestines, letting food stagnate in the small intestines and allow bacteria to migrate from the colon to the small intestine. A popular group of medications called proton pump inhibitors (for example omeprazole) that are often used to treat acid reflux and other symptoms of gastrointestinal discomfort may decrease gastric acid levels, making the upper digestive tract more hospitable to bacteria (Pimental et al., 2020). Antibiotics may also sometimes lead to excessive bacterial growth in the digestive system if the natural balance of gut bacteria is thrown off. For example, antibiotic use has been associated with pathological overgrowth of the bacteria responsible for C-diff infection (Sekrov et al., 2010). Excessive probiotic use may also increase the risk of developing SIBO.

Other medical procedures such as radiation therapy and some abdominal surgeries including hysterectomies, gastrectomies, cholecystectomies, and colectomies may also put you at risk of developing SIBO (Pimental et al., 2020). SIBO may also arise as a result of obstruction of the small intestines due to tumors, strictures, adhesions, diverticula, or fistulae. Gastroenterologists have also recently proposed that chronic SIBO may follow in the months after a case of food poisoning.

How to Treat SIBO

The goal of treatment for SIBO is the relief of uncomfortable symptoms and restoring the small intestine’s ability to clear food and absorb nutrients. This can be achieved by treating any underlying diseases, prescribing a course of SIBO-specific antibiotics, or using a SIBO diet. In the short video below Dr. Mark Pimentel, a prominent SIBO researcher and gastroenterologist at Cedars-Sinai hospital briefly describes what SIBO is and then reviews treatment options for SIBO.

Dr. Pimentel suggests that anyone who suspects they may have SIBO first undergo breath testing to confirm this and to determine which type of bacteria are present in excessive numbers. A course of antibiotics can then be prescribed to decrease bacterial numbers. Once the SIBO has been brought under control through the use of antibiotics, dietary changes may keep the GI tract functioning. This may involve changing the content of what you eat, taking in fewer complex carbohydrates that support intestinal bacteria. Dietary changes to reign in SIBO may also involve increasing the spacing between meals, allowing your digestive system ample time to process and digest food. This may mean a period of 4 to 5 hours between meals, although longer periods, such as in intermittent fasting, may also be beneficial.

​Herbal or alternative treatments such as Atrantil can also be helpful, especially if one does not want to take antibiotics.

Video: Improving Gut Health & SIBO

Antibiotics for SIBO

Antibiotics are often the first course of treatment for SIBO. Ideally, the specific antibiotics used to treat the SIBO should be chosen to target the bacterial species that are over-represented in the small intestine. Testing for SIBO may be able to determine this and thus inform the decision on which antibiotics to use. In some cases many bacterial species, each with different antibiotic sensitivities, may all be implicated in SIBO, necessitating the use of wide-spectrum antibiotics (Gasbarini et al., 2007). Antibiotic treatment of SIBO is somewhat effective, with one meta-analysis reporting that antibiotics are effective in eradicating SIBO in 70 percent of patients (Gatta et al., 2017).

Antibiotic treatment for SIBO typically lasts between 1 and 2 weeks. Several different antibiotics may be effective in treating SIBO and you and your doctor may want to work together to select the antibiotic that is most likely to address your concerns with as few side effects as possible.

Probiotics for SIBO

Probiotics are not usually recommended to treat SIBO. Since SIBO is an overgrowth of gut bacteria, introducing more bacteria into the gut may not bring relief. Scientific research supports this, with little evidence supporting the efficacy of probiotics in the treatment of SIBO (Gasbarinni et al, 2007).

Having said this, there is limited evidence of some potentially beneficial effects of probiotic use on SIBO. Probiotics may help with some of the symptoms of SIBO (Zhong et al., 2017), although the evidence in these studies is not particularly strong. Some laboratory studies have suggested that some beneficial bacteria may be able to limit the growth of harmful bacterial species (Sanz et al., 2007). For example, the bacteria strains lactobacillus and bifidobacterium, found in fermented foods like yogurt, kimchi, sauerkraut, and miso may prevent the growth of listeria in cell cultures.

Given that the evidence for probiotic treatment of SIBO is limited, and that probiotic bacteria may inadvertently colonize the small intestine, potentially contributing to SIBO (Rao et al., 2018), it may not be wise to try to treat SIBO with probiotics. Dr. Pimentel, the gastroenterologist featured in the video above, specifically cautions against ingesting probiotics if you have SIBO. If you are still interested in trying probiotics for SIBO, you should consult with your physician or with a registered dietician for guidance on how to proceed.

SIBO Diet

Changing your diet may help to relieve many of the symptoms of SIBO (Pimental et al 2020). The dietary approach to treating SIBO largely rests on reducing your intake of foods that are  difficult to digest or that are digested slowly. The foods that our body’s cells can’t or don’t digest go on to instead feed the bacteria that live in the gut. In most cases eating to treat SIBO involves adopting a low fiber diet that avoids things like complex carbohydrates, leafy vegetables, beans, and legumes.

​A SIBO diet will also probably avoid artificial sweeteners like sucralose which tend to feed gut bacteria. A low FODMAP diet may be helpful. This diet lists specific low-fermentable foods from every food group (McIntosh et al., 2017). In the short video below two registered dieticians describe the low FODMAP diet as a potential way to address symptoms of gastrointestinal distress that may be due to SIBO. As the dieticians mention, this may be a difficult diet to follow and you may find more success working with a doctor or a registered dietician.

Video: The FODMAP Diet for SIBO: What You Need to Know | UCLA Digestive Diseases

Articles Related to SIBO

Want to learn more? Here are some related articles that might be helpful.​​

Books Related to SIBO

Here are some books that may help you learn even more.

Final Thoughts on SIBO

The bacteria that live in the human gut are essential to good health and well-being. They play a crucial part in extracting nutrients from the food that you eat and in creating the chemical building blocks of your cells. However, when these bacteria become too plentiful, or when they migrate to places where they don’t belong, you may experience symptoms of gastrointestinal discomfort.

Luckily, relief may be possible. Straightforward, noninvasive laboratory tests exist to determine whether you have excessive bacteria in your digestive tract. These tests may even be able to determine the specific bacterial species that are present in excess. Treatment may also be relatively straightforward with many people responding well to a short course of antibiotics followed by dietary changes. Relief from the discomfort of SIBO may be within your reach.

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