An Overview of Small Intestine Bacterial Overgrowth (SIBO)

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Small intestinal bacterial overgrowth (SIBO) is excessive gut bacteria in the small intestine. This condition is uncommon before the age of 65, and it is estimated to affect around 10 to 15 percent of adults over the age of 65.

SIBO can contribute to symptoms ranging from the abdominal bloating to nutritional deficiencies, so getting a timely diagnosis is important. There are a few conditions that increase your risk of SIBO, including diabetes and Crohn's disease. A breath test can help with diagnosis, and sometimes a biopsy is needed to confirm the condition.

There are a number of treatment strategies that can help reduce the symptoms of SIBO, and the proper treatment of your other GI conditions (if you have any) also helps alleviate the effects of SIBO.


With SIBO, you can experience vague symptoms and it can be hard to differentiate these effects from other common gastrointestinal (GI) problems. In fact, SIBO can worsen other GI condition, while other GI conditions can worsen SIBO, resulting in a cycle of illness.

Common effects of SIBO include:

  • Abdominal bloating
  • Flatulence and gas
  • Abdominal pain
  • Abdominal distension
  • Diarrhea, sometimes with urgency or soiling accidents
  • Foul smelling stools
  • Constipation
  • Nausea
  • Weight loss
  • Fatigue

You may experience all or some of these symptoms, and they can intermittently come and go.


SIBO can interfere with your absorption of essential nutrients. The health effects of malnutrition cause vague, subtle symptoms, such as fatigue, weight loss, depression. You can also develop serious health issues, such as osteoporosis (fragile bones) and anemia (low red blood cell function).

Nutritional deficits associated with SIBO include:

Excess bacteria in the small intestine can interfere with carbohydrate absorption. Sometimes, people who have SIBO avoid carbohydrates to prevent bloating and diarrhea. Overall, carbohydrate deficiency causes weight loss and low energy.

SIBO induced changes in the small intestine prevent proper protein absorption, resulting in weight loss and decreased immune function.

With SIBO, the bile acids which are responsible for the breakdown and absorption of fat are deficient. Fat malabsorption produces visible signs, including an oily appearance of stools, smelly stools, and floating stools. Health effects include weight loss and fatigue.

Fat-soluble vitamins, A, D, E, and K, may not be properly absorbed if you have SIBO.

  • Vitamin A deficiency can cause vision problems and immune deficiency.
  • Vitamin D deficiency causes osteoporosis and depression.
  • Vitamin E deficiency interferes with healing.
  • Vitamin K deficiency can cause easy bruising and bleeding.

Vitamin B12 deficiency can occur with SIBO because the excess bacteria in the small intestine utilize the vitamin themselves, decreasing its availability for your body. Vitamin B12 deficiency can result in peripheral neuropathy, resulting in pain of the fingers and toes. This vitamin deficiency also causes megaloblastic anemia (enlarged, dysfunctional red blood cells), resulting in fatigue and irritability.

SIBO can cause iron deficiency, which results in microcytic anemia (small, dysfunctional red blood cells) and a number of other health effects, such as fatigue.


Normally, bacteria in the small intestine aid in the breakdown and absorption of nutrients and help prevent infections. Because SIBO is an overgrowth of bacteria in the small intestine, the normal pattern of bacterial functions becomes altered. The bacterial overgrowth of SIBO also results in microscopic damage to the villi lining the walls of the small intestine, which impairs the absorption of nutrients.

Risk Factors

A variety of illnesses may predispose you to SIBO. These medical conditions are generally diagnosed years before SIBO and may alter the environment of the small intestine, predisposing you to SIBO.

Conditions associated with SIBO include:

Keep in mind that you can develop SIBO even if you don't have one of the associated risk factors, and your doctor may consider diagnostic testing if you have symptoms of SIBO without an obvious predisposing cause.

How SIBO Develops

The bacterial overgrowth in SIBO is believed to result from alterations in the acidity (change in pH) of the small intestine and decreased movement of the intestinal muscles.

The pH changes make it easier for bacteria to grow in the small intestine and also allow different types of bacteria to thrive. The decreased intestinal motility keeps bacteria in the small intestine for a longer period of time than usual, disrupting the normal balance of digestive enzymes.


There are three main ways to test for SIBO—through the use of hydrogen breath testing, through testing samples of the fluid in the small intestine taken during an endoscopy, or through a trial of specific antibiotics. Each method has benefits and limitations, and the direct sampling method through endoscopy is considered to be the most reliable.

Breath testing: Breath testing is a fast, non-invasive, and safe diagnostic testing method. With this test, you would drink a solution and then have your breath analyzed a few hours later. The presence of hydrogen or methane is indicative of malabsorption. However, this test is not considered highly reliable because there are other causes of malabsorption besides SIBO, and your medications and diet throughout the weeks prior to the test can alter the results.

Jejunal aspiration: This is an invasive test in which endoscopy is used to sample fluid from the small intestine. An endoscopy is a test in which a thin camera-equipped tube is placed down the throat to visualize the upper GI structures, and a biopsy or fluid sample can be taken while the endoscope is inserted. The test can provide helpful information regarding the bacterial content of the small intestine, but there can be other causes of bacterial overgrowth, including an infection.

Antibiotic trial: Another diagnostic method involves beginning antibiotic treatment of SIBO and assessing the response. This is usually a safe process, but you should let your doctor know immediately if your symptoms worsen while taking antibiotics.


If you have SIBO, you will need treatment for the condition. Treatment options include antibiotics to treat the bacterial overgrowth, management of your underlying medical condition (such as pancreatitis or scleroderma), and nutritional supplementation. You might not need to use all of these methods, and your own treatment will be tailored to your symptoms and the effects that you are experiencing from the condition.

Antibiotics: A number of antibiotics can be used to reduce bacteria in the small intestine. Xifaxan (rifaximin) is one of the most commonly prescribed antibiotics for the treatment of SIBO. Your doctor may select a different antibiotic based on your jejunal sample or on your symptoms.

Manage underlying condition: If you have a medical problem that predisposes you to SIBO, management of that problem can reduce bacterial overgrowth in the small intestine. Your treatment plan depends on a number of factors. For example, some medical conditions, such as diverticulitis, may act up occasionally, while others, such as intestinal surgery, are permanent.

Discontinue medications: While it is not clear whether medications used for the treatment of heartburn promote SIBO, these medications can alter the intestinal pH. Some doctors recommend stopping these treatments if you are diagnosed with SIBO.

Nutritional supplementation: When you have a GI condition that causes nutritional deficiencies, your doctor may test your vitamin levels and prescribe supplementation as needed. Because SIBO associated nutritional deficits stem from malabsorption, you may need injections or intravenous (IV) supplementation rather than oral pills.

Dietary modification: Dietary modifications have not been proven effective for the treatment of SIBO. Some people with SIBO have an increase in symptoms after consuming certain foods, such as lactose or fructose-containing food. If you have a specific dietary intolerance, then avoiding the food that exacerbates your symptoms can help prevent SIBO from acting up.

You can identify dietary intolerance by using a food diary and keeping track of your symptoms.

Herbs have not been found effective for managing SIBO, and you should tell your doctor about any supplements that you use, because they may actually promote pH changes or bacterial overgrowth.

A Word From Verywell

SIBO is a condition that is becoming more commonly recognized as a cause of GI disturbance and malnutrition. Getting a diagnosis and formulating a treatment plan for SIBO may take some time, but you should begin to feel more comfortable and energetic once your condition is properly managed.

Keep in mind that SIBO can fluctuate over time, so you may be able to take a break from treatment for months, or even years, at a time. Be sure to discuss recurring symptoms with your doctor so that flare-ups can be treated promptly.

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