How to Manage SIBO (Small Intestine Bacterial Overgrowth)

Signs of a Bacterial Gut Imbalance and How to Treat It

Small intestinal bacterial overgrowth (SIBO) is excessive gut bacteria in the small intestine. SIBO symptoms may include abdominal bloating, constipation, and nutritional deficiencies. A range of conditions can lead to SIBO, such as celiac disease, Crohn's disease, and blind loop syndrome.

SIBO can affect adults and children at any age. However, it may be more prevalent and problematic for older adults (over age 50). Experts suggest that disruptions in gut bacteria may be more likely in people with a history of digestive disease and related surgeries, or who take certain medications.

This article describes symptoms and causes of SIBO. It explains who may be more at risk and reviews the steps healthcare providers take to diagnose and treat this condition.

Intestinal bacteria

SIBO Symptoms

With SIBO, your gastrointestinal (GI) symptoms can be similar to those seen in other GI problems. The cause of symptoms can work both ways, too. SIBO can worsen another co-occurring digestive disorder, and GI conditions can worsen SIBO, resulting in a cycle of illness.

Common effects of SIBO include:

Additional symptoms may occur due to specific underlying causes of SIBO. For example, a vitamin D deficiency can affect bone health. Or, SIBO that's linked to nonalcoholic fatty liver disease can lead to fatigue, weight loss, jaundice, and other fatty liver-related symptoms.

What Color Is SIBO Poop?

SIBO and related conditions can cause your stool to change colors. Yellow and green are common with malabsorption disorders; a light or clay-colored stool may suggest liver dysfunction. Phone app tools can help you identify possible causes of stool shape and color.


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 from other areas to grow in the small intestine and allow different types of bacteria to thrive.

Factors that can alter the acidity of the small intestine include:

  • Medication side effects (including antibiotics and proton pump inhibitor (PPI) drugs
  • Surgery, such as a gastric bypass procedure or bowel resection
  • Dietary preferences (for which there's increasing evidence with SIBO)

Other causes can include Helicobacter pylori (H. pylori) infection and bowel obstructions.

Slow digestion (caused by gastroparesis, hypothyroidism, blind loop syndrome, and other conditions) can keep waste in the small intestine. This decreased intestinal motility means that bacteria in the small intestine stays for a longer time than usual. This disrupts the normal balance of digestive enzymes.

What Is Blind Loop Syndrome?

Blind loop syndrome occurs when food digestion bypasses a part of your intestine, often because of bacterial overgrowth. This can be a complication of IBS, or other gastrointestinal conditions like diverticulitis or peptic ulcer disease. In addition to GI symptoms, you may experience fever or body aches due to bacterial infection, as well as malnutrition.


SIBO can interfere with your absorption of essential nutrients. Bacteria naturally found in the small intestine aid in the breakdown and absorption of nutrients and help prevent infections. The bacterial overgrowth also results in microscopic damage to the villi lining the walls of the small intestine, which impairs the absorption of nutrients.

Symptoms of malnutrition can include fatigue, weight loss, and 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:

  • Carbohydrates: 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.
  • Protein: SIBO-induced changes in the small intestine prevent proper protein absorption, resulting in weight loss and decreased immune function.
  • Fat: With SIBO, the bile acids responsible for the breakdown and absorption of fat are deficient. Fat malabsorption produces visible signs, including oily, smelly, 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 in 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 several other health effects, such as fatigue.

Foods That Trigger SIBO

There's research evidence to suggest that high-fiber diets improve SIBO symptoms. A small pilot study of healthy people eating high-fiber foods found that a temporary switch to diets that are high in sugar and low in fiber caused GI symptoms that resolved when the diet was changed back.

More research is needed to understand how diet plays a role in SIBO, and how foods affect symptoms in ways seen with other functional GI disorders, like IBS.

High-fiber foods that may be helpful include:

  • Whole grains, including oats and wheat products
  • Fresh fruits and vegetables, such as apples and avocados
  • Legumes (certain peas and beans) and lentils

Foods to avoid include high-sugar, low-fiber products:

  • Packaged baked goods
  • Sweetened cereals
  • Peanut butter
  • White bread

SIBO is affected by other dietary factors. For example, malabsorption of carbohydrates can cause bloating and gas when they ferment in the gut. The inability to digest protein well can lead to edema (swelling). In addition, problems digesting fat can lead to diarrhea, constipation, or both.

The low-FODMAP diet (it stands for fermentable oligo-, di-, mono-saccharides, and polyols) is often used in treating IBS and may help with SIBO symptoms.

Speak with a healthcare provider before making dietary changes, especially if you have an existing digestive disorder. Ask about medications and supplements, too, that can affect your digestion and nutrient absorption.

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, setting the stage for the condition to develop.

Conditions and circumstances associated with SIBO include:

Researchers note that SIBO has been detected in a third of patients with GI symptoms who took a breath test, and that smoking is another risk factor for the condition.

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


SIBO symptoms have been identified in people diagnosed with a wide range of illness, and their presence can suggest complications or greater disease severity.

Some of these conditions include:

  • Acute pancreatitis, with SIBO affecting one in four people diagnosed with severe disease
  • Diabetes, which can be aggravated by the way fats and carbohydrates are digested
  • Portal hypertension in liver cirrhosis, due to systemic inflammation and how bacteria are transported
  • Arterial stiffness (abdominal aorta, carotid arteries in the neck, arteries in the legs)

More research is needed to better understand SIBO symptoms, the complications caused by intestinal damage itself, and the ways that SIBO affects other diseases like non-alcoholic fatty liver disease.

Studies are now exploring the increase in SIBO diagnoses that occur in people with reactive arthritis or hepatic encephalopathy, conditions that serve as examples of gut-brain and gut-joint connections. They are building on an understanding of how gut bacteria relates to the immune system or cognitive function.

How to Test for SIBO

There are three main ways to test for SIBO—a breath test, analysis of samples collected from the small intestine, and use of an antibiotic trial. Each method has benefits and limitations, but the direct sampling method is considered to be the most reliable.

Breath Testing

Hydrogen breath testing is a fast, non-invasive, and safe diagnostic testing method. You drink a solution and then have your breath analyzed a few hours later. The presence of hydrogen or methane is indicative of malabsorption.

Lactulose breath tests, for example, are considered positive for SIBO with a rise in hydrogen of 20 parts per million (ppm) or more after consuming lactulose. Glucose and lactulose tests became common, but questions remain over the accuracy of results and the precise chemistry involved.

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; a biopsy or fluid sample can be taken while the endoscope is inserted.

Breath tests are more widely used, given challenges with jejunal aspiration that include its complexity and the risk of sample contamination. 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 healthcare provider know immediately if your symptoms worsen while taking antibiotics.

If SIBO symptoms respond to antibiotics, there is no need to repeat diagnostic testing.

How to Treat SIBO

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, based on your specific condition. For example, antibiotics may be useful in treating SIBO symptoms in people with IBD. But there is limited research on how effective the antibiotics are in these cases.

SIBO can fluctuate over time, so you may be able to take a break from treatment for months, or even years, at a time. Discuss recurring symptoms with your healthcare provider so that flare-ups can be treated promptly.


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 SIBO. Your healthcare provider may select a different antibiotic based on your jejunal sample or your symptoms, or because of challenges with insurance coverage for this use of rifaxmin.

Up to 44% of people will experience recurrence within nine months after one course of antibiotics. That's more often seen in older adults, people with an appendix removed, and those who have used PPI drugs for a long period. You may need antibiotics more than once.

Underlying Condition Management

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 several factors. For example, some medical conditions, such as Crohn's disease, may act up periodically, while others, such as those that result from intestinal surgery, are permanent.

Medication Discontinuation

It is not clear whether PPI medications used for the treatment of heartburn promote SIBO, with different research results indicating how these medications alter the intestinal pH and lead to SIBO.

Some healthcare providers recommend stopping these treatments if you are diagnosed with SIBO.

Nutritional Supplementation

When you have a GI condition that causes nutritional deficiencies, your healthcare provider 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 Modifications

Dietary modifications may be helpful as adjunctive therapy for the treatment of SIBO. For example, some people with the condition have an increase in symptoms after consuming certain items, such as lactose or fructose-containing foods.

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. Tell your healthcare provider about any supplements that you use, because they may actually promote pH changes or bacterial overgrowth.


SIBO is a condition that is becoming more commonly recognized as a cause of GI disturbance and malnutrition. Symptoms are due to changes in gut bacteria growth, for which there are a variety of possible causes.

Treatment for SIBO can include diet interventions and medication. Many people experience SIBO due to another co-occurring health condition, such as diabetes or liver disease, and treatment of the underlying cause is vital to their overall health.

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.

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Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
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Additional Reading
Barbara Bolen, PhD

By Barbara Bolen, PhD
Barbara Bolen, PhD, is a licensed clinical psychologist and health coach. She has written multiple books focused on living with irritable bowel syndrome.