SIBO (Small Intestinal Bacterial Overgrowth)

Facts and Definition of SIBO (Small Intestinal Bacterial Overgrowth)

  • SIBO is a condition in which colonic-type bacteria (resembling bacteria normally found in the colon) proliferate in large numbers in the small intestine.
  • SIBO may be caused by dysfunction of intestinal nerves or muscles, and anatomic abnormalities of the intestine including intestinal obstruction, or the presence of bypassed small intestine (a blind loop).
  • The symptoms of are:
  • The condition is diagnosed by culturing intestinal fluid or with hydrogen breath testing.
  • The problem may be the cause of symptoms in at least some individuals with irritable bowel syndrome (IBS).
  • SIBO is treated with antibiotics, probiotics, low-FODMAP diet, or a combination of all three.

What Does SIBO Mean?

Small intestinal bacterial overgrowth (SIBO) refers to a condition in which abnormally large numbers of bacteria (usually defined as at least 100,000 bacteria per ml of fluid) are present in the small intestine, and the types of bacteria in the small intestine resemble more the bacteria of the colon than the small intestine. There are many conditions associated with SIBO including diabetes, scleroderma, Crohn's disease, and others. There is a striking similarity between the symptoms of irritable bowel syndrome (IBS) and SIBO. It has been theorized that SIBO may be responsible for the symptoms of at least some people diagnosed with irritable bowel syndrome.

The small bowel, also known as the small intestine, is the part of the gastrointestinal tract that connects the stomach with the colon. The main purpose of the small intestine is to digest and absorb food into the body. The small intestine is approximately 21 feet in length and begins at the duodenum (into which food from the stomach empties), followed by the jejunum and then the ileum (which empties the food that has not been digested and absorbed in the small intestine into the large intestine or colon).

The entire gastrointestinal tract, including the small intestine, normally contains bacteria. The number of bacteria is greatest in the colon (usually at least 1,000,000,000 bacteria per milliliter or ml of fluid) and much lower in the small intestine (less than 10,000 bacteria per ml of fluid). Moreover, the types of bacteria within the small intestine are different than the types of bacteria within the colon. It has been suggested, however, that SIBO and its symptoms may occur with smaller numbers of bacteria, for example, 10,000 per ml of fluid.

SIBO also is known as small bowel bacterial overgrowth or bacterial overgrowth of the small bowel or intestine.

SIBO Symptoms and Signs

The symptoms of SIBO include

A small number of patients with SIBO have chronic constipation rather than diarrhea. Patients with SIBO sometimes also report symptoms that are unrelated to the gastrointestinal tract, such as body aches or fatigue. The reason for these symptoms is unclear. The symptoms of SIBO tend to be chronic. A typical patient with SIBO can experience symptoms that fluctuate in intensity over months, years, or even decades before the diagnosis is made.

How does small intestinal bacterial overgrowth cause symptoms?

When bacteria digest food in the intestine, they produce gas. The gas can accumulate in the abdomen giving rise to abdominal bloating or distension. Distension can cause abdominal pain. The increased amounts of gas are passed as flatus (flatulence or farts). The bacteria also probably convert foods including sugar and carbohydrates into substances that are irritating or toxic to the cells of the inner lining of the small intestine and colon. These irritating substances produce diarrhea (by causing secretion of water into the intestine). There also is some evidence that the production of one type of gas by the bacteria, methane, causes constipation.

Bacteria in the small intestine, when present in large numbers, can compete with the human host for the food that is eaten. This can lead to malnutrition with vitamin and mineral deficiencies. In advanced cases of SIBO, the bacteria use up enough food that there are insufficient calories for the host, thereby leading to weight loss.

SIBO Causes

The gastrointestinal tract is a continuous muscular tube through which digesting food is transported on its way to the colon. The coordinated activity of the muscles of the stomach and small intestine propels the food from the stomach, through the small intestine, and into the colon. Even when there is no food in the small intestine, muscular activity sweeps through the small intestine from the stomach to the colon.

The muscular activity that sweeps through the small intestine is important for the digestion of food, but it also is important because it sweeps bacteria out of the small intestine and thereby limits the numbers of bacteria in the small intestine. Anything that interferes with the progression of normal muscular activity through the small intestine can result in SIBO. Any condition that interferes with muscular activity in the small intestine allows bacteria to stay longer and multiply in the small intestine. The lack of muscular activity also allows bacteria to spread backward from the colon and into the small intestine.

Many conditions are associated with SIBO. A few are common.

  • Neurologic and muscular diseases can alter the normal activity of the intestinal muscles. Diabetes mellitus damages the nerves that control the intestinal muscles. Scleroderma damages the intestinal muscles directly. In both cases, abnormal muscular activity in the small intestine allows SIBO to develop.
  • Partial or intermittent obstruction of the small intestine interferes with the transport of food and bacteria through the small intestine and can result in SIBO. Causes of obstruction leading to SIBO include adhesions (scarring) from previous surgery and Crohn's disease.
  • Diverticuli (outpouchings) of the small intestine where bacteria can live and multiply and are not swept away by the intestinal activity. Diverticuli of the colon, an extremely common condition is not associated with SIBO.

How Do We Get Good Gut Bacteria, and How What Does It Do?

At birth, there are no bacteria in the gastrointestinal tract. During birth, however, bacteria from the mother's colon and vagina are swallowed by the infant, and, within a few weeks or months, they populate the infant's gastrointestinal tract.

The relationship between normal intestinal bacteria and their human host is complex. The relationship is symbiotic, which means that each benefits from the other. The bacteria benefit from the warm, moist environment of the small intestine that is ideal for growth as well as a constant flow of food passing down the gastrointestinal tract that provides a ready source for their nutrition. The human host benefits in several ways. For example, the normal bacteria stimulate the growth of the intestinal lining and the immune system of the intestine. They prevent the growth of disease-causing bacteria within the intestine. They produce vitamin K, which is absorbed and used by the host. In fact, the bacteria are important even for the muscular activity of the small intestine; without bacteria, there is reduced muscular activity.

There is a delicate balance between the bacteria of the gastrointestinal tract and the human host. The gastrointestinal tract, particularly the small intestine, contains an extensive immune system. The immune system protects the intestine from disease-causing viruses, bacteria, and parasites. (The effects of the response of the intestinal immune response to disease-causing organism have been experienced by anyone who has experienced gastroenteritis.) The interesting fact is that the intestine does not attack the normal bacteria within it, only disease-causing bacteria. Somehow, the intestine becomes tolerant of the normal bacteria and does not mount an attack against them. The intestine has other ways that may be important in protecting it from bacteria, both normal and disease-causing. As mentioned previously, muscular activity keeps the numbers of bacteria within the intestine at a low level. Mucus that is secreted into the intestine coats the intestinal lining and prevents the bacteria from coming into contact with the lining. The intestine secretes antibodies that can block, and sometimes kill, bacteria as well as substances that prevent the growth of bacteria. Finally, the lining of the intestine can produce receptors for toxic substances produced by bacteria and can prevent the substances from exerting their toxic effects.

SIBO and Irritable Bowel Syndrome (IBS)

Irritable bowel syndrome (IBS) is a common gastrointestinal condition. Patients with IBS typically complain of abdominal pain associated with bloating, gaseousness, and alterations in their bowel habit (diarrhea, constipation, alternating diarrhea and constipation, or a sense of incomplete evacuation of stool). IBS is a chronic condition. Symptoms can be continuous or vary over months, years, or even decades. While irritable bowel syndrome is not life-threatening, symptoms of irritable bowel syndrome can have a major impact on a person's quality of life and even can be debilitating. For example, a patient with diarrhea after meals may avoid eating out. Patients who experience bloating and abdominal pain after meals may develop a fear of eating. In its extreme, they may even lose weight. Even flatulence can be socially limiting.

Irritable bowel syndrome has been a frustrating condition for both physicians and patients because it is difficult to diagnose and treat. Irritable bowel syndrome is difficult to diagnose because there is no diagnostic test that is abnormal. The diagnosis is made on the basis of typical symptoms and tests that exclude other diseases that might be causing the symptoms such as ulcers, infections, tissue inflammation, cancers, and obstruction of the intestine. Tests to rule out other conditions include computerized tomography (CT) scans, barium X-rays, upper gastrointestinal endoscopies, and colonoscopies. Physicians have to rely heavily on their clinical judgment to decide when enough testing has been done and to confidently make a diagnosis of IBS. Physicians are frustrated further by the fact that the treatment for IBS is not helpful in many patients.

There is a striking similarity between the symptoms of IBS and SIBO. It has been theorized that SIBO may be responsible for the symptoms of at least some patients with irritable bowel syndrome. The estimates run as high as 50% of patients with irritable bowel syndrome. Support for the SIBO theory of IBS comes from the observation that many patients with IBS are found to have an abnormal hydrogen breath test, and some patients with irritable bowel syndrome have improvement of their symptoms after treatment with antibiotics, the primary treatment for SIBO. Furthermore, it has been reported that successful treatment of symptoms with antibiotics causes the hydrogen breath test to revert to normal, suggesting that bacteria indeed are causing the symptoms. Although this theory is tantalizing and there is much anecdotal information that supports it, the rigorous scientific studies that are necessary to prove the theory have just begun. Nevertheless, many physicians have already begun to treat patients with IBS for SIBO. The intriguing issue yet to be elucidated is the reason why individuals who appear to have normal small intestines develop SIBO and IBS. The most popular theory is that patients with IBS have a subtle abnormality in the function of their intestinal muscles that allows SIBO to occur. Another theory is that there is an immunologic defect that allows colonic bacteria to live in the small intestine.

Causes of Increased Production of Gas (Flatulence, Farting)

There are three situations in which abnormally increased amounts of gas are produced in the colon.

  1. Malabsorption of sugars and carbohydrates: Reduced digestion or absorption by the small intestine allows increased amounts of sugar and carbohydrate to reach the colon where greater amounts of gas are produced. The most common example of malabsorption leading to increased production of gas is lactose (milk sugar) intolerance. Lactose intolerance is due to a genetic lack of an enzyme in the lining of the small intestine that digests lactose, the sugar in milk. Other causes of malabsorption that can lead to excessive production of gas include: (1) genetically-determined malabsorption of other sugars such as sucrose, sorbitol, and fructose; (2) diseases of the pancreas that result in inadequate production of pancreatic enzymes that are necessary for digesting sugars and carbohydrates in the small intestine; and (3) diseases of the lining of the small intestine (for example, celiac disease) that reduce the sugar and carbohydrate-digesting enzymes in the lining and reduce absorption of sugars and carbohydrates in the body.
  2. Rapid intestinal transit: Normal digestion and absorption of sugars and carbohydrates requires time. If food passes through the small intestine too rapidly, there is not enough time for digestion and absorption to be completed, and more sugar and carbohydrate reach the colon. The best example of rapid intestinal transit is in individuals who have had a large portion of their small intestine removed surgically. There are also a small number of individuals with intact small intestine who, for unexplained reasons, have abnormally rapid transit through the small intestine.
  3. Small intestinal bacterial overgrowth (SIBO): In patients with SIBO, large numbers of gas-producing bacteria (normally present in the colon) are present in the small intestine. The abundant bacteria in the small intestine compete with the small intestine for the digestion of sugars and carbohydrates, but unlike the small intestine, the bacteria produce large amounts of gas.

What Tests Are Used To Diagnose SIBO?

Culturing Bacteria From the Small Intestine

One method of diagnosing bacterial overgrowth is culturing (growing) the bacteria from a sample of fluid taken from the small intestine. The culturing must be quantitative, meaning that the actual number of bacteria must be determined. Essentially, the bacteria in a known quantity of fluid are counted. Culturing requires a long flexible tube to be passed through the nose, down the throat and esophagus, and through the stomach under X-ray guidance so that fluid can be obtained from the small intestine.

There are several problems with diagnosing SIBO by culturing. Passage of the tube is uncomfortable and expensive, and the skill necessary to pass the tube is not commonly available. The quantitative culturing of intestinal fluid is not a routine procedure for most laboratories, and, therefore, the accuracy of the cultures is questionable. Finally, with the tube, only one, or at the most a few, locations of the small intestine can be sampled. Usually it is the duodenum. It is possible that the overgrowth involves just the jejunum or ileum, and may be missed if only the duodenal fluid is sampled. Because of all these potential problems, quantitative culturing for intestinal bacteria usually is utilized only for research purposes.

Hydrogen Breath Test (HBT)

Bacteria that live in the colon are capable of digesting and using sugars and carbohydrates as food. When the bacteria normally present in the colon digest sugars and carbohydrates, they produce gas, most commonly carbon dioxide, but also smaller amounts of hydrogen and methane. (The types of bacteria normally found in the esophagus, stomach, and small intestine produce little gas.) Most of the sugars and carbohydrates that we eat are digestible and are digested and absorbed in the small intestine, never reaching the colonic bacteria. Moreover, greater than 80% of the gas that is produced by bacteria in the colon is used up by other bacteria within the colon. As a result, relatively little of the gas that is produced remains in the colon to be eliminated, and it is eliminated as flatus (farts). Although the overwhelming majority of the hydrogen and methane produced by colonic bacteria is used up by other bacteria, small amounts of these gases are absorbed through the lining of the colon and into the blood. The gases circulate in the blood and go to the lungs, where they are eliminated in the breath. These gases can be measured in the breath with special analyzers (usually a gas chromatograph).

Hydrogen Breath Test Procedure

For the hydrogen breath test, individuals fast for at least 12 hours. At the start of the test, the individual fills a small balloon with a single breath of air and then ingests a small amount of the test sugar (usually lactulose or glucose). Samples of breath are analyzed for hydrogen and methane every 15 minutes for the next three or more hours.

Lactulose is a sugar that is digested only by colonic bacteria and not by the human host. The ingested lactulose travels through the small intestine undigested and reaches the colon where the bacteria produce gas. In the normal individual, there is a single peak of gas in the breath following the ingestion of lactulose when the lactulose enters the colon. Individuals with SIBO have two peaks of gas in the breath. The first abnormal peak occurs as the lactulose passes the gas-producing bacteria in the small intestine, and the second normal peak occurs as the lactulose enters the colon.

The situation is slightly different when glucose is used for the hydrogen breath test. Glucose is a sugar that is digested and absorbed by everyone. None of it reaches the colon. However, if large amounts of glucose are ingested (50-100 grams), the glucose is steadily absorbed in the small intestine. As a result, the concentration of glucose in the small intestine decreases steadily as the glucose travels down the small intestine until eventually there is no more glucose in the small intestine. If the glucose passes through a segment of the small intestine that contains overgrowing bacteria (for example, SIBO is present), the bacteria produce gas from the glucose, and the gas is excreted in the breath. Normal individuals excrete no gas in their breath after ingesting glucose because the glucose never reaches the gas-producing bacteria that normally are present only in the colon.

Limitations of the Hydrogen Breath Test

There are several limitations of the hydrogen breath test for the diagnosis of SIBO.

  • Hydrogen breath testing with lactulose may be able to diagnose only 60% of patients with SIBO, and glucose may be only slightly better. Since glucose is absorbed completely before it completes its passage through the small intestine, it may not be able to diagnose SIBO of the distal small intestine (ileum). A major problem is that there is no "gold standard" for the diagnosis of SIBO since culture of the bacteria has its own limitations, as discussed previously. Without such a gold standard, it is difficult to know just how effective hydrogen breath test is for the diagnosis of SIBO.
  • Any condition that impairs the digestion or absorption of sugars and carbohydrates in the small intestine can produce an abnormal hydrogen breath test when dietary sugars (for example, glucose) are used for testing. Therefore, conditions other than SIBO, such as pancreatic insufficiency and celiac disease, can result in abnormal breath tests. In the former instance, the pancreatic enzymes that are necessary for the digestion of carbohydrates are missing, and in the latter condition, the lining of the small intestine is destroyed and digested food cannot be absorbed. Hydrogen breath testing using lactulose is not affected by impaired digestion or absorption.
  • There may be similarities in the pattern of gas production with SIBO and rapid intestinal transit, thus making distinctions difficult, for example, early production of hydrogen or methane.
  • Some normal individuals may have slow transit through the small intestine making prolonged testing -- up to five hours -- necessary and many individuals are unwilling to undergo such prolonged testing.
  • A small number of individuals with SIBO may have bacteria that do not produce hydrogen or methane, and, therefore, their SIBO cannot be detected with the hydrogen breath test.
  • Some individuals produce only methane or a combination of hydrogen and methane. There is much less experience with methane as compared with hydrogen for the diagnosis of SIBO, however, and the production of methane is more complex than the production of hydrogen. Therefore, it is not clear if the pattern of the production of methane after ingestion of sugars can be interpreted in the same way as the production of hydrogen.
  • A positive hydrogen breath test does not always mean that a patient's symptoms are caused by SIBO. For example, Crohn's disease of the small intestine, small intestine strictures (narrowing due to scarring), or other anatomical abnormalities of the small intestine can cause symptoms of bloating, distension, pain, and diarrhea from the obstruction of the intestine that they cause. These conditions also can cause bacterial overgrowth, which can produce similar symptoms. How can it be determined whether the underlying condition or the bacteria is causing the symptoms? The only way to establish whether the symptoms are caused by the intestinal disease or by the SIBO is to treat and suppress the bacteria. If the symptoms disappear, then it is likely that SIBO rather than the underlying disease is responsible for the symptoms. If symptoms don't improve, however, it is possible either that the symptoms are those of the underlying disease or, alternatively, that suppression of the bacteria was ineffective.

What Is the Treatment for Classic SIBO and SIBO Associated with IBS?

"Classic" SIBO

SIBO has been recognized for many years as a problem with severe disorders of intestinal muscles and intestinal obstruction. The treatment has been antibiotics, and they are very effective. The difficulty is that the disease causing the SIBO often cannot be corrected. As a result, symptoms frequently return when the antibiotics are stopped, and it may be necessary to treat the patient with antibiotics repeatedly or even continuously.

SIBO Associated With IBS

There are very few rigorous, scientific studies on the treatment of irritable bowel syndrome with therapies that are directed specifically to the possibility of underlying SIBO. That has not stopped physicians from trying unproven treatments. The discussion of treatment that follows is based on the minimal scientific evidence that is available (two trials) as well as the anecdotal (observed but not scientifically demonstrated) experience of physicians who see patients with irritable bowel syndrome.

The two most common treatments for SIBO in patients with IBS are oral antibiotics and probiotics. Probiotics are live bacteria that, when ingested by an individual, result in a health benefit. The most common probiotic bacteria are lactobacilli (also used in the production of yogurt) and bifidobacteria. Both of these bacteria are found in the intestine of normal individuals. There are numerous explanations for how probiotic bacteria might benefit individuals. However, the beneficial action has not been identified clearly. It may be that the probiotic bacteria inhibit other bacteria in the intestine that may be causing symptoms, or it may be that the probiotic bacteria act on the host's intestinal immune system to suppress inflammation.

Several antibiotics either alone or in combination have been reported in scientific studies to be successful in treating IBS. Treatment success, when measured by either symptom improvement or by the normalization of the hydrogen breath test, ranges from 40%-70%. When one antibiotic fails, the doctor may add another antibiotic or change to a different antibiotic. However, the doses of antibiotics, the duration of treatment, and the need for maintenance therapy to prevent recurrence of SIBO have not been adequately studied. Most physicians use standard doses of antibiotics for one to two weeks. Probiotics may be used alone, in combination with antibiotics, or for prolonged maintenance. When probiotics are used, it probably is best to use one of the several probiotics that have been studied in medical trials and shown to have an effect on the small intestine, though not necessarily in SIBO. The commonly sold probiotics in health-food stores may not be effective. Moreover, they often do not contain the bacteria stated on the labels or the bacteria are dead. The following are some treatment options:

  • Neomycin (Neo-Fradin, Neo-Tab) orally for 10 days. Neomycin is not absorbed from the intestine and acts only within the intestines.
  • Levofloxacin (Levaquin) or ciprofloxacin (Cipro) for seven days.
  • Metronidazole (Flagyl) for seven days.
  • Levofloxacin (Levaquin) combined with metronidazole (Flagyl) for seven days.
  • Rifaximin (Xifaxan) for seven days. Rifaximin like neomycin is not absorbed from the intestine, and, therefore, acts only within the intestine. Because very little rifaximin is absorbed into the body, it has few important side effects. Higher than normal doses of rifaximin (1,200 mg/day for seven days) were superior to the standard lower doses (800 or 400 mg/day) in normalizing the hydrogen breath test in patients with SIBO and IBS. However, it is not yet known whether the larger dose is any better at suppressing symptoms.
  • Commercially available probiotics such as VSL#3 or Flora-Q, which are mixtures of several different bacterial species, have been used for treating SIBO and IBS, but their effectiveness is not known. Bifidobacterium infantis 35624 is the only probiotic that has been demonstrated to be effective in treating patients with IBS.

Treatment with Antibiotics Versus Probiotics

It is the author's personal belief that for short-term (one to two weeks) treatment, antibiotics are more effective than probiotics. However, antibiotics do have certain disadvantages. Specifically, symptoms tend to recur after treatment is discontinued, and prolonged or repeated courses of treatment may be necessary in some patients. Physicians are reluctant to prescribe prolonged or repeated courses of antibiotics because of concern over long-term side effects of the antibiotics and the emergence of bacteria that are resistant to the antibiotics. Physicians have less concern over long-term side effects or the emergence of resistant bacteria with probiotics and, therefore, are more willing to prescribe probiotics repeatedly and for prolonged periods. One option is to initially treat the patient with a short course of antibiotics and then long term with probiotics. Long-term studies comparing antibiotics, probiotics, and combinations of antibiotics and probiotics are badly needed.

Where Can I Find Out What Research Is Being Done for SIBO?

One of the major impediments to understanding the role of SIBO in causing disease is the lack of a good test for diagnosis. In the last few years, a new technique for studying intestinal bacteria has been developed that is promising. Bacterial RNA is extracted from samples of stool and then analyzed. The DNA analysis can determine the types of bacteria present as well as their numbers. Perhaps this new technique will be useful in clarifying the importance of SIBO.

SIBO Symptoms

Flatulence (Gas)

  • Flatulence is the state of having excessive stomach and/or intestinal gas (waste gas produced during digestion) that is usually released from the anus with sound and/or odor.
  • Causes of excess gas in the digestive tract are
    • swallowed air,
    • breakdown of undigested foods,
    • lactase intolerance, and
    • malabsorption of certain foods.
Syed, SZ. "Bacterial Overgrowth." Medscape. Updated: Mar 17, 2016.