SIBO stands for small intestinal bacterial overgrowth: too many bacteria living in the small intestine, the part of the gut between the stomach and the colon. It is also called small bowel bacterial overgrowth (SBBO) or small intestinal bacterial overgrowth syndrome⁴. Doctors diagnose it when a sample of small-intestinal fluid contains more than 1,000 bacteria per milliliter¹, or, far more often, with a breath test. Symptoms range from mild bloating to chronic diarrhea, weight loss and malabsorption⁵.

The colon is home to trillions of microbes that ferment fiber. The small intestine is different: it is where most nutrients are absorbed, and in health it holds relatively few bacteria. When the body’s defenses against bacteria in the small intestine fail, bacteria that normally live in the mouth or colon can multiply there, ferment food before it is absorbed, and cause symptoms¹¹.

Older definitions required more than 100,000 colony-forming units per milliliter (CFU/mL) of fluid. In 2020, a US clinical guideline lowered the threshold to more than 1,000 CFU/mL¹. Even so, a US expert review published the same year noted that the definition of SIBO still “lacks precision and consistency”, largely because scientists still know little about what a normal small-intestinal microbiome looks like².

How a healthy gut keeps bacteria out of the small intestine

The body has several defenses that keep bacterial numbers low in the small intestine¹¹:

Stomach acid kills most of the bacteria swallowed with food and saliva.
The migrating motor complex (MMC) is a wave of contractions that sweeps through the stomach and small intestine roughly every 90 to 120 minutes between meals, carrying leftover food and bacteria into the colon. Eating interrupts it⁶.
The ileocecal valve, where the small intestine joins the colon, stops colonic bacteria from flowing backwards.
Bile, digestive enzymes and the immune system in the gut lining also keep bacterial growth in check.

When one or more of these defenses fails, SIBO can develop.

What causes SIBO?

SIBO is almost always the result of another problem. Finding that problem matters, because treating the bacteria without addressing it often leads to relapse. Our guide to the root causes of SIBO covers each in detail.

Slow gut movement

Weak or missing migrating motor complexes are one of the main drivers. The absence of the MMC has been linked to gastroparesis, intestinal pseudo-obstruction and SIBO⁶. Conditions that slow the gut raise the risk. In a 2007 study of 50 people with a history of an underactive thyroid (hypothyroidism), 54% had a positive breath test, compared with 5% of 40 healthy controls⁷. Diabetes can damage the nerves that control gut movement, with the same effect¹¹.

Food poisoning is another well-studied trigger. Bacteria such as Campylobacter jejuni, E. coli and Salmonella release a toxin called cytolethal distending toxin B (CdtB). In animal studies, antibodies the body makes against this toxin cross-react with vinculin, a protein in gut nerve cells, and produce an IBS-like condition. In a 2015 study of more than 2,000 people with diarrhea-predominant IBS, levels of both anti-CdtB and anti-vinculin antibodies were higher than in people with inflammatory bowel disease, celiac disease or no gut disease⁹. People who have had Campylobacter food poisoning have a 2.7 to 5.6 times higher risk of developing IBS, and in animal studies the same infection leads to SIBO⁸.

Low stomach acid and structural changes

Low stomach acid (hypochlorhydria) removes the first barrier. It can result from aging, long-term Helicobacter pylori infection or acid-reducing medicines called proton pump inhibitors (PPIs). A 2013 meta-analysis of 11 studies with 3,134 people found that PPI users were about twice as likely to have SIBO. The link was strongest in studies that diagnosed SIBO by culturing intestinal fluid¹⁰.

Changes in the shape of the gut can also trap bacteria. Examples include scar tissue (adhesions) after abdominal surgery, narrowed areas from Crohn’s disease and other inflammatory bowel diseases, pouches in the intestinal wall (diverticula), and surgery that removes the ileocecal valve³¹¹. In some people, fungi also overgrow in the small intestine, a condition called small intestinal fungal overgrowth (SIFO).

The three gas types

When microbes in the small intestine ferment carbohydrates, they produce gas. Human cells do not make hydrogen or methane, so finding these gases in the breath means gut microbes are producing them¹². Overgrowth is grouped by the main gas:

Overgrowth type	Main gas	Main microbes	Typical bowel pattern
Hydrogen-dominant SIBO	Hydrogen (H₂)	Bacteria such as Enterobacteriaceae (the E. coli family)	Bloating, abdominal pain, diarrhea¹⁴
Intestinal methanogen overgrowth (IMO)	Methane (CH₄)	Archaea, mainly Methanobrevibacter smithii	Bloating, constipation¹⁴
Hydrogen sulfide overgrowth	Hydrogen sulfide (H₂S)	Sulfate-reducing bacteria such as Desulfovibrio, and Fusobacterium	Diarrhea¹⁴

Methane-dominant overgrowth is now called intestinal methanogen overgrowth (IMO), because the methane is made by archaea, which are a separate group of microbes from bacteria. Archaea do not ferment food themselves. They use the hydrogen made by bacteria and turn it into methane¹. Methane slows the gut down: in a 2006 animal study, infusing methane into the small intestine of dogs slowed transit by an average of 59%¹³.

Hydrogen sulfide is also made from the hydrogen that other bacteria release. In a 2022 study that combined breath tests with stool sequencing in people with IBS, higher breath hydrogen sulfide went with more sulfide-producing bacteria and with diarrhea, while higher breath methane went with more Methanobrevibacter and with constipation¹⁴. A 2025 study that sampled fluid from the small intestine found that breath levels of both gases matched the microbes living there¹⁵.

Symptoms and nutrient problems

Bloating, diarrhea and abdominal pain or discomfort are the classic symptoms of SIBO. In more severe cases, fat is poorly absorbed and stools become pale, greasy and floating (steatorrhea)². Gas produced in a narrow tube stretches the intestinal wall, which is felt as bloating, fullness and pain.

The bacteria also interfere with nutrients:

Fat and fat-soluble vitamins. Bacteria break down bile acids before they can do their job of absorbing fat. This can lead to fat malabsorption and low levels of vitamins A, D, E and K³¹¹.
Vitamin B12. Bacteria use up vitamin B12 before the body can absorb it, so B12 deficiency can develop. Folate, in contrast, is often high, because bacteria make it²¹¹.
Brain fog. In a 2018 study of 38 people with gas and bloating, those with brain fog were more likely to have SIBO (68% vs. 28%) and D-lactic acidosis, an excess of acid made by bacteria. All of those with brain fog were taking probiotics, and the brain fog cleared in 77% after they stopped the probiotics and took antibiotics¹⁸.

SIBO and celiac disease

SIBO can change the lining of the small intestine. In a 2010 study comparing duodenal biopsies from 67 people with SIBO and 55 without, shortened, flattened villi (villous blunting) were more common in SIBO (24% vs. 7%), but more than half of the SIBO biopsies looked normal¹⁶. Villous blunting is also the hallmark of celiac disease, so the two can be confused.

SIBO is also a common reason why people with celiac disease keep having symptoms despite a strict gluten-free diet. In a 2003 study of 15 celiac patients who still had symptoms after 6 to 8 months on the diet, 10 had SIBO, and their symptoms went away after antibiotic treatment¹⁷.

SIBO and IBS

Irritable bowel syndrome (IBS) is diagnosed from a pattern of symptoms, mainly abdominal pain with changes in bowel habits, after other diseases have been ruled out. In a 2021 survey of more than 73,000 adults in 33 countries, 4.1% of internet respondents met the current (Rome IV) criteria for IBS, and 10.1% met the older Rome III criteria²⁰.

The two conditions overlap. A 2020 meta-analysis of 25 studies with more than 3,000 people with IBS found that people with IBS had 3.7 times the odds of having SIBO compared with people without IBS¹⁹:

With breath tests, 35.5% of people with IBS tested positive, compared with 29.7% of controls.
With fluid culture at the 1,000 CFU/mL threshold, 33.5% of people with IBS had SIBO, compared with 8.2% of controls.
SIBO was more common in diarrhea-predominant IBS, and methane-positive tests were more common in constipation-predominant IBS.

The authors rated the overall quality of the evidence as low, mainly because studies used different tests and selection criteria¹⁹. So SIBO is one possible explanation for IBS symptoms in a subset of people, not the cause of most IBS. Our SIBO vs. IBS guide goes into more detail.

SIBO and leaky gut

The lining of the intestine is held together by protein seals called tight junctions. When they loosen, the gut becomes more permeable, often called leaky gut. Laboratory work shows that bacteria in contact with the small intestine trigger the release of zonulin, a protein that opens the tight junctions and lets more material pass through²¹. The researchers suggested this may be a defense that flushes out bacteria, but it also shows how overgrowth could make the gut lining leakier.

SIBO has also been linked to conditions outside the gut:

Rosacea. In a 2008 study, SIBO was found in 52 of 113 people with rosacea, compared with 3 of 60 controls. After SIBO was cleared with rifaximin, the skin cleared in 20 of 28 people and improved greatly in 6 more, while it stayed the same or worsened in all 20 who took a placebo²².
Restless legs syndrome. In a 2011 study of 32 people with restless legs syndrome, 69% had a positive breath test, compared with 28% of 25 controls from the general population²³.

These studies show an association. They do not prove that SIBO causes these conditions.

Is SIBO contagious or dangerous?

Is SIBO contagious?

No. SIBO is not an infection you catch from another person. It develops when bacteria that normally live in your own colon or mouth multiply in the small intestine because the body’s defenses, such as stomach acid, gut movement and the ileocecal valve, stop working properly⁴. Food poisoning itself can spread between people, and it is one of the ways those defenses get damaged⁸.

Is SIBO dangerous?

SIBO is rarely life-threatening, but it should not be ignored. Some people have only mild symptoms, while others develop chronic diarrhea, weight loss and malabsorption⁵, including the vitamin deficiencies described in our symptoms guide. How serious it becomes depends mostly on the underlying condition that caused it⁴. Warning signs such as blood in the stool, unintended weight loss or difficulty swallowing need prompt medical attention whatever the cause; our symptom checker lists them.

How SIBO is diagnosed

Small-intestinal fluid culture

The reference test is to take a sample of fluid from the upper small intestine during an endoscopy and grow the bacteria in a laboratory. More than 1,000 CFU/mL counts as SIBO¹. The test is invasive and expensive, the sample can be contaminated by bacteria from the mouth and stomach on the way down, and a single sample from the top of the small intestine can miss an overgrowth further along².

Breath tests

Because fluid culture is difficult, most people are diagnosed with a breath test. The day before, you avoid fermentable carbohydrates and fiber, then fast for at least 8 hours. On the day, you give a baseline breath sample, drink a sugar solution, and then give breath samples every 15 to 20 minutes for 90 to 120 minutes, or longer at some laboratories. If bacteria ferment the sugar before it reaches the colon, the gases they make pass into the blood and are breathed out¹¹²⁴.

A 2017 North American consensus of gastroenterologists set the standard cut-offs, which a 2020 US guideline adopted²⁴¹:

Hydrogen: a rise of 20 parts per million (ppm) or more above baseline within 90 minutes suggests SIBO.
Methane: a level of 10 ppm or more at any point suggests IMO.
Hydrogen sulfide: standard tests do not measure it. There is no agreed cut-off yet; the company behind the main three-gas test treats 3 ppm or more as positive²⁶.

The consensus recommends 75 g of glucose or 10 g of lactulose²⁴. The two sugars behave differently:

Glucose is absorbed quickly in the upper small intestine, so it rarely reaches the colon and causes fewer false positives, but it can miss overgrowth further down.
Lactulose is not absorbed, so it travels the whole small intestine, but it always ends up in the colon. If it gets there quickly, colonic bacteria can produce a rise that looks like SIBO. In a 2011 study that tracked a lactulose test meal with imaging in 40 people with IBS, 5% or more of the meal had already reached the colon at the time hydrogen rose in 22 of 25 positive tests²⁵.

A 2020 meta-analysis found that lactulose tests diagnosed SIBO 3.6 times more often than glucose tests in people with IBS¹⁹, which is one reason results need to be interpreted alongside symptoms. Once you have results, our breath test interpreter shows how your readings compare with the published thresholds.

How SIBO is treated

Treatment usually has three parts: reducing the overgrowth, easing symptoms, and addressing the cause. To weigh the main options against each other, see our side-by-side comparison of SIBO treatments.

Antibiotics

Rifaximin is the most studied antibiotic for SIBO. It is barely absorbed into the bloodstream, so it acts mainly inside the gut¹. A 2017 meta-analysis of 32 studies with 1,331 patients found that it cleared SIBO in about 71% of cases, with side effects in about 5%. The authors noted that the quality of the studies was generally poor²⁷.

Methane is harder to clear with rifaximin alone. In a 2010 review of the records of 74 people with methane on their breath test, methane disappeared in 87% of those who took rifaximin plus neomycin for 10 days, compared with 33% on neomycin alone and 28% on rifaximin alone²⁸.

Herbal antimicrobials are an alternative; our guide to natural antimicrobials for SIBO covers the evidence.

Diet

Diet changes ease symptoms but do not clear SIBO on their own. The most widely used approach is the low-FODMAP diet, which removes short-chain carbohydrates that bacteria ferment quickly, then reintroduces them one by one. In a 2026 online survey of 98 people with IBS, SIBO or IMO who had followed the diet, most reported fewer symptoms, especially less bloating, but fewer than half completed both phases²⁹. Our SIBO diet guide compares the main diets.

An elemental diet is a liquid formula of pre-digested nutrients that is absorbed in the upper small intestine, leaving little for bacteria further down. In a 2004 study of 93 people with IBS and an abnormal breath test, 80% had a normal test after 14 days on the formula alone, and 85% after up to 21 days³⁰.

Preventing SIBO from coming back

Clearing the bacteria does not fix the reason they grew. In a 2008 study of 80 people treated successfully with rifaximin, SIBO had returned in about 13% after 3 months, 28% after 6 months and 44% after 9 months. Relapse was more likely in older people, people who had had their appendix removed, and long-term PPI users³¹. Our relapse prevention guide covers the full strategy.

Prokinetics

Prokinetics are medicines or supplements that stimulate gut movement. Erythromycin, an antibiotic that also acts on the gut’s motilin receptors, triggers MMC-like contractions when given to healthy people³³. In a 2009 review of 64 patients whose SIBO had been treated successfully, people who took no prokinetic had symptoms again after an average of 60 days, compared with 139 days for low-dose erythromycin and 242 days for tegaserod taken at bedtime³². SIBO practitioners usually recommend taking prokinetics at bedtime, to support the MMC during the overnight fast³⁴.

Meal spacing and stress

Because eating interrupts the MMC⁶, SIBO practitioners recommend spacing meals 4 to 5 hours apart without snacks, and fasting for about 12 hours overnight³⁴. These recommendations are based on how the MMC works rather than on trials.

Stress affects the MMC too. In a 1986 study of 37 healthy volunteers, periods of psychological stress during the day reduced the number of migrating motor complexes compared with a stress-free day³⁵. Our guide to stress, the vagus nerve and SIBO covers approaches that may help.

Works Cited & Scientific References 35

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What is Small Intestinal Bacterial Overgrowth (SIBO)?