In short: SIBO happens when the body’s defenses against bacteria in the small intestine fail. The main defenses are stomach acid, the migrating motor complex (the wave of contractions that sweeps the small intestine between meals), digestive secretions, the ileocecal valve and the immune system¹. The most common causes are slow gut movement, low stomach acid, previous gut surgery and conditions such as diabetes, scleroderma, cirrhosis and inflammatory bowel disease. Finding the cause matters because treating the bacteria without addressing it often leads to relapse¹⁶.

Small intestinal bacterial overgrowth (SIBO) is almost always a consequence of another problem. This guide explains the body’s defenses, the conditions that weaken them, and how much each one raises the risk.

The body’s defenses against SIBO

The small intestine normally holds relatively few bacteria. Several mechanisms keep it that way¹:

Stomach acid, at a pH of about 1 to 3, kills most bacteria swallowed with food.
Pancreatic and bile secretions contain enzymes and bile acids with antibacterial effects.
The migrating motor complex (MMC), a wave of contractions that sweeps through the stomach and small intestine during fasting and is interrupted by eating. Its absence is associated with SIBO².
The ileocecal valve, between the small intestine and the colon, which stops colonic bacteria from flowing back.
The immune system of the gut lining.

When one or more of these fails, bacteria can multiply in the small intestine.

Slow gut movement

Weak or missing migrating motor complexes are one of the main drivers of SIBO, and many conditions and medicines slow the gut¹².

Food poisoning and post-infectious IBS

Gastroenteritis is a well-studied trigger. A 2017 meta-analysis of 45 studies found that about 10% of people developed IBS within a year of infectious enteritis, a 4.2 times higher risk than in people without a recent infection⁷. After Campylobacter infection, the risk of IBS is 2.7 to 5.6 times higher, and in animal studies the same infection leads to SIBO⁸.

One proposed mechanism involves cytolethal distending toxin B (CdtB), a toxin made by food-poisoning bacteria. In animal studies, antibodies against CdtB cross-react with vinculin, a protein in gut nerve cells, producing an IBS-like condition with altered gut function. In a 2015 study of more than 2,000 people with diarrhea-predominant IBS, levels of these antibodies were higher than in people with inflammatory bowel disease, celiac disease or no gut disease⁶. See our IBS guide and blood tests guide.

Hormonal and metabolic conditions

Underactive thyroid. In a 2007 study of 50 people with a history of hypothyroidism, 54% had SIBO on a glucose breath test, compared with 5% of 40 controls³.
Diabetes. A 2022 meta-analysis of 14 studies with more than 1,400 people with diabetes found SIBO in 29%⁴. Diabetes can damage the nerves that control gut movement¹.

Connective tissue disease

In systemic sclerosis (scleroderma), the gut muscle can stiffen and weaken. A 2021 meta-analysis found SIBO in about 34% of people with systemic sclerosis, nearly 13 times the risk of healthy controls, and diarrhea was a strong predictor⁵.

Medicines

Opioid painkillers and other medicines that slow the gut raise the risk of SIBO¹.

Methane

Methane, made by archaea in methane overgrowth (IMO), itself slows the gut: in a 2006 animal study, methane slowed small-intestinal transit by 59%¹⁷. This can create a cycle in which slow transit favors overgrowth and methane slows transit further.

Low stomach acid

Reduced stomach acid weakens the first line of defense¹:

Acid-reducing medicines. A 2013 meta-analysis of 11 studies with 3,134 people found that users of proton pump inhibitors (PPIs) were about twice as likely to have SIBO; the link was strongest in studies using fluid culture⁹. In one study of older adults, 77% of long-term PPI users had SIBO, compared with 58% of non-users¹⁵.
Helicobacter pylori infection. A 2023 meta-analysis of 874 people found that H. pylori infection was linked to 1.8 times the odds of SIBO, mainly in younger people¹⁰. See our H. pylori guide.

Other digestive conditions

Condition	How often SIBO is found	Evidence
Cirrhosis	41%, vs. 11% of controls; 51% in decompensated cirrhosis	2018 meta-analysis of 21 studies¹²
Chronic pancreatitis	36% overall; 22% excluding lactulose tests; 4.1 times the odds of controls	2016 meta-analysis of 9 studies¹¹
Inflammatory bowel disease	22%; higher with strictures or previous bowel surgery	2019 meta-analysis of 11 studies¹³
Celiac disease	18%; 5.1 times the odds of healthy controls	2022 meta-analysis of 14 studies¹⁴
Systemic sclerosis	34%; about 13 times the risk of controls	2021 meta-analysis⁵
Diabetes	29%	2022 meta-analysis of 14 studies⁴

Structural changes and surgery

Changes to the shape of the gut can create areas where food and bacteria stagnate¹:

Strictures, for example from Crohn’s disease. In the 2019 IBD meta-analysis, stricturing Crohn’s disease raised the odds of SIBO about 7.5-fold¹³.
Removal of the ileocecal valve, which lets colonic bacteria flow back. Previous bowel surgery, especially removal of this valve, raised the odds of SIBO in Crohn’s disease¹³.
Gastric bypass and gastrectomy. In one study, SIBO rose from 15% before Roux-en-Y gastric bypass to as much as 40% afterwards, and another study found SIBO in 62% of people after gastrectomy¹⁵.
Small-intestinal diverticula, pouches in the intestinal wall¹.
Appendectomy was linked to a higher risk of SIBO relapse in a 2008 study¹⁶.

Immune deficiency

Inherited or acquired immune deficiencies, including severe malnutrition, also raise the risk of SIBO¹.

Finding your cause

Because SIBO is usually secondary, a clinician will typically look for an underlying cause, especially if SIBO comes back. The AGA expert review notes that the definition and causes of SIBO are still being refined¹⁸. Depending on your history, this may involve reviewing medicines (PPIs, opioids), checking thyroid function and blood sugar, testing for celiac disease or H. pylori, or imaging if surgery or strictures are suspected. Our diagnosis guide covers testing for SIBO itself.

Why the cause matters: relapse

In a 2008 study of 80 people treated successfully with antibiotics, SIBO returned in 44% within 9 months. Relapse was more likely in older people, those who had had their appendix removed, and long-term PPI users¹⁶. Addressing the cause where possible, supporting gut movement with prokinetics and following a relapse prevention plan all aim to lower that risk.

Common questions

What is the most common cause of SIBO?

There is no single most common cause. Slow gut movement (from food poisoning, diabetes, thyroid disease, scleroderma or medicines) and low stomach acid (from PPIs, H. pylori or aging) are among the most frequent¹.

Can stress cause SIBO?

Stress affects gut movement. In a 1986 study of healthy volunteers, psychological stress reduced the number of migrating motor complexes¹⁹. Whether stress alone causes SIBO has not been shown. See our guide to stress and SIBO.

Do PPIs cause SIBO?

They raise the risk. PPI users were about twice as likely to have SIBO in a 2013 meta-analysis⁹, and long-term PPI use was linked to SIBO relapse¹⁶. Do not stop a prescribed PPI without talking to your doctor.

Works Cited & Scientific References 19

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Root Causes of SIBO: Why Does Overgrowth Happen?