SIBO: Mechanisms, Symptoms and Testing

Small intestinal bacterial overgrowth has moved from a niche gastroenterology diagnosis to one of the most discussed conditions in functional practice. Patients arrive having read that it explains their bloating, and many practitioners test for it routinely. SIBO is real and treatable, and in the right patients recognising it transforms their care. It is also overdiagnosed, partly because the most widely used test is imperfect and partly because its symptoms overlap with many other conditions. Getting SIBO right means understanding why it happens as well as how to test for it.

What SIBO is

The small intestine normally contains far fewer bacteria than the colon. Several defences keep it that way: stomach acid, which kills many swallowed organisms; bile and pancreatic secretions; intestinal immunity; the ileocaecal valve, which limits backflow from the colon; and, most importantly, the migrating motor complex, a cyclical wave of muscular activity that sweeps contents through the small intestine between meals.

SIBO occurs when these defences fail and bacteria accumulate in the small intestine. American gastroenterology guidance defines it by a bacterial count above a threshold in fluid aspirated from the small intestine, and in practice more often by breath testing. The bacteria ferment carbohydrates, producing gas, and can interfere with digestion and absorption.

A related condition, intestinal methanogen overgrowth, describes excess methane producing archaea, principally Methanobrevibacter smithii. Methane slows gut transit and is associated with constipation and bloating rather than diarrhoea. It is now considered separately from hydrogen producing SIBO.

Why it happens

SIBO is almost always a consequence of something else. Identifying that something else matters more than the diagnosis itself.

The relationship with proton pump inhibitors has been studied extensively, with mixed findings; any effect appears modest. The relationship with irritable bowel syndrome is also debated. Some studies found high rates of positive breath tests in irritable bowel syndrome, but many of these used lactulose tests, which are prone to false positives in people with rapid gut transit.

Symptoms and consequences

• Bloating and distension, often worse after meals
• Abdominal discomfort, flatulence
• Diarrhoea in hydrogen predominant overgrowth; constipation with methanogen overgrowth
• In more severe or prolonged cases, malabsorption with weight loss, fatty stools and deficiencies

A characteristic laboratory pattern can occur: low vitamin B12, because bacteria consume it, and normal or high folate, because some bacteria produce it. Deficiencies of fat soluble vitamins and iron can also develop. None of the symptoms is specific, which is why testing and clinical context both matter.

Testing

Breath tests

Breath testing measures hydrogen and methane in exhaled breath after a sugar substrate is swallowed. If bacteria in the small intestine ferment the sugar, gas levels rise early. A North American consensus proposed that a rise in hydrogen of at least 20 parts per million from baseline within 90 minutes suggests SIBO, and that a methane level of at least 10 parts per million at any point suggests methanogen overgrowth.

2 substrates are used, with different strengths.

Preparation matters: recent antibiotics, laxatives, bowel preparation, some diets and smoking can affect results. Protocols and interpretation vary between laboratories, and different criteria can produce different diagnoses in the same patient.

Small bowel aspirate

Culture of fluid obtained at endoscopy is often described as the reference standard, but it is invasive, samples only the proximal small intestine and has technical limitations, so it is used mainly in specialist settings.

Empirical treatment

In some cases, particularly where risk factors are clear, clinicians treat empirically and assess response.

Who should be tested

Testing is most useful when there is a plausible predisposing condition, such as previous surgery, diabetic neuropathy, systemic sclerosis or unexplained malabsorption, and when the result will change management. Testing everyone with bloating, particularly with lactulose, is likely to produce many false positive results and unnecessary treatment. Other conditions with similar symptoms, including coeliac disease, lactose and fructose malabsorption, bile acid diarrhoea, pancreatic insufficiency and inflammatory bowel disease, should be considered alongside.

Treatment

Antibiotics

Rifaximin, a poorly absorbed antibiotic that acts mainly within the gut, is the most studied treatment and is recommended in gastroenterology guidance. Other antibiotics are also used. For methanogen overgrowth, combinations including neomycin or other agents have been studied. Antibiotic treatment should be prescribed by a qualified clinician.

Addressing the cause

This is the most important step for long term success. Recurrence after antibiotic treatment is common, particularly when the underlying cause persists. Improving glucose control in diabetes, reviewing opioids and acid suppression, treating hypothyroidism and managing anatomical problems where possible all reduce recurrence.

Diet

Dietary changes that reduce fermentable carbohydrate, such as a low FODMAP approach, can reduce symptoms but do not eradicate overgrowth. Elemental diets, liquid formulas absorbed in the upper small intestine, have shown high normalisation of breath tests in small studies, but are expensive, unpalatable and require supervision.

Other approaches

Herbal antimicrobial preparations have been compared with rifaximin in a small study with encouraging results, but the evidence is limited and product quality varies. Prokinetic agents are sometimes used to support motility after treatment, particularly where motility is impaired. Probiotics have mixed and limited evidence in SIBO.

Small intestinal fungal overgrowth

Small intestinal fungal overgrowth, SIFO, describes excess fungi, mainly Candida species, in the small intestine. It has been reported in some patients with unexplained gut symptoms, particularly those with immune suppression or taking acid suppressants, but it is diagnosed by aspirate and culture, has no validated breath test, and evidence about its prevalence and treatment is limited. It is best considered in selected patients under specialist care.

An illustrative case

A 61 year old woman with type 2 diabetes for 18 years has had bloating, loose stools and weight loss for a year. Her glucose control is poor, and she has diabetic neuropathy. Blood tests show a low B12 and a high folate. Her doctor excludes coeliac disease and arranges a glucose breath test, which shows an early rise in hydrogen. She is treated with rifaximin, her B12 is replaced, and, crucially, her diabetes treatment is intensified to improve glucose control, which may help her gut motility over time. Her symptoms improve. 6 months later they begin to return, and a second course of treatment is combined with a review of the medicines affecting her motility. The overgrowth was treatable, but managing her diabetes was the long term solution.

A consequence, not a destination

SIBO is best understood as a consequence of failing defences rather than a primary disease. Testing selectively, choosing the right test, interpreting it cautiously, treating it with appropriate agents and, above all, finding and addressing the underlying cause gives patients the best chance of lasting improvement.