SIBO: Symptoms, Causes, Diagnosis and Treatment

What Is SIBO?

Small Intestinal Bacterial Overgrowth (SIBO) occurs when bacteria that normally reside in the large intestine colonise the small intestine in abnormally high numbers. The small intestine should be largely bacteria-free — it is the site of nutrient absorption, and bacterial overgrowth here disrupts this process dramatically. SIBO produces bloating, gas, abdominal pain, altered bowel habits, and nutritional deficiencies, and is significantly underdiagnosed as a cause of chronic digestive symptoms. It is estimated to underlie a substantial proportion of IBS diagnoses — some research suggests 30–80% of IBS patients may have concurrent SIBO, though methodology varies widely. For the broader digestive health context, see our complete gut health guide.

SIBO Symptoms

SIBO symptoms overlap significantly with IBS: bloating (often worse as the day progresses and after eating), gas and flatulence, abdominal pain or discomfort, diarrhoea (in hydrogen-dominant SIBO), constipation (in methane-dominant SIBO — now termed intestinal methanogen overgrowth or IMO), nausea, and in chronic cases, nutritional deficiencies including B12, fat-soluble vitamins (A, D, E, K), and iron. The hallmark distinction from simple IBS is often the severity and predictability of post-meal bloating, and nutrient deficiency in the absence of obvious dietary cause.

What Causes SIBO?

The small intestine is normally kept relatively bacteria-free by several mechanisms: stomach acid (which kills most ingested bacteria), bile and pancreatic enzymes (which have antimicrobial properties), the migrating motor complex (MMC — a housekeeping wave of contractions that sweeps bacteria downstream between meals), and the ileocecal valve (which prevents backflow from the large intestine). SIBO occurs when one or more of these mechanisms fails. Common underlying causes include: low stomach acid (from acid-suppressing medications like proton pump inhibitors, or from ageing), dysmotility conditions (gastroparesis, scleroderma, Parkinson’s disease), structural abnormalities (adhesions, strictures, blind loops from surgery), immune deficiency, hypothyroidism, and — most commonly — prior GI infection that disrupts migrating motor complex function.

How SIBO Is Diagnosed

Breath testing is the standard non-invasive diagnostic method. Lactulose or glucose breath tests measure hydrogen and methane gas produced when bacteria ferment a test substrate — abnormal patterns of gas production at specific time points indicate SIBO. Breath tests are not perfect — false positives and false negatives occur — and results must be interpreted alongside clinical history. Small intestinal aspiration and culture (the gold standard) is invasive and rarely performed in practice. Clinical diagnosis based on symptoms and response to treatment is common in practice.

SIBO Treatment

Antibiotics

Rifaximin is the most studied antibiotic for SIBO — it is gut-specific (minimally absorbed systemically), has a broad antimicrobial spectrum, and does not significantly disturb the colonic microbiome. A 2-week course of rifaximin produces significant symptom improvement in approximately 50–70% of hydrogen-dominant SIBO patients. For methane-dominant SIBO (IMO), the combination of rifaximin and neomycin or metronidazole is more effective. Recurrence after antibiotic treatment is common (40–50% within 9 months) if the underlying cause is not addressed.

Elemental Diet

An elemental diet — a liquid formula providing pre-digested nutrients that are absorbed in the early small intestine before reaching bacteria — starves bacteria of substrate and can eradicate SIBO without antibiotics. Two to three weeks of exclusive elemental diet achieves SIBO eradication in approximately 80% of cases but is expensive, challenging to adhere to, and not widely available.

Prokinetics

Addressing the underlying motility problem — using prokinetic agents to restore the migrating motor complex — is the most important strategy for preventing SIBO recurrence. Prokinetics include low-dose naltrexone, ginger, 5-HTP, and in some cases prescription medications (prucalopride, domperidone). Taking prokinetics between meals (when the MMC operates) helps sweep bacteria toward the large intestine.

Dietary Approaches

Specific carbohydrate diet (SCD), the bi-phasic SIBO diet, and low-FODMAP diets reduce substrate availability for bacteria and reduce symptom severity during treatment, though they do not eradicate SIBO alone. Intermittent fasting and spacing meals 4–5 hours apart supports MMC function. See our guide to IBS symptoms and treatments for overlapping dietary strategies.

FAQ

What is SIBO?
Small intestinal bacterial overgrowth — a condition where bacteria colonise the small intestine in abnormally high numbers, causing bloating, gas, digestive discomfort, and nutrient deficiencies.

How do I know if I have SIBO?
Symptoms include severe bloating that worsens through the day, gas, altered bowel habits, and nutritional deficiencies. Diagnosis is confirmed by hydrogen/methane breath test interpreted alongside clinical history.

Can SIBO be cured?
SIBO can be eradicated with antibiotics or elemental diet, but recurrence is common without addressing the underlying cause — particularly dysmotility. Long-term prokinetic use reduces recurrence significantly.

Is SIBO the same as IBS?
Not exactly — SIBO is a specific bacterial overgrowth syndrome while IBS is a functional diagnosis. SIBO may underlie many IBS cases, and treating SIBO can resolve IBS symptoms in those with concurrent SIBO.

What foods make SIBO worse?
High-FODMAP foods and simple carbohydrates provide the most substrate for bacterial fermentation in SIBO — temporarily reducing these reduces symptoms during treatment.