What is SIBO? Complete guide 2026

What is SIBO?

SIBO stands for Small Intestinal Bacterial Overgrowth. It is a condition in which there is an abnormal increase of bacteria in the small intestine, a part of the digestive tract that normally contains a relatively low number of microorganisms.

In a healthy digestive system, the highest concentration of bacteria is found in the large intestine (colon), where they perform essential functions such as fibre fermentation and vitamin production. The small intestine, by contrast, is designed primarily for nutrient absorption and maintains a much smaller bacterial population thanks to defence mechanisms including gastric acid, intestinal motility (the rhythmic movement that pushes contents forward) and the ileocaecal valve that separates the two intestines.

When these mechanisms fail, bacteria from the colon can migrate to or proliferate in the small intestine. There, they ferment food before the body can absorb it properly, producing gases such as hydrogen, methane and hydrogen sulphide. This process is responsible for the hallmark symptoms of SIBO: abdominal bloating, pain, altered bowel habits and, in chronic cases, nutritional deficiencies.

SIBO is estimated to affect between 2% and 20% of the general population, although figures vary widely depending on the diagnostic criteria used. Prevalence is significantly higher in people with Irritable Bowel Syndrome (IBS), where studies have found rates of between 30% and 85%. This has led many researchers to consider SIBO as a frequent underlying cause of IBS.

SIBO symptoms

SIBO symptoms can vary considerably from one person to another, both in type and in severity. This means it is often confused with other digestive conditions and diagnosis can be delayed. The most common symptoms include:

Main digestive symptoms

• Abdominal bloating (distension): This is the most frequent and often the most bothersome symptom. Bacterial fermentation of food in the small intestine produces gases that cause visible distension and an uncomfortable feeling of fullness, especially after meals.
• Abdominal pain and cramping: Gas build-up and intestinal inflammation cause pain that tends to be felt in the central and upper abdomen. It may be constant or come in episodes.
• Diarrhoea: Predominant in hydrogen-type SIBO. Bacteria alter water and electrolyte absorption, and also produce fatty acids that stimulate fluid secretion in the intestine.
• Constipation: More commonly associated with methane-type SIBO (also known as IMO, Intestinal Methanogen Overgrowth). Methane gas slows intestinal transit, resulting in hard stools and infrequent bowel movements.
• Excessive gas and flatulence: A direct consequence of bacterial fermentation. Many people report that gas worsens throughout the day and is particularly intense after eating foods rich in fermentable carbohydrates.
• Nausea: Especially common after meals, it can contribute to loss of appetite and insufficient caloric intake.

Systemic symptoms

• Chronic fatigue: Nutrient malabsorption, systemic inflammation and disrupted sleep due to nocturnal digestive discomfort all contribute to persistent tiredness that does not improve with rest.
• Brain fog: Difficulty concentrating, memory problems and a feeling of mental confusion. This has been linked to D-lactate production by certain bacteria and to systemic inflammation.
• Nutritional deficiencies: Bacteria compete with the body for nutrients. The most common deficiencies include vitamin B12, iron, fat-soluble vitamins (A, D, E, K) and essential fatty acids. This can manifest as anaemia, muscle weakness, skin problems or brittle hair.
• Unintentional weight loss: In advanced cases, the combination of malabsorption, nausea and dietary restriction can lead to significant weight loss and malnutrition.
• Joint pain and inflammation: Increased intestinal permeability (leaky gut) allows bacterial toxins to enter the bloodstream, triggering inflammatory responses that can affect the joints.

Causes of SIBO

SIBO is not a disease with a single cause. It normally results from disruption of one or more of the mechanisms that keep the bacterial population of the small intestine in check. The main causes include:

Impaired intestinal motility

The migrating motor complex (MMC) is a pattern of muscular contractions that occurs between meals and during sleep, functioning as a "broom" that sweeps food residues and bacteria towards the colon. When this mechanism weakens or is disrupted, bacteria can accumulate in the small intestine. The most common causes of dysmotility include:

• Previous infectious gastroenteritis (food poisoning), which can damage the nerves that control the MMC
• Diabetes mellitus with autonomic neuropathy
• Untreated hypothyroidism
• Scleroderma and other connective tissue diseases
• Chronic opioid use, which slows motility

Anatomical abnormalities

Any change in the structure of the digestive tract can create areas where bacteria accumulate:

• Previous abdominal surgery, especially bariatric surgery or intestinal resections
• Adhesions (scar tissue) that create pockets or strictures
• Small intestinal diverticula
• Ileocaecal valve dysfunction, which allows bacteria to reflux from the colon into the small intestine

Reduced gastric acid

Stomach acid is one of the first defensive barriers against ingested bacteria. Insufficient production allows more bacteria to survive and reach the small intestine:

• Long-term use of proton pump inhibitors (PPIs) such as omeprazole
• Atrophic gastritis
• Natural ageing (acid production decreases with age)

Immune impairment

The intestinal immune system produces immunoglobulin A (IgA), which helps control bacterial populations. Conditions such as immunodeficiency, chronic stress or coeliac disease can compromise this defence.

Diagnosing SIBO

Diagnosing SIBO can be challenging because its symptoms overlap with those of many other digestive conditions. However, specific methods exist that can help confirm the diagnosis.

Breath test (hydrogen and methane)

The breath test is currently the most widely used diagnostic method owing to its non-invasive nature and accessibility. The procedure involves:

1. Preparation: The patient follows a restricted diet (low in fibre and fermentable sugars) for 24 hours beforehand and fasts overnight.
2. Substrate: A solution of lactulose or glucose dissolved in water is consumed. Lactulose is not absorbed and travels the entire length of the small intestine, whereas glucose is absorbed in the first section.
3. Samples: Breath samples are collected every 15-20 minutes over 2-3 hours.
4. Measurement: Levels of hydrogen (H2), methane (CH4) and, in some more advanced laboratories, hydrogen sulphide (H2S) are measured.

A significant rise in hydrogen or methane in the early stages of the test (before the substrate reaches the colon) suggests the presence of fermenting bacteria in the small intestine. The most widely accepted criteria according to the 2017 North American Consensus are:

• Hydrogen-type SIBO: A rise of ≥20 ppm of H2 above baseline within the first 90 minutes
• Methane-type SIBO (IMO): CH4 level ≥10 ppm at any point during the test

Jejunal aspirate culture

Historically considered the "gold standard", this involves extracting a fluid sample from the small intestine during an endoscopy and culturing the bacteria present. A count above 10³ CFU/mL is considered positive. However, its invasive nature, high cost and difficulty in culturing all bacterial species mean it is used less and less in clinical practice.

Clinical evaluation

In many cases, an experienced gastroenterologist may suspect SIBO based on the patient's clinical history, predominant symptoms and response to previous treatments. Factors such as a history of food poisoning, long-term PPI use or a previous diagnosis of refractory IBS can raise clinical suspicion.

SIBO treatment

SIBO treatment has three main goals: reduce the bacterial overgrowth, relieve symptoms and prevent relapse. In most cases a combination of approaches is required.

Antibiotics

Rifaximin is the most studied and widely used antibiotic for hydrogen-type SIBO. Its main advantage is that it acts locally in the gut without being significantly absorbed into the bloodstream, which minimises systemic side effects. A typical course lasts 14 days. For methane-type SIBO, rifaximin is usually combined with neomycin or metronidazole, since methane-producing archaea do not respond well to rifaximin alone.

It is important to note that the recurrence rate of SIBO after antibiotics is significant (up to 40-50% in some studies), which underscores the need to address the underlying causes rather than just treating the symptoms.

Herbal antimicrobials

A study published in Global Advances in Health and Medicine showed that certain herbal antimicrobial protocols can be as effective as rifaximin. The most commonly used include:

• Oregano oil (carvacrol)
• Berberine (found in plants such as Oregon grape root)
• Allicin from garlic (especially effective against methane producers)
• Neem

These treatments typically last between 4 and 6 weeks and can be an option for patients who prefer to avoid antibiotics or who have not responded to them.

Therapeutic diet

Dietary modification is a fundamental pillar of SIBO treatment. The most commonly used dietary strategies include:

• Low FODMAP diet: The most studied and recommended approach. It reduces the fermentable carbohydrates that feed bacteria in the small intestine.
• Elemental diet: A liquid formula with pre-digested nutrients that are absorbed in the first section of the small intestine, effectively "starving" the bacteria. Studies have shown breath test normalisation rates of 80-85% within 14 days, although it is difficult to follow due to its taste and cost.
• Bi-Phasic diet: Developed by Dr Nirala Jacobi, it combines elements of the Low FODMAP diet with additional restrictions across two phases.

Prokinetics

To prevent relapse, many gastroenterologists prescribe prokinetics, medications that stimulate the migrating motor complex. The most commonly used include prucalopride, low-dose erythromycin and low-dose naltrexone. Natural options such as ginger and Iberogast are also available.

The Low FODMAP diet and SIBO

The Low FODMAP diet, developed by researchers at Monash University in Australia, is one of the most effective tools for managing SIBO symptoms. FODMAP is an acronym encompassing five types of short-chain carbohydrates that are poorly absorbed in the small intestine: Fermentable, Oligosaccharides, Disaccharides, Monosaccharides And Polyols.

In the context of SIBO, these carbohydrates are particularly problematic because, when not absorbed properly, they remain available for bacteria in the small intestine, which ferment them and produce hydrogen, methane and other gases. By reducing FODMAP intake, you reduce the "fuel" available to these bacteria, which in turn decreases gas production and the associated symptoms.

How to follow the Low FODMAP diet with SIBO

The Low FODMAP diet is structured in three phases:

1. Elimination phase (2-6 weeks): All high-FODMAP foods are removed. This is the most restrictive phase, but it usually provides significant symptom relief. Safe foods include rice, potatoes, carrots, spinach, chicken, fish, eggs, firm bananas and strawberries.
2. Reintroduction phase (6-8 weeks): FODMAP groups are reintroduced one by one to identify which ones cause symptoms and in what quantities. This is especially important for people with SIBO, as tolerance may change as treatment reduces the overgrowth.
3. Personalisation phase (long-term): A personalised diet is established that includes the widest possible variety of foods, avoiding only those that cause significant symptoms.

What to eat during the elimination phase

A selection of low-FODMAP foods that are safe during SIBO treatment includes:

• Proteins: Chicken, turkey, fish, eggs, firm tofu, tempeh
• Grains: Rice, gluten-free oats (in controlled portions), quinoa, corn
• Vegetables: Carrots, courgette, cucumber, spinach, bell pepper, aubergine, green beans
• Fruits: Firm banana, blueberries, strawberries, grapes, orange, kiwi
• Fats: Olive oil, MCT oil, chia seeds (limited portions), macadamia nuts

Nutrition during SIBO treatment

One of the greatest challenges of SIBO is maintaining adequate nutrition during treatment. The combination of malabsorption caused by bacterial overgrowth, the dietary restrictions of treatment and symptoms that reduce appetite can lead to significant nutritional deficiencies.

Common nutritional challenges

• Insufficient caloric intake: Fear of eating (in anticipation of symptoms) and Low FODMAP diet restrictions can result in a caloric intake well below daily requirements.
• Protein deficit: Many plant-based protein sources (legumes, soy) are high in FODMAPs, which limits options for people following vegetarian or vegan diets.
• Meal preparation fatigue: Cooking every meal from scratch with Low FODMAP ingredients is exhausting, especially when you are already suffering from chronic fatigue.
• Micronutrient deficiencies: Malabsorption can cause deficits in B12, iron, vitamin D, zinc and magnesium, even when the diet appears adequate.

The role of meal supplements

A meal supplement formulated for the Low FODMAP diet can be an extremely valuable tool during SIBO treatment. It offers several advantages:

• Guarantees adequate caloric and protein intake without the need to cook
• Eliminates uncertainty about the FODMAP content of each ingredient
• Is easy to digest, which can reduce the burden on an already compromised digestive system
• Can be especially useful on days when symptoms are worse and eating solid food is difficult

However, choosing the right product is important. Most supplements on the market contain ingredients that are problematic for people with SIBO: inulin, chicory root, FOS (fructo-oligosaccharides), soy protein, lactose or sugar alcohols such as erythritol and sorbitol. KLARGUT FODMAP Meal Shake has been scientifically formulated for the Low FODMAP diet, avoiding all of these ingredients and providing plant-based protein (pea + rice), gluten-free oats, MCT oil and chia seeds in every serving.

Frequently asked questions about SIBO