Understanding Small Intestinal Bacterial Overgrowth (SIBO): A Functional Nutrition Approach

Small Intestinal Bacterial Overgrowth (SIBO) is a condition characterized by an excessive growth of bacteria in the small intestine, leading to a number of gastrointestinal symptoms. Unlike the large intestine, where a high bacterial count is normal, the small intestine is meant to have relatively low bacterial levels. SIBO disrupts this balance, affecting nutrient absorption and causing discomfort. Symptoms associated with SIBO can include: bloating, diarrhoea, constipation, gas, fatigue, nausea, joint pain and even depression.

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Types of SIBO: Hydrogen and Methane

SIBO can be categorized based on the type of gas produced by the overgrown bacteria:

  • Hydrogen-Dominant SIBO: Typically associated with diarrhoea and is identified by a rise in hydrogen levels during a breath test. Numerous bacteria have been associated with SIBO, including Enterococcus, Escherichia coli, and Klebsiella.
  • Methane-Dominant SIBO: This type is often linked to constipation and involves methane production by archaea rather than bacteria​. Methanobrevibacter smithii is the archaea linked to IMO when it overgrows in either the small or large intestines.
  • Mixed SIBO: Mixed SIBO occurs when both hydrogen gas and methane gas are elevated on a SIBO breath test, suggesting overgrowth of both methane-producing and hydrogen-producing bacteria.


Diagnosis is often made through a breath test that measures hydrogen and methane levels after ingesting a sugar solution.  However, the testing can be costly for the average South African so we often go on symptoms.

It is super important to recognise that overgrowth is a symptom of underlying dysfunction and imbalances. Identifying and addressing these causative factors makes a functional approach to SIBO more effective than conventional treatment techniques.

Functional Nutrition Approach to Addressing SIBO

Functional nutrition addresses SIBO through the 5R Framework for Gut Health:

  1. Remove: Eliminate dietary triggers and infections using elimination diets or targeted antimicrobial treatments. Both herbal antimicrobials (e.g., oil of oregano, peppermint oil, garlic) and prescription meds (e.g., rifaximin) are used based on the type of SIBO​
  2. Replace: Supplement digestive enzymes and acids that may be deficient, enhancing digestion and absorption​. I often see low levels of elastase and high levels of steatocrit in a stool test.
  3. Reinoculate: Introduce beneficial bacteria through probiotics and prebiotics to restore a balanced gut microbiome​. However, one has to be super careful with SIBO not to overdo the probiotics and prebiotics (initially anyway).
  4. Repair: Support the gut lining with nutrients like zinc, omega-3 fatty acids, and glutamine to ensure overall gut health. It may also be important to include supplements that are high in immunoglobulins.
  5. Rebalance: Address lifestyle factors such as stress, sleep, and exercise, which significantly impact gut health.  This is absolutely key.

Dietary Interventions

Nutritional therapy is critical in managing SIBO. A low FODMAP diet, which restricts fermentable carbohydrates, is often recommended to reduce bacterial overgrowth.  I prefer to also significantly limit grains. An elemental diet, which involves consuming easily digestible nutrients in a liquid form, can be effective in severe cases.

Long term outlook

When addressing SIBO using a functional nutrition approach, commitment for the long term is crucial. Whilst the initial diet can provide significant relief, the complete protocol may span 4-6 months, and in some cases, even longer.   Discontinuing the intervention early generally leads to a regression and a return of symptoms.