Understanding Small Intestinal Bacterial Overgrowth (SIBO)

We recently shared an article on the potential for mapping your gut microbiome, which is the home to bacteria that live within the large intestine. Today we dissect another condition associated with the gut known as Small Intestinal Bacterial Overgrowth (SIBO). As the name would suggest, this is a condition of microbial imbalance in the small intestine, which means it can’t be diagnosed via the MetaBiomeTM test (though the signs will most definitely be there) and must be diagnosed via simple breath testing. 

SIBO is a common underlying contributor to gastrointestinal complaints including reflux, bloating, inconsistent bowel motions and Irritable Bowel Syndrome (IBS) but unfortunately, it often goes undiagnosed or overlooked.

Many modern lifestyle factors create risk for SIBO such as the reliance on antibiotics, stress, abdominal surgery, occurrences of gastroenteritis and overconsumption of refined carbohydrates contribute.


As the name implies, SIBO is an overgrowth of bacteria in the small intestine. While bacterium naturally occur throughout the digestive tract, in a healthy system the small intestine should have relatively lower levels of bacteria, with the highest concentrations found in the colon. This is not the case with SIBO and the excessive numbers of bacteria present in the small intestine can wreak havoc.

The small intestine is where we absorb nutrients from our food. The increase of bacteria in this region causes nutrients to get broken down and/or fermented (rather than absorbed and used for energy or cell growth and repair) leading to nutritional deficiencies, food sensitivities, gut permeability, poor immune health, inflammation and abdominal discomfort.


  • Abdominal pain/discomfort
  • Bloating
  • Flatulence
  • Constipation
  • Diarrhoea
  • Reflux
  • Fatigue
  • Nutrient deficiencies (iron and B12, especially)
  • Altered mood (anxiety and/or depression)


SIBO can be diagnosed by undertaking a simple breath test, administered by a health care professional, that measures the levels of hydrogen and methane gas present in the breath over a period of time. If results are conclusive, dietary change, herbal remedies and lifestyle changes are essential to get the body back into balance and reverse the symptoms and nutritional deficiencies SIBO may have caused.

The SIBO Bi-Phasic Diet is the most up to date and effective dietary protocol to help eliminate bacterial overgrowth from the small intestine and involves a lower FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols), SCD (Specific Carbohydrate Diet) and Dr Allison Siebecker’s SIBO specific food guide. The Bi-Phasic Diet is broken down into two phases:

Phase 1: this phase involves reducing fermentable starches and fibres, in order to starve bacteria of their preferred fuel source, resulting in die-off. It is based on reducing certain food groups (e.g. dairy, legumes, starchy vegetables, onion, garlic, mushrooms, fruit, grains, sweeteners and specific nuts and seeds), whilst repairing damage to the integrity of the intestinal lining with suitable gut healing nutrients. This phase is divided into two parts (restricted and semi restricted) and individual symptoms will determine how quickly you move through each phase of restriction. Depending on the individual at hand, this phase should take 4-6 weeks in total, before commencing phase 2.

Phase 2: this phase involves the continuation of a low fibre diet (not as restrictive as phase 1) in conjunction with herbal antimicrobials to remove the remaining overgrown bacteria. In this phase, a prokinetic supplement is also recommended to aid the normal functioning of the digestive tract and increase gastrointestinal motility. It is important to note that not all SIBO cases are treated the same and the supplement protocol should differ for individuals who are expressing either hydrogen dominance or methane dominance.


When you undertake a breath test to diagnose SIBO, the presence of methane and hydrogen gases produced by bacteria in the small intestine is measured after ingesting a sugary solution. For those experiencing hydrogen dominance, the overload and/or the wrong type of bacteria in the small intestines causes the unabsorbed sugar to ferment. The process of fermentation creates hydrogen gas as a by-product and this is what the breath test will measure. On the other hand, methane dominance is a little more complex and involves a different class of organisms called archaea. An increase in methane gas after a breath test indicates an overgrowth not of bacteria, but of these methane-producing archaea. The archea, which can be detected via MetaBiomeTM, feed off hydrogen and produce methane as a by product3. Another interesting point to note is that symptoms expressed in patients with hydrogen or methane dominance are also linked. More often than not, hydrogen producers are more likely to experience diarrhea and methane producers often struggle with constipation. This is why it is very important that you test for SIBO (as we always say, ‘test, don’t guess’), that your results are interpreted correctly by a trained health professional who can then advice you on the safest and most effective treatment plan.


It is not unlikely for individuals who test positive for SIBO to also experience a co-infection known as SIFO (Small Intestine Fungal Overgrowth). SIFO is similar to SIBO however instead of the presence of excessive bacteria, there is an excessive number of fungal organisms in the small intestine. This condition is also successfully treated with the SIBO Bi-Phasic Diet diet outlined above.

If you think you may be at risk of SIBO or need support in optimising your gut health, please book your complimentary 15-minute consultation with Holistic Nutritionist Elly Mclean. You can learn more about Elly here.

For more information on this condition, please listen to episode 132 of Health, Happiness & Human Kind here with SIBO expert Dr Nirala Jacobi or episode 282 on Dissecting IBS with Steph Lowe and Elly McLean. 


  1. Hicks, R, 2016. What is Small Intestinal Bacterial Overgrowth (SIBO)? WebMD. Accessed 29 May 2017.
  2. Jacobi, N, 2017. The SIBO Bi-Phasic Diet, 1st Ed [PDF] p. 2. Accessed 30 May 2017.
  3. Kresser, C, 2014. RHR: SIBO and Methane – What’s the Connection? Accessed 6 June 2017.

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