SIBO: rebalancing gut bacteria by addressing root causes

SIBO symptoms

SIBO is caused by microbial bacteria producing methane, hydrogen or a combination of both or sulphur-reducing microbial species residing in the small intestine. Symptoms can differ from person to person, although the most common SIBO symptoms can include:

• Bloating and abdominal distention
• Loose bowel motions or diarrhoea‍
• Food allergies, intolerances and sensitivities‍
• Abdominal pain and/or cramping
• Excessive, smelly flatulence‍
• Constipation‍
• Alternating constipation and diarrhoea
• Belching/burping
• Nausea
• Brain fog & memory loss
• Histamine intolerance
• Joint pain‍
• Reflux/heartburn‍
• Skin complaints such as hives, eczema, psoriasis, acne or rashes
• Joint pain
• Intestinal hyper-permeability
• Sleep disruption
• Anxiety, depression and neuropsychological symptoms

Methane-dominant SIBO is usually associated with constipation, whereas hydrogen-dominant SIBO can present with symptoms of diarrhoea or loose stools. Less common sulphur reducing bacteria can produce a gas odour that resembles rotten egg.

SIBO symptoms can both mask and worsen symptoms of other digestive disorders such as coeliac disease, and IBS. SIBO is found in up to 60% of people diagnosed with IBS (irritable bowel syndrome) making diagnosis difficult (see our article on IBS and SIBO to find out more). And for patients diagnosed with inflammatory bowel disease (IBD), studies reveal they are 9.5 times more likely to develop SIBO.

SIBO can cause systemic inflammation and trigger intestinal hyperpermeability (also known as ‘leaky gut’) of the digestive lining by breaking the junctions between cells, allowing large proteins to cross over into the bloodstream. These proteins are detected by the immune system and can trigger new food reactions. A vicious cycle can occur where food reactions cause further inflammation, exacerbating SIBO symptoms.

Additionally, in all SIBO types, nutritional deficiencies can occur due to poor absorption of Vitamins B12, D, A and E and minerals such as iron and calcium.

What causes SIBO?

Healthy digestion relies on a sequence of events occurring. Once the food is broken down by chewing and saliva in the mouth, it is further broken down by hydrochloric acid in the stomach and moves to the small intestines where most nutrients are absorbed. The timely movement of food occurs via a wave-like muscular constriction called ‘peristalsis’, and allows proper absorption of nutrients. The migrating motor complex (MMC) is a different and stronger wave-like constriction occurring around every 90 minutes and is a necessary ‘cleaning cycle’ of the digestive system. The disruption of any of these processes can lead to SIBO.

Common causes can include:

• Low stomach acid
• Acid reducing medications such as PPI’s (proton pump inhibitors e.g. Nexium)
• Coeliac disease
• IBS
• IBD (Crohn’s disease, ulcerative colitis)
• Diverticulitis
• Slow motility/peristalsis
• Chronic constipation
• Hypothyroid (low thyroid hormone)
• Food poisoning/infection/parasites (Enterococcus, Klebsiella, H. pylori, E.coli )
• Chronic stress
• Poor diet (e.g. high sugar, alcohol, processed carbohydrates)
• Abdominal surgery
• Traumatic brain injury, concussions
• Side effects of medications e.g. opiates, antispasmodics, PPIs
• Scarring and adhesions of the small intestines
• Pancreatitis
• Endometriosis
• Gastroparesis
• Scleroderma
• Diabetes
• Mould toxicity
• Ehlers-Danlos Syndrome (EDS)
• Ileocecal valve dysfunction

There are 3 main types of SIBO, with each involving overgrowth of different aerobic and anaerobic microbial species:

1. Hydrogen producing bacteria

The abnormal presence of colonic bacteria in the small intestines means that fermentation of foods is occurring much higher up the digestive system than it should be. The small intestines are very sensitive to the excessive production of hydrogen gas, predominantly from Bacteroidetes spp., which causes abdominal bloating and diarrhoea. Other low oxygen (microaerophilic) hydrogen-producing species are Streptococcus and Escherichia coli, along with anaerobic bacteria, such as Lactobacillus and Bacteroides.

2. Methane producing archaea 

Constipation is a result of methane-producing species of non-bacterial, single-celled species called archaea, such as Methanobrevibacter smithii and Methanospaera stadmagnae. M. smithii and M. stadmagnae. These microbes feed on the hydrogen produced by species of bacteria, creating a methane gas byproduct which is also responsible for abdominal bloating and slows transit time or migrating motor complex of the GIT, leading to  constipation or irregular bowel motions.

3. Hydrogen sulphide producing bacteria

The third type of SIBO is due to the hydrogen sulphide producing bacteria, commonly Desulfovibrio spp or Fusobacterium spp. This SIBO type is less common and tests negative on traditional breath testing  which only tests for hydrogen and methane gas which these species don’t produce.

The by-product of these species is hydrogen sulphide gas, which is highly toxic to the cells of the intestinal walls and is distinguished by the foul odour of rotten eggs. Hydrogen sulphide metabolisation is normal in the cecum and in the colon, but not when it occurs  in the small intestine.  These species reduce sulphate to hydrogen sulphide gas  and are also referred to as sulphur reducing bacteria (SRB). High concentrations of hydrogen sulphide are involved in gut inflammation.

SIBO treatment – the conventional approach

Diagnosis via conventional testing alone is imperfect and is made via either hydrogen and methane breath testing, or the gold standard is jejunal aspirate testing. This test extracts a small sample of fluid from the middle part of the digestive system called the jejunum via an endoscope. The limitations of jejunal aspirate tests are cost, the invasive nature of the testing, and potential for false negatives due to difficulties in growing cultures.

Conventional methods of SIBO treatment usually includes antibiotics such as rifaximin, and whilst it may kill undesirable species, it is indiscriminate and also kills beneficial species. This can allow opportunistic species to overgrow in much the same way as weeds that grow back in the garden when the ground is cleared. In addition, studies show that rifaximin is not effective at treating SIBO symptoms.

Usually, SIBO takes a long time to heal, and requires a holistic approach to uncover the factors involved in causing or aggravating SIBO, along with a staged approach that patients are supported through.

SIBO test Melbourne and Australia-wide

Diagnosing SIBO accurately is essential for effective treatment. The most common diagnostic tool for SIBO is a breath test that measures hydrogen and methane gas levels. These gases are produced by certain bacteria and archaea in the small intestine.

Unlike a Helicobacter pylori test, which detects the presence of H. pylori in the stomach, the SIBO breath test is specifically designed to identify bacterial overgrowth in the small intestine. It involves collecting breath samples after consuming a specific sugar solution (e.g., lactulose or glucose) and analysing them for gas production over time.

Our functional medicine approach goes beyond breath testing to develop a comprehensive understanding of your condition. In addition to the SIBO breath test, we may also recommend:

• Food allergy, intolerance, or sensitivity testing
• Gut microbiome analysis
• Digestive function and nutrient absorption assessments
• Stool testing for bacteria, including Enterococcus, Klebsiella, H. pylori, and E. coli
• Other functional tests tailored to your specific symptoms

These tests help uncover underlying factors contributing to SIBO and guide a personalised treatment plan. Our practitioners combine test results with a detailed health history to identify triggers such as antibiotic use, genetic predispositions, and lifestyle factors.

Through this holistic approach, we ensure that every aspect of your health is considered, leading to more effective and lasting relief from SIBO symptoms.‍

See how our approach helps our patients achieve better health and richer lives.

Jenny came into the program with significant health concerns, which included bloating, constipation, brain fog, and migraines. These, plus other ongoing issues had severely impacted her ability to work, as she struggled with unpredictable health fluctuations. After finding little help from allopathic medicine specialists, Jenny turned to us as a last resort, hoping for answers and a path to recovery.

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Our unique model of care was designed with you in mind. Find out how, then book a call today