Small Intestinal Bacterial Overgrowth

Dr Aisling Dwyer MB BCh BAO (Medicine, Surgery and Obstetrics), MSc (Personalised Nutrition)​

Small intestinal bacterial overgrowth is increasingly recognised as a cause of abdominal bloating, pain and diarrhoea. Historically believed to afflict only those who had structural abnormalities of the gastrointestinal tract1, it is actually an increasingly common cause of digestive symptoms: up to 78% of individuals with irritable bowel syndrome, one of the most widespread gastrointestinal complaints worldwide, have been found to have SIBO on breath testing.

What is SIBO?

Small Intestinal Bacterial Overgrowth or SIBO is the excessive growth of bacteria in the small intestine. The small intestine usually is colonised by some bacteria but much less than the large intestine. When there is an abnormally high quantity of bacteria in the small intestine, there is increased bacterial fermentation of food as it enters from the stomach. This results in increased gas production, usually hydrogen and sometimes methane gases. In the short term, increased gas production can lead to bloating, flatulence, nausea and abdominal pain. Long term, bacterial overgrowth can lead to local intestinal mucosal inflammation. This can damage the lining of the intestinal tract, flattening villi and thinning the mucosa which can in turn, prevent optimal absorption of nutrients, in some cases leading to vitamin and mineral deficiencies.

What causes SIBO?

The two most common causes of SIBO are reduced gastric acid secretion and impaired small intestinal motility3. Stomach acid inhibits the growth of bacteria that is ingested in our food. Normal intestinal motility keeps the contents of our small intestine moving and prevents stasis of food and bacteria, which can lead to bacterial overgrowth.

Causes of reduced acid production:

  • Aging (natural process)
  • Medication – long term acid suppressant use including Proton Pump Inhibitors (PPIs)

Causes of reduced small intestinal motility:

  • Irritable Bowel Syndrome
  • Crohn’s Disease
  • Systemic diseases such as Diabetes Mellitus, systemic sclerosis, liver disease
  • Coeliac Disease
  • Medications such as opiates
  • Structural abnormalities in the small intestine such as post gastric surgery

Additional contributing factors

Recurrent or long-term antibiotic use is also a risk factor for the development of SIBO. Antibiotics can alter the composition of bacteria in the small intestine leading to increased growth of pathogenic bacteria. For more about antibiotics and the microbiome, take a look at this article in the Probiotics Learning Lab: Probiotics and Antibiotics.

Poor function of the the ileocaecal valve, located at the junction between the ileum (small intestine) and the caecum (start of the large intestine), is also a risk factor for SIBO. This valve prevents the “backflow” of colonic contents from re-entering the small intestine, but individuals with a dysfunctional ileocaecal valve are at increased risk of developing SIBO as colonic bacteria can enter and colonise the small intestine more easily4.

Individuals with immune deficiencies, such as with HIV, are also prone to bacterial overgrowth.

doctor with patient

What are the symptoms of SIBO?

Symptoms of SIBO may be related to the underlying cause of SIBO (low stomach acid, poor motility), the manifestation of SIBO itself, or the consequences of malabsorption. Common symptoms include:

  • Nausea
  • Bloating
  • Abdominal distension
  • Flatulence
  • Abdominal pain and cramping
  • Diarrhoea (less commonly, constipation)
  • Fatigue or poor concentration5

Signs of corresponding malabsorption could include:

  • Bulky, difficult to flush stool with high fat content due to fat malabsorption (known as steatorrhoea)
  • Weight loss
  • Anaemia
  • Deficiency of vitamin B12 or fat-soluble vitamins A, D, E, K5

How is SIBO diagnosed?

SIBO is typically diagnosed based on patient history, followed by a diagnostic test. Healthy individuals have less than 103 CFU (or colony forming units) of bacteria per millilitre of digestive fluid in the small intestine. There are currently two diagnostic tests used for SIBO:

  • Jejunal aspiration - a direct measurement of the numbers of bacteria in the small intestine
  • Breath test - an indirect measurement of the bacteria numbers, gleaned from the measurement of the by-products of their fermentation activity.

Small bowel aspiration and culture

SIBO can be diagnosed when there is greater than 10CFU of bacteria cultured per mL of digestive fluids from the small intestine. This aspiration can be performed on endoscopy, but it is not routinely practised as it is time consuming and expensive, and is an invasive procedure with some risk attached to performing it.

Breath Test

Hydrogen gas is produced by bacteria in the gastrointestinal tract as a by-product of fermentation of simple carbohydrates. During this diagnostic test, glucose or another simple carbohydrate is given to a patient, and the hydrogen and methane* gases exhaled in their breath over the following 90 minutes, is measured. This is under the premise that hydrogen is rapidly produced by bacterial fermentation in the small intestine. The gases are absorbed into the bloodstream and excreted in the breath. A rise of 20ppm in exhaled hydrogen above baseline within 90 minutes of oral ingestion of 75g of glucose is considered diagnostic. There are many benefits with this type of testing including its wide availability, it is inexpensive, non-invasive and technically easy to perform. However, there is an increased risk of false positives as some individuals have faster colonic transit, and hydrogen may be produced in the colon. It is also relatively poor at diagnosing SIBO in the distal small intestine (the furthest end of the small intestine) as glucose is absorbed proximally (in the nearest end). Meaning that the glucose may not reach the distal small intestine and trigger bacterial fermentation here.

*Human cells are incapable of producing hydrogen and methane gases. Although methane is not produced by bacteria, the archaea that produce it use hydrogen as a substrate so its presence suggests increased hydrogen production. A rise of greater than 10 ppm of methane is diagnostic of methanogenic archaea overgrowth.

Management of SIBO

There are three areas to address when managing SIBO:

  1. The underlying cause of SIBO
  2. Malabsorption and nutritional deficiencies
  3. The bacterial overgrowth itself with antibiotics.

As discussed above, there are various underlying causes of SIBO. Medication use can be reviewed and potentially stopped, such as proton pump inhibitors and opiates, under the guidance of a healthcare practitioner. Avoiding fermentable carbohydrates such as in the low FODMAP diet can reduce bacterial fermentation in SIBO and could be considered, again under the guidance of a healthcare practitioner6. Managing IBS requires an individualised approach - you can read more about this in our article on remedies for IBS.

Addressing nutritional deficiencies is very important. Vitamin B12 and fat-soluble vitamins A, D, E and K may need to be supplemented. Damage to the lining of the intestinal tract can also prevent enzyme production which may require supplementation with digestive enzymes3.

Although there is no universally accepted standardised treatment for SIBO, the mainstay of treatment of SIBO currently is with antibiotics to reduce bacterial colonisation in the small intestine5. R*******n is the best studied antibiotic for this purpose as it has poor systemic bioavailability which means that it mostly works locally in the gastrointestinal tract7. The British Society of Gastroenterology use 550mg of r*******n twice daily for 7 days in those with abnormal breath tests8.

Best probiotics for SIBO

Although it may be seen as contradictory to use probiotics in small intestinal bacterial overgrowth, one particular probiotic yeast, Saccharomyces boulardii, has been identified as beneficial.

Saccharomyces boulardii can be found in Optibac Probiotics S. boulardii

As a yeast, Saccharomyces boulardii can be taken alongside antibiotics and its functioning is unaffected. It has known anti-inflammatory effects in the gut9 and can inactivate pathogenic toxins10 and stimulate enterocyte (cells of the intestinal lining) maturation11.

In a pilot clinical study of 40 patients diagnosed with SIBO due to the autoimmune condition, systemic sclerosis, the effects of Saccharomyces boulardii on hydrogen production and SIBO eradication was assessed and compared with m***********e, a common antibiotic used in the treatment of SIBO12. The patients were divided into 3 groups; one group were given m***********e alone for 1 week, another group were given m***********e with Saccharomyces boulardii for 1 week and the third group were given Saccharomyces boulardii alone for 1 week. Two months later, hydrogen breath tests were repeated. The group that achieved the best results was the m***********e and Saccharomyces boulardii group, with SIBO eradicated in 55% of participants at 2 months. Saccharomyces boulardii therapy alone eradicated 33% which was better than the group given m***********e alone (with just 25% SIBO eradication). Of note, the Saccharomyces boulardii group had the lowest level of adverse effects from treatment, and taking SB alongside m***********e appeared to reduce the risk of antibiotic side-effects from 53% to 36%12. The results of this clinical study suggest Saccharomyces boulardii as a potential beneficial adjunct to antibiotic therapy when treating SIBO.

Key Points

  • Small Intestinal Bacterial Overgrowth is the excessive growth of bacteria in the small intestine, where there is usually minimal bacterial colonisation.
  • The symptoms of SIBO are due to the gas produced by bacterial fermentation of carbohydrates, and the local inflammation caused by the presence of excessive bacteria in the small intestine.
  • Common symptoms of SIBO include bloating, nausea, diarrhoea, indigestion and abdominal pain.
  • SIBO is caused by factors that reduce gastric acid production or reduce small intestinal motility. Common causes include IBS, long term PPI use, recurrent or long-term antibiotic use.
  • In the presence of symptoms and risk factors for SIBO, clinical diagnosis usually involves a hydrogen breath test.
  • Along with addressing the underlying cause and nutritional deficiencies caused by SIBO, the mainstay of treatment is antibiotics.
  • The diagnosis and management of SIBO should be carried out by a health care practitioner. 

You can find the Saccharomyces boulardii strain in Optibac Saccharomyces Boulardii

If you liked this article, read more about the research behind Saccharomyces boulardii over on our Probiotics Database. 


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