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SIBO – What is it, how to diagnose

Author: PhD Natalia Drabińska

The previous article described the importance of intestinal microbiota and dysbiosis, i.e. a state in which the balance of the number and type of intestinal microorganisms is disturbed. One example of intestinal dysbiosis is SIBO.

SIBO, which is an abbreviation of Small Intestinal Bacterial Overgrowth, is a condition with an excessive amount of bacteria in the small intestine, which causes gastrointestinal symptoms. The small intestine should contain up to 103 CFU (colony-forming units) of bacteria, which results from unfavourable living conditions. Factors preventing the excessive growth of bacteria in the small intestine include:

  • low pH due to the presence of gastric juice
  • bile
  • migrating myoelectric complex (MMC)
  • intestinal peristalsis
  • proteolytic and lipolytic enzymes excreted by the pancreas
  • ileocecal valve
  • secretory IgA

As you can guess, disorders or dysfunctions in these areas, especially in intestinal peristalsis, may contribute to the development of SIBO.

The factors additionally increasing the risk of SIBO are:

  • Functional and motor disorders occurring in i.a.: irritable bowel syndrome, intestinal pseudo-obstruction
  • Anatomical abnormalities (after bariatric and ileocaecal valve surgeries, narrowing of the intestinal lumen, postoperative adhesions)
  • Intestinal inflammatory diseases, including ulcerative colitis, Crohn’s disease
  • Autoimmune diseases, such as Hashimoto, rheumatoid arthritis, celiac disease
  • Other diseases, such as diabetes, chronic pancreatitis, cirrhosis, Helicobacter pylori infection, kidney failure, rosacea and others
  • Certain medications, including acid reflux medications like proton pump inhibitors, non-steroidal anti-inflammatory drugs
  • Age 

Symptoms of SIBO

The problem in diagnosing SIBO is the non-specificity of symptoms. SIBO is most often manifested by bloating and excessive accumulation of gases, which results from bacterial fermentation. In addition, the symptom of SIBO is abdominal pain, a feeling of fullness, abdominal discomfort, chronic diarrhoea or constipation. An alarming symptom is also unjustified weight loss.

Other symptoms of SIBO can be caused by nutrient malabsorption, intestinal inflammation, increased intestinal barrier permeability, and activation of the immune system that result from pathological fermentation in the small intestine.

Diagnosis of SIBO

Due to the non-specificity of symptoms, SIBO is often diagnosed late or not at all. To date, there is also no common position regarding the SIBO diagnostic procedure recognized by various medical societies.

It is recognized that the gold standard in the diagnosis of SIBO is the quantitative microbiological examination of the contents of the small intestine. A positive result is considered to be >105 CFU or 103 CFU in 1 mL of intestinal content, depending on the studies. Although this is the most reliable diagnostic method, it is not often used due to the nature of the sample collection. To collect the content of the small intestine, an endoscopic examination is needed, which is very invasive, unpleasant for the patient, complicated, time-consuming and very expensive. Therefore, alternative, indirect methods of diagnosing SIBO have been adopted.

Hydrogen test

The hydrogen breath test is a diagnostic method based on measuring the concentration of hydrogen in the exhaled air after oral intake of 75 g of glucose or 10 g of lactulose. A positive result is considered to be a concentration of hydrogen above 20 ppm within 90 minutes of ingestion of sugars. Unfortunately, this method can give a false positive result (in the case of lactulose) or a false negative result (in the case of glucose). Most often, the hydrogen test is used when among the symptoms of the gastrointestinal tract, diarrhoea is dominating.

Hydrogen-methane test

It may happen that despite the overgrowth of microorganisms in the small intestine, the result of the hydrogen test will be negative. This is due to the fact that methane-producing microorganisms belonging to archaea, and not bacteria, can also grow in the small intestine. This type of overgrowth is called IMO, which is Intestinal Methane Overgrowth. In this case, the hydrogen test will not be able to detect abnormalities. Therefore, it is often proposed to use hydrogen-methane tests that simultaneously measure the level of both gases. IMO is diagnosed when the level of methane in the breath after oral intake of lactulose or glucose exceeds 10 ppm. The hydrogen-methane test is most often used when the patient complains of constipation.

Preparation for hydrogen and hydrogen-methane test

It is very important to prepare properly for hydrogen and hydrogen-methane tests, which, if neglected, may result in incorrect results. 

Before the test:

  • Avoid antibiotics (at least for 4 weeks)
  • Avoid taking prokinetic drugs and laxatives (at least for a week before)
  • A day before follow a low-FODMAP diet, which eliminates easily fermentable foods
  • Fast for at least 8-16 hours
  • Take care of oral hygiene, but avoid toothpaste containing xylitol
  • Avoid chewing gums containing polyols
  • Drink a glass of water
  • Avoid smoking
  • Avoid physical activity

Treatment of SIBO


When the result of the hydrogen or hydrogen-methane test turns out to be positive, the treatment of SIBO should be carried out by a doctor specializing in gastroenterology. Never initiate the treatment of SIBO by yourself!

Usually, the management of a patient with SIBO begins with antibiotic therapy, most often the introduction of rifaximin, which has a bactericidal effect on the digestive tract.

Sometimes prokinetic drugs are also used as supportive therapy. Prokinetic drugs are a group of drugs that stimulate peristalsis of the upper digestive system. Examples of prokinetic agents are:

  • Bethanechol
  • Cisapride
  • Metoclopramide


At a later stage of treatment, diet therapy is introduced. The most commonly used diet in the treatment of SIBO is a diet low in fermentable polysaccharides, disaccharides, monosaccharides and polyols, called low-FODMAPs. The task of the low-FODMAP diet is to maximally limit the intake of products that could be easily fermented by microorganisms living in the intestine, which would stimulate their further growth. 

Other diets proposed as a treatment for SIBO are:

  • Specific Carbohydrate Diet – Removal of all carbohydrate products other than elemental sugar sources
  • Ketogenic diets and low-carb diets
  • Gluten-free diet
  • Paleo diet
  • Elemental diet
  • And others

However, for other diets, there is insufficient scientific or clinical evidence to support their effectiveness.


An important element of SIBO treatment is the compensation for nutritional deficiencies. Both SIBO itself as well as the introduced diet therapy, which is based on the elimination of many food products, can contribute to deficiencies. People with SIBO are at particular risk of deficiencies in fat-soluble vitamins (A, D, E and K), vitamin B12 and iron (especially women). 

Notably, supplementation should always be consulted with a medical doctor, as some substances may negatively affect the condition of the intestines or their motility. For example, iron supplementation can cause constipation, abdominal pain, and nausea [1].

In the case of SIBO, you should also be wary of prebiotic supplements, which can aggravate symptoms resulting from over-fermentation.

In recent years, there has been a discussion about whether the use of probiotics can support SIBO therapy. However, the results of scientific studies are still inconclusive [2-4].

What’s next?

It may happen that despite successful treatment, the symptoms of SIBO return after a few months and is just as troublesome as at the beginning. We must remember that SIBO is a symptom of abnormalities in the body, not a cause and will not go away without eliminating the root cause. Therefore, in the case of SIBO, it is important not only to treat symptomatically but also to look at the whole organism holistically. It is important to consult a medical doctor who will help us find what contributed to the growth of bacteria in the intestine in the first place and deepen the diagnosis towards other potential diseases.


[1] Low MSY, Speedy J, Styles CE, De‐Regil LM, Pasricha SR. Daily iron supplementation for improving anaemia, iron status and health in menstruating women. Cochrane Database of Systematic Reviews 2016, Issue 4. Art. No.: CD009747. DOI: 10.1002/14651858.CD009747.pub2.

[2] Zhong C, Qu C, Wang B, Liang S, Zeng B. Probiotics for preventing and treating small intestinal bacterial overgrowth: a meta-analysis and systematic review of current evidence. J Clin Gastroenterol. 2017;51:300–311. 

[3] Rosania R, Giorgio F, Principi M, Amoruso A, Monno R, Di Leo A, Ierardi E. Effect of probiotic or prebiotic supplementation on antibiotic therapy in the small intestinal bacterial overgrowth: a comparative evaluation. Curr Clin Pharmacol. 2013;8:169–172. 

[4] Rao SSC, Rehman A, Yu S, Andino NM.Brain fogginess, gas and bloating: a link between SIBO, probiotics and metabolic acidosis. Clin Transl Gastroenterol. 2018;9:162.

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