The dietary management of SIBO

The dietary management of SIBO

The definition of small intestinal bacterial overgrowth (SIBO) lacks general consensus. It is generally thought to develop when there is an increased concentration of bacteria within the small intestine, which disrupts functioning.1,2 At present, our understanding of microbiota populations within a healthy gut microbiome is limited, which complicates the definition of SIBO.
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What is SIBO?

The definition of small intestinal bacterial overgrowth (SIBO) lacks general consensus. It is generally thought to develop when there is an increased concentration of bacteria within the small intestine, which disrupts functioning.1,2 At present, our understanding of microbiota populations within a healthy gut microbiome is limited, which complicates the definition of SIBO.1

Microbiome sampling techniques are improving, which could further our understanding of the composition of a healthy gut microbiome and therefore allow us to determine which bacterial strains exist in the presence of disease.

Diagnosis of SIBO

The gold standard diagnostic process for SIBO involves microbial examination of intestinal aspirates.4 However, hydrogen-breath tests (HBT) (which measure hydrogen and methane production by gut microbiota) are more frequently used as it is a non-invasive, cheaper diagnostic tool.3

The HBT involves drinking a solution of lactulose or glucose and providing breath samples every 20 minutes over a 3-hour period. The bacterial fermentation of carbohydrates in the intestine produces hydrogen. In approximately 15%-30% of the population who have a specific strain of gut bacteria (Methanobrevibacter smithii), the hydrogen is converted to methane.5 A positive SIBO case, diagnosed by a glucose HBT, will show a rise in breath hydrogen. A positive SIBO case, diagnosed by a lactulose HBT, will show a double peak of hydrogen and methane breath production.6

There are significant limitations in the diagnosis of SIBO. For example, confounding factors need to be tightly controlled to ensure they do not influence test results. HBT requires the patient to adhere to strict guidelines prior to the testing. This may include the avoidance of low glycaemic index (GI) carbohydrates and fibre-rich foods for 24-hours prior to the test as well as no cigarette smoking or exercise for two hours prior to the test.

Medications that can increase the risk of developing SIBO, including proton pump inhibitors, should be discontinued during the days leading up to the test. If these guidelines are not followed correctly, the hydrogen content and excretion in the breath can be affected, which may negatively impact results, thus leading to inaccuracies in interpretation of results and diagnosis.6

Additional diagnostic limitations are outlined below:

  • HBT is not a validated diagnostic tool
  • The ability to accurately interpret results and define SIBO is limited1
  • HBT assumes that the patient has a normal gut transit time; it assumes that mouth-to-cecum transit time is always greater than 90 minutes, however studies have identified that there is great individual variation6
  • Functional symptoms associated with SIBO are similar to IBS and other GI disorders, which could lead to mis-diagnosis
  • There are a subset of people who are asymptomatic with SIBO2

In light of the above, test results should be interpreted with caution by a suitably qualified medical professional, alongside a detailed clinical history. Even then, results are not free from ambiguity and they only complete part of the picture.

Treatment of SIBO

Treatment for SIBO must address the underlying causes and symptoms as well as correcting any nutritional deficiencies.1

Antibiotic treatment is widely used to selectively target bacterial strains that cause SIBO. The prescribed antibiotics should be based on laboratory results which determine the sensitivity of the microbial strains to particular antibiotics. However, multiple strains of gut bacteria are present in SIBO, each with different sensitivities to antibiotics, which makes treatment difficult.

Commonly used antibiotics include Tetracycline and Rifaximin. There is no consensus on choice, dose and duration of antibiotic therapy, however long-term treatment with broad-spectrum antibiotics should be avoided to minimise the adverse effects of antibiotics.3

The effects of antibiotics on the gut microbiome

A systematic review identified that antibiotic therapy can lead to dysbiosis, which is defined as an imbalance of microbial diversity in the gut microbiome. Changes within the gut microbiome can cause a variety of symptoms including antibiotic-associated diarrhoea, occurring in 2–25% of people taking antibiotics.7

The dietary management of SIBO

Dietary therapies for SIBO are currently only supported by anecdotal evidence. Therefore, more research is needed before they can be routinely recommended. If the SIBO is associated with malnutrition and weight loss, the nutritional intervention should be focused on nutrition support and correction of nutrient deficiencies.

The low FODMAP diet

At present, the LFD can be used alongside medication (antibiotic therapy) to help manage symptoms associated with SIBO, but it does not eliminate SIBO.8,9 The LFD limits intake of fermentable, oligosaccharides, disaccharides, monosaccharides and polyols, which are a group of poorly absorbed short-chain carbohydrates, fermented in the large intestine by gut microbiota.9

It is known that FODMAP dietary exclusions can alter the gut microbiome. However, further research is required to determine the effect of dietary manipulation on gut microbiota and whether it is able to address the changes caused by SIBO.8,10


Correction of nutrient deficiencies

SIBO can result in the malabsorption of nutrients in the intestinal lumen, which can lead to deficiencies of the fat-soluble vitamins (A, D, E, K). Vitamin B12 deficiency is also commonly observed in SIBO patients due to reduced populations of gut microbiota which are needed to bind to vitamin B12 to permit absorption in the ileum.11 Additionally, folate levels can be raised due to increased synthesis of folate by microbiota in the small bowel.12

Biochemistry and clinical signs should be monitored to detect nutritional deficiencies. Antibiotic treatment alongside nutrient supplementation and dietary counselling are often effective in reversing nutrient deficiencies caused by SIBO.13

The use of probiotics

Nutritional strategies can selectively increase the population of beneficial microbes within the gut and therefore may prove to be beneficial in the treatment of SIBO. This section will explore the role of probiotics in the management of SIBO.

Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host.8 There are currently no approved health claims for probiotics in the UK.9

There is a lack of randomised controlled trials (RCTs) examining the effects of probiotics on SIBO. A systematic review including 18 studies, identified that probiotics can decontaminate SIBO, reduce hydrogen production and relieve abdominal pain. However long-term use of probiotics was shown to be ineffective in preventing SIBO. More studies are needed to evaluate the efficacy of probiotics strains in the presence of SIBO.14

Probiotics can be useful during the antibiotic treatment of SIBO. A systematic review which examined 82 RCTs suggested that probiotics are associated with a reduction in antibiotic-associated diarrhoea. Additionally, probiotics may increase the efficacy of antibiotics. One study found that the use of Rifaximin alongside a probiotic (Lactobacillus casei) resolved symptoms of SIBO more effectively than antibiotic use alongside a prebiotic.15

Further research is needed to determine which probiotic strains have the greatest efficacy in preventing diarrhoea and which specific antibiotics are most responsive to probiotic supplementation.11


SIBO can be difficult to diagnose due to underlying GI disturbances presenting with similar symptoms. At present, antibiotic therapy is the preferred treatment, however dietary manipulation (i.e. a low FODMAP diet) alongside targeted supplementation (i.e. probiotics or nutrition supplements) may help to manage symptoms and nutritional deficiencies associated with SIBO.

Weight loss is often associated with SIBO and can present further challenges, making nutrition support a clinical priority. Patients that present with suspected SIBO should be supported to ensure that testing is undertaken within the NHS or a suitable private facility which specialises in gastroenterology. This will ensure results are interpreted accurately and that appropriate, evidence-based clinical treatment is given.

Footnotes - 

[1] Quigley EMM, Murray JA, Pimentel M. AGA Clinical Practice Update on Small Intestinal Bacterial Overgrowth: Expert Review. Gastroenterology. 2020 Jul 1;159(4):1526–32.

[2] Bures J, Cyrany J, Kohoutova D, Förstl M, Rejchrt S, Kvetina J, et al. Small intestinal bacterial overgrowth syndrome. World Journal of Gastroenterology. 2010;16(24):2978–90. Available from:

[3] Rubio-Tapia A, Barton SH, Rosenblatt JE, Murray JA. Prevalence of small intestine bacterial overgrowth diagnosed by quantitative culture of intestinal aspirate in celiac disease. Journal of Clinical Gastroenterology. 2009 Feb;43(2):157–61. Available from:

[4] Corazza GR, Menozzi MG, Strocchi A, Rasciti L, Vaira D, Lecchini R, et al. The diagnosis of small bowel bacterial overgrowth. Reliability of jejunal culture and inadequacy of breath hydrogen testing. Gastroenterology. 1990;98(2):302–9. Available from:

[5] Ghoshal UC. How to interpret hydrogen breath tests. Journal of Neurogastroenterology and Motility. 2011;17(3):312–7. Available from:

[6] Ghoshal UC. How to interpret hydrogen breath tests. Journal of Neurogastroenterology and Motility. 2011;17(3):312–7. Available from:

[7] National Institute of Clinical Excellence (NICE). Diarrhoea – antibiotic associated | Topics A to Z | CKS | 2018. Available from:

[8] Ong DK, Mitchell SB, Barrett JS, Shepherd SJ, Irving PM, Biesiekierski JR, et al. Manipulation of dietary short chain carbohydrates alters the pattern of gas production and genesis of symptoms in irritable bowel syndrome. Journal of Gastroenterology and Hepatology (Australia). 2010;25(8):1366–73. Available from:

[9] Gibson PR. History of the low FODMAP diet. Journal of Gastroenterology and Hepatology [Internet]. 2017;32:5–7. Available from:

[10] Liu J, Chey WD, Haller E, Eswaran S. Low-FODMAP Diet for Irritable Bowel Syndrome: What We Know and What We Have Yet to Learn. Vol. 71, Annual Review of Medicine. Annual Reviews Inc.; 2020. p. 303–14. Available from:

[11] Nutritional consequences of intestinal bacterial overgrowth. PubMed. 1994. Available from:

[12] Camilo E, Zimmerman J, Mason JB, Golner B, Russell R, Selhub J, et al. Folate synthesized by bacteria in the human upper small intestine is assimilated by the host. Gastroenterology. 1996;110(4):991–8. Available from:

[13] Dukowicz AC, Lacy BE, Levine GM. Small intestinal bacterial overgrowth: A comprehensive review. Vol. 3, Gastroenterology and Hepatology. Millenium Medical Publishing; 2007. p. 112–22. Available from:

[14] Zhong C, Qu C, Wang B, Liang S, Zeng B. Probiotics for Preventing and Treating Small Intestinal Bacterial Overgrowth. Journal of Clinical Gastroenterology. 2017;51(4):00–11. Available from:

[15] Rosania R, Giorgio F, Principi M, Amoruso A, Monno R, di Leo A, et al. Effect of Probiotic or Prebiotic Supplementation on Antibiotic Therapy in the Small Intestinal Bacterial Overgrowth: A Comparative Evaluation. Current Clinical Pharmacology. 2013;8(2):169–72. Available from: