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Small Intestinal Bacterial Overgrowth (SIBO)

Is SIBO the cause of your IBS symptoms?

Small Intestine Bacterial Overgrowth or SIBO has been estimated to be involved in over half of all cases of IBS (1), with some studies finding it in as many as 70% or more of those with IBS.

What is SIBO?

Small Intestine Bacterial Overgrowth (SIBO) is, as the name implies, bacterial overgrowth of the small intestine. A healthy small intestine is usually home to very few bacteria, about ten thousand per ml. A person with SIBO has around one million bacteria per ml

In the large intestine, which houses about one hundred billion per ml, bacteria fulfil numerous beneficial functions via their ability to ferment undigested food particles.

With SIBO, because of abnormally large amounts of bacteria in the small intestine, the process of fermentation begins within its narrow confines, producing gases and other by-products in an area which is not adapted to deal with them..

In contrast to healthy subjects, the small intestine of people with SIBO contain bacteria from the large intestine such as E.coli, Enterococcus, Klebsiella pneumonia, and Proteus mirabilis, (2, 3, 4) that ferment carbohydrates into gas (hydrogen, methane, hydrogen sulphide) (5, 6) causing symptoms such as bloating, distension, abdominal discomfort, and pain. (10)

The gases also have an effect on bowel movement with hydrogen having a stronger link to diarrhea and methane having a nearly exclusive link to constipation. (7,8),

SIBO causes GI dysfunction and symptoms by several mechanisms, including inflammation, immune activation, alteration in motility, increase in intestinal permeability, deconjugation of bile salts, and secondary lactase deficiency. (9,10,11,12)

Bacteria in the small intestine produce toxic by-products after fermentation, which can damage the inner lining of the small intestine. (13). A study on small intestine biopsies in patients with SIBO revealed thinning of the mucosa and crypts and increased inflammation. (14)

What are the symptoms of SIBO?

SIBO symptoms include:

  • Bloating/abdominal distension after eating
  • Gas and belching
  • Reflux, bad breath
  • Abdominal pain
  • Food Intolerances
  • Constipation 
  • Diarrhea 
  • Nutrient deficiencies:.e.g vitamin B12 & Iron
  • Weight loss/weight gain
  • Fatigue 
  • Brain fog
  • Fibromyalgia
  • Restless legs
  • Rosacea

What causes SIBO?

The body has a number of mechanisms in place to inhibit the overgrowth of bacteria in the small intestine. Normally bacteria in the small intestine are kept at low levels by:

  • Certain antibacterial secretions in the gut, like gastric acid, pancreatic juices and bile, which keep bacterial growth in check.
  • Antimicrobial peptides and immunoglobulins secreted by small intestinal epithelial cells.
  • The migrating motor complex (MMC), a nerve propulsion which sweeps bacteria and food from the small intestine between meals stopping colonisation of bacteria.
  • The ileocecal valve, which prevents a backflow of bacteria and the translocation of bacterial species from the large intestine.

SIBO develops when one or more of these mechanisms that control bacterial overgrowth are disrupted. 

Conditions that may predispose you to SIBO

  1. Hypochlorhydria (low stomach acid)
  2. Pancreatic enzyme deficiency
  3. Impaired motility in small intestine
  4. Small intestinal obstructions, adhesions and diverticuli.
  5. An episode of gastroenteritis (food poisoning, travelers diarrhea)
  6. Nerve damage that affects the GI tract
  7. Medications such as opiates and proton pump inhibitors
  8. Multiple courses of antibiotics
  9. Mechanical factors due to previous GI surgery
  10. Impaired function of the ileocecal valve
  11. Chronic stress
  12. Any disease that slows motility (diabetes, scleroderma, hypothyroidism)

How do I find out if I have SIBO?

The most common method to diagnose SIBO is a hydrogen/methane breath test following a 24-hour prep diet and an overnight fast. This test involves drinking a prepared lactulose solution, and measuring the presence of methane and hydrogen gases on the breath. Because bacteria produce hydrogen and methane when they ferment sugars, a rise in these gases above a certain amount within the first 100 minutes of the test indicate a bacterial overgrowth in the small intestine.

Based on the results of the breath test, there are four forms of SIBO.

Hydrogen: overgrowth of bacteria in the small intestine ferment fibers to produce hydrogen.

Methane:  a group of archaea called methanogens selectively feed on hydrogen produced by other bacteria and produce methane. Reflux and belching are more common in patients with elevated methane, and methane production is highly correlated with constipation. (16)

Combination: when Hydrogen and Methane gases are both elevated.

Hydrogen sulfide: not as common but some people with SIBO will have elevated hydrogen sulfide production. In this situation, sulphate-reducing bacteria feed on hydrogen produced by other bacteria and produce hydrogen sulfide.

Learn more about the test here.

How is SIBO treated?

With SIBO treatment, the overall goal is to reduce bacteria in the small intestine, repair the intestinal lining, and prevent relapse by addressing the underlying causes that led to SIBO in the first place. To do this, we take a comprehensive approach that includes several interventions.

At the Digestive Wellness Clinic I use a 5 phase protocol, incorporating diet, herbal medicines and nutritional supplements, to ensure SIBO is cleared and relapse prevented.

  1. Remove foods from your diet that cause inflammation, feed overgrowths and irritate the gut wall, using a specialised eating plan.   
  2. Stimulate production of and/or supplement stomach acid, bile and enzymes if indicated.
  3. Herbal antimicrobials to reduce the bacterial overgrowth. Physicians at Johns Hopkins and the University of Pittsburgh showed that SIBO treatment using herbal antimicrobial supplements was as effective as rifaximin, the conventional antibiotic most commonly used to treat SIBO. (15) Herbal medicines have the added benefit of being able to treat other dysbiosis issues, such as fungal overgrowth, parasites, and overgrowth of bacteria in the large intestine.
  4. After anti-microbial treatment Improve small intestine motility with herbal prokinetics to prevent relapse.
  5. Support gut immunity and repair damaged gut lining.

As one of the first practitioners in Australia to treat SIBO, I have years of experience in treating hundreds of SIBO patients. Over this time I have developed a deep understanding of SIBO and what works best to treat it.

What next?

To learn more about the testing and treatment options available it is recommended you take a free 15 minute phone consultation. During this call you can learn more about the programme and have all your questions answered. This call is to determine if we are a good fit for one another rather than a history or complete consultation. There is no obligation, and no strings attached.

It is quick and easy to book your free 15-minute phone consultation using the online calendar. Just click the button below, choose a date and time convenient for you, enter your details, and Matt will call you at your chosen time.

Book Free Phone Consult


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  2. Sachdev AH, Pimentel M. Gastrointestinal bacterial overgrowth: pathogenesis and clinical significance. Ther Adv Chronic Dis 2013;4:223–31
  3. Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 1977;31:107–33.
  4. Bouhnik Y, Alain S, Attar A, et al. Bacterial populations contaminating the upper gut in patients with small intestinal bacterial overgrowth syndrome. Am J Gastro-enterol 1999;94:1327–31.
  5. Sachdev AH, Pimentel M. Antibiotics for irritable bowel syndrome: rationale and current evidence. Curr Gastroenterol Rep 2012;14:439–45.
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  7. Pyleris E, Giamarellos-Bourboulis EJ, Tzivras D, Koussoulas V, Barbatzas C, Pimentel M. The prevalence of overgrowth by aerobic bacteria in the small intestine by small bowel culture: relationship with irritable bowel syndrome. Dig Dis Sci. 2012; 57(5):1321-1329.
  8. Pimentel M, Park S, Mirocha J, Kane SV, Kong Y. The effect of a nonabsorbed oral antibiotic (rifaximin) on the symptoms of the irritable bowel syndrome: a randomized trial. Ann Intern Med. 2006; 145(8):557- 563.
  9. Ghoshal UC, Srivastava D. Irritable bowel syndrome and small intestinal bacterial overgrowth: meaningful association or unnecessary hype. World J Gastroenterol 2014;20:2482–91.
  10. Ghoshal UC, Shukla R, Ghoshal U, et al. The gut microbiota and irritable bowel syndrome: friend or foe? Int J Inflam 2012;2012:151085.
  11. .Mathias JR, Clench MH. Review: pathophysiology of diarrhea caused by bacterial overgrowth of the small intestine. Am J Med Sci 1985;289:243–8.
  12. Pimentel M, Kong Y, Park S. IBS subjects with methane on lactulose breath test have lower postprandial serotonin levels than subjects with hydrogen. Dig DisSci 2004;49:84–7
  13. Bala L, Ghoshal UC, Ghoshal U, Tripathi P, Misra A, Gowda GA, Khetrapal CL. Malabsorption syndrome with and without small intestinal bacterial overgrowth: a study on upper-gut aspirate using 1H NMR spectroscopy. Magn Reson Med. 2006;56:738–744.
  14. Haboubi NY, Lee GS, Montgomery RD. Duodenal mucosal morphometry of elderly patients with small intestinal bacterial overgrowth: response to antibiotic treatment. Age Ageing. 1991;20:29–32
  15. Chedid V, Dhalla S, Clarke JO, Roland BC, Dunbar KB, Koh J, Justino E, Tomakin E, Mullin GE. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med. 2014 May;3(3):16-24.
  16. Chatterjee, S., Park, S., Low, K., Kong, Y. & Pimentel, M. The degree of breath methane production in IBS correlates with the severity of constipation. Am. J. Gastroenterol. 102, 837–841 (2007)
The Digestive Wellness Clinic
12 Junction St Woollahra, NSW 2025 Tel: (02) 8001 6344