Official reprint from UpToDate®
www.uptodate.com ©2016 UpToDate®

Treatment of small intestinal bacterial overgrowth

Mark Pimentel, MD, FRCP(C)
Section Editor
J Thomas Lamont, MD
Deputy Editor
Shilpa Grover, MD, MPH


Small intestinal bacterial overgrowth (SIBO) is a condition of excessive colonization of the small intestine by bacteria (most commonly anaerobic bacteria). It can be associated with mucosal inflammation and nutrient malabsorption. Affected patients may be asymptomatic or have one or more symptoms including bloating, abdominal discomfort, diarrhea, dyspepsia, and, in severe cases, weight loss.

This topic review will discuss the treatment of SIBO. The etiology, pathogenesis, clinical manifestations, and diagnosis of SIBO are presented separately. (See "Small intestinal bacterial overgrowth: Etiology and pathogenesis" and "Clinical manifestations and diagnosis of small intestinal bacterial overgrowth".)


The mainstay of treatment of small intestinal bacterial overgrowth (SIBO) is antibiotic therapy. If present, the underlying cause/disease should be treated. Dietary manipulation and surgical therapy may also be helpful.

Treatment of the underlying disease — The underlying cause of SIBO may be small intestinal stasis due to anatomic abnormalities (eg, diverticulosis, surgical blind loops or strictures), abnormal small intestinal motility (eg, drug-induced dysmotility, diabetes), abnormal communication between the proximal and distal intestine (eg, fistula), or may be multifactorial in etiology (eg, hypochlorhydria, chronic pancreatitis, associated with irritable bowel syndrome) (table 1). These are discussed separately. (See "Small intestinal bacterial overgrowth: Etiology and pathogenesis", section on 'Epidemiology'.)

Nonsurgical conditions associated with intestinal stasis should be corrected when possible. This includes the elimination or substitution of drugs known to decrease intestinal motility (eg, narcotics, benzodiazepines).


Subscribers log in here

To continue reading this article, you must log in with your personal, hospital, or group practice subscription. For more information or to purchase a personal subscription, click below on the option that best describes you:
Literature review current through: Sep 2016. | This topic last updated: Jun 6, 2016.
The content on the UpToDate website is not intended nor recommended as a substitute for medical advice, diagnosis, or treatment. Always seek the advice of your own physician or other qualified health care professional regarding any medical questions or conditions. The use of this website is governed by the UpToDate Terms of Use ©2016 UpToDate, Inc.
  1. Parodi A, Sessarego M, Greco A, et al. Small intestinal bacterial overgrowth in patients suffering from scleroderma: clinical effectiveness of its eradication. Am J Gastroenterol 2008; 103:1257.
  2. Soudah HC, Hasler WL, Owyang C. Effect of octreotide on intestinal motility and bacterial overgrowth in scleroderma. N Engl J Med 1991; 325:1461.
  3. Compare D, Pica L, Rocco A, et al. Effects of long-term PPI treatment on producing bowel symptoms and SIBO. Eur J Clin Invest 2011; 41:380.
  4. Lombardo L, Foti M, Ruggia O, Chiecchio A. Increased incidence of small intestinal bacterial overgrowth during proton pump inhibitor therapy. Clin Gastroenterol Hepatol 2010; 8:504.
  5. Law D, Pimentel M. Proton pump inhibitor therapy does not affect hydrogen production on lactulose breath test in subjects with IBS. Dig Dis Sci 2010; 55:2302.
  6. Hutchinson S, Logan R. The effect of long-term omeprazole on the glucose-hydrogen breath test in elderly patients. Age Ageing 1997; 26:87.
  7. Thorens J, Froehlich F, Schwizer W, et al. Bacterial overgrowth during treatment with omeprazole compared with cimetidine: a prospective randomised double blind study. Gut 1996; 39:54.
  8. Fried M, Siegrist H, Frei R, et al. Duodenal bacterial overgrowth during treatment in outpatients with omeprazole. Gut 1994; 35:23.
  9. Ratuapli SK, Ellington TG, O'Neill MT, et al. Proton pump inhibitor therapy use does not predispose to small intestinal bacterial overgrowth. Am J Gastroenterol 2012; 107:730.
  10. Buchman AL, Scolapio J, Fryer J. AGA technical review on short bowel syndrome and intestinal transplantation. Gastroenterology 2003; 124:1111.
  11. Vanderhoof JA, Young RJ, Murray N, Kaufman SS. Treatment strategies for small bowel bacterial overgrowth in short bowel syndrome. J Pediatr Gastroenterol Nutr 1998; 27:155.
  12. Singh VV, Toskes PP. Small Bowel Bacterial Overgrowth: Presentation, Diagnosis, and Treatment. Curr Treat Options Gastroenterol 2004; 7:19.
  13. Quigley EM, Abu-Shanab A. Small intestinal bacterial overgrowth. Infect Dis Clin North Am 2010; 24:943.
  14. Shah SC, Day LW, Somsouk M, Sewell JL. Meta-analysis: antibiotic therapy for small intestinal bacterial overgrowth. Aliment Pharmacol Ther 2013; 38:925.
  15. Lauritano EC, Gabrielli M, Lupascu A, et al. Rifaximin dose-finding study for the treatment of small intestinal bacterial overgrowth. Aliment Pharmacol Ther 2005; 22:31.
  16. Scarpellini E, Gabrielli M, Lauritano CE, et al. High dosage rifaximin for the treatment of small intestinal bacterial overgrowth. Aliment Pharmacol Ther 2007; 25:781.
  17. Yang J, Lee HR, Low K, et al. Rifaximin versus other antibiotics in the primary treatment and retreatment of bacterial overgrowth in IBS. Dig Dis Sci 2008; 53:169.
  18. Scarpellini E, Giorgio V, Gabrielli M, et al. Rifaximin treatment for small intestinal bacterial overgrowth in children with irritable bowel syndrome. Eur Rev Med Pharmacol Sci 2013; 17:1314.
  19. Attar A, Flourié B, Rambaud JC, et al. Antibiotic efficacy in small intestinal bacterial overgrowth-related chronic diarrhea: a crossover, randomized trial. Gastroenterology 1999; 117:794.
  20. Tahan S, Melli LC, Mello CS, et al. Effectiveness of trimethoprim-sulfamethoxazole and metronidazole in the treatment of small intestinal bacterial overgrowth in children living in a slum. J Pediatr Gastroenterol Nutr 2013; 57:316.
  21. Bouhnik Y, Alain S, Attar A, et al. Bacterial populations contaminating the upper gut in patients with small intestinal bacterial overgrowth syndrome. Am J Gastroenterol 1999; 94:1327.
  22. Malik BA, Xie YY, Wine E, Huynh HQ. Diagnosis and pharmacological management of small intestinal bacterial overgrowth in children with intestinal failure. Can J Gastroenterol 2011; 25:41.
  23. Lauritano EC, Gabrielli M, Scarpellini E, et al. Small intestinal bacterial overgrowth recurrence after antibiotic therapy. Am J Gastroenterol 2008; 103:2031.
  24. Pimentel M, Morales W, Chua K, et al. Effects of rifaximin treatment and retreatment in nonconstipated IBS subjects. Dig Dis Sci 2011; 56:2067.
  25. Food and Agriculture Organization of the United Nations. Health and nutritional properties of probiotics in food including powder milk with live lactic acid bacteria. http://www.who.int/foodsafety/publications/fs_management/en/probiotics.pdf (Accessed on July 22, 2010).
  26. Stotzer PO, Blomberg L, Conway PL, et al. Probiotic treatment of small intestinal bacterial overgrowth by Lactobacillus fermentum KLD. Scand J Infect Dis 1996; 28:615.
  27. Hegar B, Hutapea EI, Advani N, Vandenplas Y. A double-blind placebo-controlled randomized trial on probiotics in small bowel bacterial overgrowth in children treated with omeprazole. J Pediatr (Rio J) 2013; 89:381.
  28. Gaon D, Garmendia C, Murrielo NO, et al. Effect of Lactobacillus strains (L. casei and L. Acidophillus Strains cerela) on bacterial overgrowth-related chronic diarrhea. Medicina (B Aires) 2002; 62:159.
  29. Scientific concepts of functional foods in Europe. Consensus document. Br J Nutr 1999; 81 Suppl 1:S1.
  30. Rosania R, Giorgio F, Principi M, et al. Effect of probiotic or prebiotic supplementation on antibiotic therapy in the small intestinal bacterial overgrowth: a comparative evaluation. Curr Clin Pharmacol 2013; 8:169.
  31. Cole CR, Frem JC, Schmotzer B, et al. The rate of bloodstream infection is high in infants with short bowel syndrome: relationship with small bowel bacterial overgrowth, enteral feeding, and inflammatory and immune responses. J Pediatr 2010; 156:941.
  32. Taylor SF, Sondheimer JM, Sokol RJ, et al. Noninfectious colitis associated with short gut syndrome in infants. J Pediatr 1991; 119:24.
  33. Klaus J, Spaniol U, Adler G, et al. Small intestinal bacterial overgrowth mimicking acute flare as a pitfall in patients with Crohn's Disease. BMC Gastroenterol 2009; 9:61.