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Small intestinal bacterial overgrowth: Etiology and pathogenesis

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


Small intestinal bacterial overgrowth (SIBO) is a condition in which colonic bacteria are seen in excess in the small intestine. When present, this overabundance of organisms can result in intestinal symptoms and, in extreme cases, malabsorption.

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


Overview — The stomach and proximal small bowel normally contain relatively few bacteria due to the presence of gastric acidity and the effects of peristalsis. Lactobacilli, enterococci, gram-positive aerobes, or facultative anaerobes predominate in concentrations of 104 organisms/mL in the mid to distal jejunum [1]. The concentration of coliforms rarely exceeds 103 organisms/mL [2]. Bacteroides, the predominant organism in the colon, is rarely found in the proximal small bowel.

The microbiology of the terminal ileum represents an intermediary zone between the aerobic flora found in the stomach and proximal small bowel and the dense population of anaerobic organisms found in the colon. The concentration of organisms may be as high as 109/mL and includes enterobacteria and other coliforms. If the ileocecal valve is dysfunctional or surgically absent, the microbiology of the terminal ileum resembles that of the colon. (See "Spatial organization of intestinal microbiota in health and disease", section on 'Stomach and duodenum'.)

In the colon, the concentration of microorganisms may exceed 1012/mL. The organisms are predominantly anaerobes such as Bacteroides, Lactobacillus, Clostridium, and bifidobacteria, although multiple species coexist. (See "Spatial organization of intestinal microbiota in health and disease", section on 'Bacteria in the colon'.)

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Literature review current through: Nov 2017. | This topic last updated: Feb 16, 2016.
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  1. Walker MM, Talley NJ. Review article: bacteria and pathogenesis of disease in the upper gastrointestinal tract--beyond the era of Helicobacter pylori. Aliment Pharmacol Ther 2014; 39:767.
  2. Khoshini R, Dai SC, Lezcano S, Pimentel M. A systematic review of diagnostic tests for small intestinal bacterial overgrowth. Dig Dis Sci 2008; 53:1443.
  3. Phillips SF, Quigley EM, Kumar D, Kamath PS. Motility of the ileocolonic junction. Gut 1988; 29:390.
  4. Roland BC, Ciarleglio MM, Clarke JO, et al. Low ileocecal valve pressure is significantly associated with small intestinal bacterial overgrowth (SIBO). Dig Dis Sci 2014; 59:1269.
  5. Riordan SM, McIver CJ, Wakefield D, et al. Small intestinal mucosal immunity and morphometry in luminal overgrowth of indigenous gut flora. Am J Gastroenterol 2001; 96:494.
  6. Mackie RI, Sghir A, Gaskins HR. Developmental microbial ecology of the neonatal gastrointestinal tract. Am J Clin Nutr 1999; 69:1035S.
  7. Choung RS, Ruff KC, Malhotra A, et al. Clinical predictors of small intestinal bacterial overgrowth by duodenal aspirate culture. Aliment Pharmacol Ther 2011; 33:1059.
  8. Pimentel M. Evaluating a bacterial hypothesis in IBS using a modification of Koch's postulates: part 1. Am J Gastroenterol 2010; 105:718.
  9. Vantrappen G, Janssens J, Hellemans J, Ghoos Y. The interdigestive motor complex of normal subjects and patients with bacterial overgrowth of the small intestine. J Clin Invest 1977; 59:1158.
  10. Shah ED, Basseri RJ, Chong K, Pimentel M. Abnormal breath testing in IBS: a meta-analysis. Dig Dis Sci 2010; 55:2441.
  11. Posserud I, Stotzer PO, Björnsson ES, et al. Small intestinal bacterial overgrowth in patients with irritable bowel syndrome. Gut 2007; 56:802.
  12. Pyleris E, Giamarellos-Bourboulis EJ, Tzivras D, et al. The prevalence of overgrowth by aerobic bacteria in the small intestine by small bowel culture: relationship with irritable bowel syndrome. Dig Dis Sci 2012; 57:1321.
  13. Kim G, Morales W, Funari V, et al. Duodenal Aeromonas SPP Are Increased in Number in a Rat Model of Post-Infectious IBS: Translation of Data From Deep Sequencing of the Microbiome in Humans With IBS. Gastroenterology 2013; 144:S542.
  14. Giamarellos-Bourboulis E, Tang J, Pyleris E, et al. Molecular assessment of differences in the duodenal microbiome in subjects with irritable bowel syndrome. Scand J Gastroenterol 2015; 50:1076.
  15. Bures J, Cyrany J, Kohoutova D, et al. Small intestinal bacterial overgrowth syndrome. World J Gastroenterol 2010; 16:2978.
  16. Jones RM, Neish AS. Recognition of bacterial pathogens and mucosal immunity. Cell Microbiol 2011; 13:670.
  17. 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.
  18. Kirsch M. Bacterial overgrowth. Am J Gastroenterol 1990; 85:231.
  19. Shindo K, Machida M, Koide K, et al. Deconjugation ability of bacteria isolated from the jejunal fluid of patients with progressive systemic sclerosis and its gastric pH. Hepatogastroenterology 1998; 45:1643.
  20. Donaldson RM Jr. Role of enteric microorganisms in malabsorption. Fed Proc 1967; 26:1426.
  21. Pai RK. A practical approach to small bowel biopsy interpretation: celiac disease and its mimics. Semin Diagn Pathol 2014; 31:124.
  22. Sherman P, Lichtman S. Small bowel bacterial overgrowth syndrome. Dig Dis 1987; 5:157.
  23. Su J, Smith MB, Rerknimitr R, Morrow D. Small intestine bacterial overgrowth presenting as protein-losing enteropathy. Dig Dis Sci 1998; 43:679.
  24. Justus PG, Fernandez A, Martin JL, et al. Altered myoelectric activity in the experimental blind loop syndrome. J Clin Invest 1983; 72:1064.
  25. Hoog CM, Lindberg G, Sjoqvist U. Findings in patients with chronic intestinal dysmotility investigated by capsule endoscopy. BMC Gastroenterol 2007; 7:29.
  26. Taylor SF, Sondheimer JM, Sokol RJ, et al. Noninfectious colitis associated with short gut syndrome in infants. J Pediatr 1991; 119:24.
  27. 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.
  28. Greenson JK. The biopsy pathology of non-coeliac enteropathy. Histopathology 2015; 66:29.
  29. Bongaerts GP, Tolboom JJ, Naber AH, et al. Role of bacteria in the pathogenesis of short bowel syndrome-associated D-lactic acidemia. Microb Pathog 1997; 22:285.
  30. Schnabl B, Brenner DA. Interactions between the intestinal microbiome and liver diseases. Gastroenterology 2014; 146:1513.
  31. Lichtman SN, Keku J, Schwab JH, Sartor RB. Evidence for peptidoglycan absorption in rats with experimental small bowel bacterial overgrowth. Infect Immun 1991; 59:555.
  32. O'Brien DP, Nelson LA, Kemp CJ, et al. Intestinal permeability and bacterial translocation are uncoupled after small bowel resection. J Pediatr Surg 2002; 37:390.
  33. Mouzaki M, Comelli EM, Arendt BM, et al. Intestinal microbiota in patients with nonalcoholic fatty liver disease. Hepatology 2013; 58:120.