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The Intestinal Flora and Small Intestinal Bacterial Overgrowth (SIBO)

The human gastrointestinal tract is made up of 300-500 different bacterial species with varying densities throughout. The proximal bowel contains a less dense population of aerobic bacteria. As you move distally through the small intestine and into the colon the bacteria transition to predominately anaerobes and the density increases dramatically. In cases of small bacterial overgrowth, you will see an increase in the population of bacteria in the proximal small intestine, commonly of species of Streptococci, Bacteroides, Escherichia, and Lactobacilli. (1)

The normal gut flora has many beneficial effects to the intestine, including:

  • Conversion of unabsorbed dietary sugars to short chain fatty acids (SCFAs) to be used as an energy source by the colonic mucosa

  • Production of certain nutrients, such as folate and vitamin K

  • Protecting the host from colonization of pathogenic species

  • Maintaining the integrity of the epithelial barrier and development of mucosal immunity

Defining Small Intestinal Bacterial Overgrowth:

Small intestinal bacterial overgrowth (SIBO) is the presence of more than 10^5 colony-forming units/mL from intestinal aspirate. (2) Common types of bacteria associated with bacterial overgrowth include: Streptococci, E. coli, Staphylococci, Micrococci, and Klebsiella.

There are many possible causes of SIBO:

1. Disordered anatomy: diverticula, surgical blind loops, small bowel obstruction, intestinal resection with dilation, strictures

2. Motor disorders: chronic intestinal pseudo-obstruction, autonomic neuropathy, amyloidosis, hypothyroidism, scleroderma

3. Immunological factors: immunodeficiency, malnutrition, corticosteroids, antibiotics, oral contraceptives

4. Non-immune mechanisms: exocrine pancreatic insufficiency, bile salt deficiency, malabsorption syndromes, bile salt deficiency

SIBO can cause both morphological and metabolic derangements to the intestine. 

  • Deconjugation of bile acids in the proximal small bowel can result in disruption of fat digestion and production of lithocholic acid. 

  • The lithocholic acid is poorly absorbed, remains in the lumen of the intestine, and is then directly toxic to the enterocytes. 

  • The fat maldigestion and malabsorption that occurs also can result in deficiencies of the fat-soluble vitamins A, D, E, and K (1)

  • Biopsies of SIBO diseased duodenum may reveal reduction in villus height, crypt depth, and total mucosal thickness; all of which can be reversed following successful treatment. (3) 

For further information on the pathophysiology behind bacterial overgrowth, please refer to this article.

Diagnosis of small intestinal bacterial overgrowth utilizes various techniques including direct aspirate culture, hydrogen breath testing, and clinical picture. There are many limitations with diagnostic testing that can lead to false positives and false negatives.

Since bacterial overgrowth commonly recurs, it often requires prolonged treatment and/or periodic antibiotic therapy. The choice of antibiotic is usually one that is effective against Gram negative and anaerobic bacteria. (2) It is important to effectively treat patients, but also be mindful to not promote the establishment of antibiotic resistance.

If you wish to read more in depth discussion on diagnosis and treatment of small intestinal bacterial overgrowth please visit this page. 


  1. Dibaise JK, Young RJ, Vanderhoof JA. Enteric Microbial Flora, Bacterial Overgrowth, and Short-Bowel Syndrome. Clinical Gastroenterology and Hepatology. 2006;4(1):11-20. doi:10.1016/j.cgh.2005.10.020.

  2. 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(1):41‐45. doi:10.1155/2011/604643

  3. Langnas AN, Goulet O, Quigley EMM, Tappenden KA. Intestinal Failure Diagnosis, Management, and Transplantation. Malden, MA: Blackwell; 2008.

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