What Causes Small Intestinal Bacterial Overgrowth (SIBO)?

The small intestinal microflora are usually limited in number, less than 105 colony-forming units per mL of intestinal fluid. This number is somewhat arbitrary, because of the intense reluctance of most intestinal bacteria to grow in culture.

Stomach shaped out of bacteria. Image Credit: lanatoma / Shutterstock
Stomach shaped out of bacteria. Image Credit: lanatoma / Shutterstock

There are many reasons why colonic bacteria should grow up into the intestine and proliferate to produce small intestinal bacterial overgrowth (SIBO).

These include:

Anatomic Causes

These often produce stagnation of bacteria, which leads to their overgrowth, both because of lack of normal pushing down of the bacteria and because food is retained for too long a duration

  • Surgical procedures that cause the formation of anastomoses or blind loops in the intestine, such as following a Billroth II or Roux-en-Y procedure
  • Fistulas or strictures of the small bowel as occurs in Crohn’s disease, following radiation, and major bowel reconstruction, which can also promote the abnormal passage of bacteria between the upper and lower small bowel
  • Medical conditions that can cause diverticulum formation, such as Crohn’s disease
  • Diverticulosis of the small bowel with the formation of sacs that allow more bacteria than normal to grow, which are more common in males, and may be associated with disorders, such as myopathies and neuropathies, or connective tissue disorders like progressive systemic sclerosis

Dysmotility of the Small Bowel

Failure of normal gut movements encourages food stagnation and bacterial proliferation. This may be due to diverse causes including:

  • Chronic diabetes resulting in neuropathic gastroparesis
  • Scleroderma
  • Bowel ischemia
  • Chronic pancreatitis
  • Age-related slowing of the digestive tract
  • Following a viral infection
  • Amyloidosis
  • Hypothyroidism

Immunodeficiency Syndromes

  • AIDS
  • Severe nutritional deficiency

Miscellaneous Factors

  • Liver cirrhosis with portal hypertension and ascites is associated with retrograde waves in the first part of the duodenum, irregular and abnormal migrating motility complex (MMC).
  • Non-alcoholic liver cirrhosis
  • Celiac disease especially when the patient does not respond to gluten-free dietary modification
  • Irritable bowel syndrome

Evidence is yet to accumulate as to whether this is a cause or effect of SIBO. Methane production on breath tests are found to be strongly linked with a subgroup of IBS patients who complain of constipation, who also have weak and infrequent MMC. The role of proton pump inhibitors in this association with IBS is yet to be tested, though it is well known that hypochlorhydria contributes to SIBO.

Elderly patients

In elderly patients, SIBO is probably caused by a reduction in small intestinal dysmotility, though hypochlorhydria and immune cellular deficiency may play subsidiary roles.

Chronic pancreatitis

In chronic pancreatitis, there is mucosal inflammation, which results in reduced intestinal movements, besides the dysmotility induced by the narcotic analgesics typically prescribed in this condition. In scleroderma, about half of patients have been found to have SIBO, especially if they have symptoms related to the gut.


Complications of such overgrowth include:

  • Malnutrition due to the absorption of nutrients by the excessive bacterial growth
  • Mucosal inflammation due to the endotoxins released by the high bacterial number and the non-native bacteria growing up from the colon, which can increase intestinal permeability and further reduce intestinal absorption of nutrients from ingested food.

Normal Barriers to SIBO

The two most common underlying factors include too little gastric acid and less-than-normal intestinal motility.

Hydrochloric acid in the stomach is capable of killing most organisms that enter the stomach from the oropharynx. Thus, bacteria are rarely found in the stomach and upper small intestine. Hypochlorhydria is a risk factor and is often associated with Helicobacter pylori colonization or with aging, though SIBO itself may cause false-positives for H. pylori due to its reaction with urea on testing. Proton pump inhibitors, such as omeprazole and histamine 2 receptor blockers, may also promote SIBO when used on a long-term basis, such as 4 weeks.

Motility of the small bowel is maintained by propulsive forces created by the circular and longitudinal smooth muscle of the small bowel wall. These form MMCs, which push food down the digestive tract rapidly and prevent bacteria from colonizing the upper small intestine.

Other factors include:

  • Mucosal integrity
  • Mucus production to form a layer over the mucosal surface
  • The potent enzymes present in the intestinal, pancreatic and biliary secretions
  • Protective intestinal commensal bacteria
  • Mechanical and physiological actions of the ileocecal valve, which protects the terminal ileum from the colonic flora backwash


Further Reading

Last Updated: Feb 27, 2019

Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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