Bacterial Overgrowth

What is bacterial overgrowth?

Small-bowel bacterial overgrowth can occur from alterations in intestinal anatomy or GI motility, or lack of gastric acid secretion. This condition can lead to vitamin deficiencies, fat malabsorption, and malnutrition. Diagnosis is by breath test or quantitative culture of intestinal fluid aspirate. Treatment is with oral antibiotics.

Under normal conditions, the proximal small bowel contains < 105 bacteria/mL, mainly gram-positive aerobic bacteria. This low bacterial count is maintained by normal peristalsis, normal gastric acid secretion, mucus, secretory IgA, and an intact ileocecal valve.


Usually, bacterial overgrowth occurs when anatomic alterations promote stasis of intestinal contents. These conditions include small-bowel diverticulosis, surgical blind loops, postgastrectomy states (especially in the afferent loop of a Billroth II), strictures,
or partial obstruction. Intestinal motility disorders associated with diabetic neuropathy, systemic sclerosis, amyloidosis, and idiopathic intestinal pseudo-obstruction can also impair bacterial clearance. Achlorhydria and idiopathic changes in intestinal motility may cause bacterial overgrowth in elderly people.


The excess bacteria consume nutrients, including vitamin B12 and carbohydrates, leading to caloric deprivation and vitamin B12 deficiency. However, because the bacteria produce folate, this deficiency is rare. The bacteria deconjugate bile salts, causing failure of micelle formation and subsequent fat malabsorption. Severe bacterial overgrowth also damages the intestinal mucosa. Fat malabsorption and mucosal damage can produce diarrhea.

What are the symptoms of a bacterial overgrowth?

Many patients are asymptomatic and present with only weight loss or nutrient deficiencies. Some have significant diarrhea or steatorrhea.

Diagnosis for bacterial overgrowth

  • 14C-xylose breath test or quantitative culture of intestinal aspirate
  • Upper GI series with small-bowel follow-through

Some clinicians advocate response to empiric antibiotic therapy as a diagnostic test. However, because bacterial overgrowth can mimic other malabsorptive disorders (eg, Crohn’s disease) and adverse effects of the antibiotics can worsen symptoms, establishing a definitive etiology is preferred.

The standard for diagnosis is quantitative culture of intestinal fluid aspirate showing bacterial count > 105/mL. This method, however, requires endoscopy. Breath tests, using substrates like glucose, lactulose Some Trade Names
, and xylose, are noninvasive and easy to do. The 14C‑xylose breath test seems to perform better than the other breath tests. In addition, an upper GI series with small-bowel follow-through should be done to identify predisposing anatomic lesions.

What is the treatment for bacterial overgrowth?

Treatment is with 10 to 14 days of oral antibiotics. Empiric regimens include tetracycline Some Trade Names

250 mg qid, amoxicillin Some Trade Names

/clavulanic acid 250 to 500 mg tid, cephalexin Some Trade Names

250 mg qid, trimethoprim-sulfamethoxazole Some Trade Names

160/800 mg bid, and metronidazole Some Trade Names

250 to 500 mg tid or qid. Antibiotics should be changed based on culture and sensitivity results. Underlying conditions and nutritional deficiencies (eg, vitamin B12) should be corrected.

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