Small intestinal bacterial overgrowth

To see contributor disclosures related to this article, click on this reference: ^[1]

Physicians can earn CME/MOC credit by using this article to address a clinical question and completing a brief evaluation about how they applied the information in their practice.

AMBOSS designates this internet point-of-care activity for a maximum of 0.5 AMA PRA Category 1 Credit(s)™. Physicians should claim only the credit commensurate with the extent of their participation in the activity.

For answers to questions about AMBOSS CME, including how to redeem CME/MOC credit, see “Tips and links” at the bottom of this article.

Small intestinal bacterial overgrowth (SIBO) is excessive growth of bacteria in the small intestine that causes gastrointestinal symptoms. Causes include structural abnormalities (e.g., due to postsurgical complications), motility disorders, biochemical abnormalities, and immune dysregulation. Growth is typically a mixture of aerobic and anaerobic gram-negative coliforms, which produce gas through fermentation of small intestinal contents and impair intestinal function. Clinical features include flatulence, bloating, abdominal discomfort, and diarrhea. Severe SIBO can cause malabsorption, micronutrient deficiencies, and weight loss. Diagnosis is performed with a quantitative culture of duodenal aspirate (gold standard test) or a hydrogen breath test. Treatment involves antibiotics, and further management is based on the underlying condition and/or nutritional deficiencies.

Intestinal methanogen overgrowth is characterized by pathological overgrowth of methane-producing archaea. Symptoms include constipation. Diagnosis is confirmed with a methane breath test, and treatment involves antibiotics.

SIBO is a pathologically excessive growth of bacteria in the small intestine that causes gastrointestinal symptoms. ^[2][3]

• Structural abnormalities ^[2]
  • Postsurgical complications, e.g.:
    • Short bowel syndrome
    • Blind loop syndrome: bacterial overgrowth in the bypassed intestinal segment (blind loop), e.g., due to gastrectomy
    • Adhesions
  • Strictures and/or fistulae e.g., due to Crohn disease, radiation injury
  • Small bowel diverticulosis
  • Volvulus or intussusception
  • Small-bowel cancer
• Motility disorders ^[2]
  • Irritable bowel syndrome (IBS)
  • Paralytic ileus, e.g., due to opiate use
  • Systemic disorders, e.g., diabetic autonomic neuropathy, systemic sclerosis, amyloidosis
• Biochemical abnormalities ^[2]
  • Achlorhydria, e.g., due to atrophic gastritis, proton pump inhibitors
  • Chronic pancreatitis, exocrine pancreatic insufficiency
  • Liver disease, cirrhosis
• Immune disorders ^[2]
  • Common variable immunodeficiency
  • Selective IgA deficiency
  • HIV
  • Inflammatory bowel disease ^[4]
• Multifactorial ^[3]
  • CKD
  • Advanced age

SIBO is caused by conditions that impair stool movement, create a favorable microenvironment for bacteria, and/or reduce immune defenses.

The following result from bacterial overgrowth. ^[5]

• ↑ Deconjugation of the bile acids
• ↑ Production of folate
• Rare: ↓ absorption of vitamin B₁₂, fat-soluble vitamins, zinc, and iron

Symptoms are caused by bacterial fermentation of intestinal contents, intestinal inflammation, and/or changes in intestinal permeability and motility. ^[2][3]

• Common symptoms ^[2][3]
  • Bloating
  • Flatulence
  • Abdominal pain or discomfort
  • Diarrhea (more common in SIBO) and/or constipation (more common in intestinal methanogen overgrowth)
  • Nausea
• Signs of severe disease: rare; typically caused by structural abnormalities, e.g., blind loop syndrome ^[2][3]
  • Steatorrhea
  • Weight loss
  • Other signs of malabsorption, e.g.:
    • Signs of anemia
    • Signs of micronutrient deficiencies, e.g., vitamin B₁₂ deficiency

Intestinal methanogen overgrowth (IMO) ^[2][3]

• Definition: pathological overgrowth of methane-producing archaea in the gastrointestinal tract
• Clinical features
  • Similar to clinical features of SIBO
  • Most common: constipation
• Diagnostics: methane concentration ≥ 10 ppm on hydrogen breath testing
• Treatment: antibiotic therapy, e.g., rifaximin in combination with neomycin

Approach ^[2]

• Consider SIBO in patients with typical clinical features and a condition or anatomic abnormality associated with SIBO (e.g., IBS). ^[2]
• Consider routine laboratory studies to assess for signs of nutritional deficiencies, e.g., iron-deficiency anemia.
• Confirm SIBO with one of the following:
  • Hydrogen breath testing (most commonly used)
  • Small bowel aspirate
• Consider further investigations, e.g., endoscopy, to detect underlying conditions guided by patient history and examination.
• Consider gastroenterology referral to assess for alternative diagnoses, e.g., other causes of malabsorption.

Laboratory studies ^[2][3]

Laboratory studies are not routinely indicated. Findings may be normal or show nonspecific abnormalities.

• CBC: anemia, e.g., due to iron deficiency and/or vitamin B₁₂ deficiency
• Abnormal micronutrient levels, e.g.: ^[2][3]
  • ↑ Folate
  • ↓ Vitamin B₁₂
  • ↑ or ↓ Vitamin K

Confirmatory tests

Hydrogen breath testing ^[2][6]

Hydrogen breath testing is generally preferred for confirming SIBO and is usually performed in combination with a methane breath test for IMO.

• Procedure
  • Discontinue antibiotics for 4 weeks and prokinetic agents and laxatives for 1 week before testing.
  • Measure exhaled hydrogen after patient consumes a carbohydrate load. ^[2]
  • Repeat testing may be needed, as sensitivity and specificity are limited. ^[2]
• Options
  • Glucose hydrogen breath test: higher sensitivity and specificity ^[6]
  • Lactulose hydrogen breath test
• Findings: An increase of ≥ 20 ppm above baseline within 90 minutes confirms SIBO. ^[2]

Small bowel aspirate ^[2][3]

Small bowel aspirate is the gold standard test; however, collection is invasive, and the risk of contamination is high.

• Procedure
  • Duodenal or jejunal fluid is aspirated during endoscopy.
  • Obtain quantitative aerobic and anaerobic cultures.
• Findings
  • Typically mixed colonic flora (most commonly gram-negative coliforms, e.g., Escherichia coli)
  • A bacterial count of ≥ 10³ CFU/mL confirms SIBO. ^[2][3]

• See "Etiology of chronic diarrhea."
• See "Differential diagnoses of malabsorption."

The differential diagnoses listed here are not exhaustive.

General principles ^[2][3]

• Identify and treat underlying conditions.
• Start antibiotic therapy to modulate gut flora and control symptoms.
• Correct nutritional deficiencies as needed, e.g., via parenteral vitamin B₁₂ replacement.
• Existing evidence does not support probiotic therapy or fecal transplant.

Antibiotic treatment ^[3]

• There is limited data to guide treatment decisions.
• Empiric treatment recommendations cover aerobic and anaerobic bacteria. ^[2][3]
• Options include:
  • Rifaximin (off-label) for 7–10 days ^[3]
  • Amoxicillin/clavulanate (off-label)
  • Ciprofloxacin (off-label)
  • Doxycycline (off-label)