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Small Intestinal Bacterial Overgrowth (SIBO)

What is small intestinal bacterial overgrowth (SIBO)?

Small intestinal bacterial overgrowth (SIBO) is an overgrowth of nonpathogenic bacteria in the small intestine [2]. Normally, there is only a small amount of bacteria in the small intestine (they are mostly in the large intestine), but they may overgrow under certain conditions. The main symptom is abdominal bloating.

SIBO Causes and Risk Factors

A. Disruption of natural barriers, which allows bacteria to colonize the small intestine [1,2,3,4]:

  • Reduced or absent secretion of gastric acid (hypo- or achlorhydria) due to gastritis caused by Helicobacter pylori, autoimmune gastritis in pernicious anemia, resection of the vagal nerve (vagotomy), use of proton-pump inhibitors
  • Gastrointestinal surgery: partial stomach removal, gastric bypass (bariatric surgery), removal of the last part of the small intestine including the removal of the ileo-cecal valve that prevents bacteria to enter from large to small intestine, extensive resection of the small intestine, mainly in infants, resulting in short bowel syndrome (SBS).
  • Immune deficiency due to HIV/AIDS, IgA deficiency, severe malnutrition, liver cirrhosis [5], chronic lymphocytic leukemia [6], common variable immunodeficiency and severe malnutrition
  • Abnormal connection (fistula) between the small and large intestine, for example, in Crohn’s disease [7]

B. Impaired digestion or absorption of carbohydrates:

  • Celiac disease [1,2]
  • Crohn’s disease [1,7]
  • Short bowel syndrome [1]
  • Chronic pancreatitis [1,8]
  • Possibly: fructose malabsorption, lactose intolerance

C. Decreased motility of the small intestine [1,2]:

  • Neurological disorders: diabetic autonomic neuropathy with delayed gastric emptying (gastroparesis), myotonic dystrophy, Parkinson disease, Chagas enteropathy
  • Infiltration of the small intestinal wall: scleroderma, amyloidosis
  • Hypothyroidism

D. Blind pouches in the small intestine [1,2]:

  • Diverticles in the small intestine
  • Blind loop syndrome
  • Megacolon in Chagas disease

E. Obstruction of the small intestine [1,4]:

  • Tumors
  • Pseudotumors, polyps, strictures and adhesions in Crohn’s disease
  • Radiation enteritis

F. The following conditions have been associated with SIBO:

  • Old age (associated with malnutrition, decreased mobility, increased prevalence of diabetes) [1,2,13,14]
  • Chronic alcoholism [2]
  • Irritable bowel syndrome [1,2]
  • End stage renal disease [1,2]
  • Acromegaly [10]
  • Cystic fibrosis [11,12]
  • Fibromyalgia [2,15]

SIBO Symptoms

Symptoms of SIBO may include [1,2]:

  • Abdominal bloating (distension) and pain
  • Excessive gas (flatulence)
  • Stomach upset (dyspepsia)
  • Chronic diarrhea
  • Symptoms caused by nutrient malabsorption: weight loss, fatigue, anemia (see Chart 1)

Chart 1. Nutrient Malabsorption in SIBO



Lactose Bloating, diarrhea
Fructose Bloating, diarrhea
Fats Greasy stools – steathorrhea, weight loss
Proteins Muscle wasting, swelling, weight loss
Vitamin A Dry eyes, night blindness
Vitamin B12, folate Macrocytic anemia, peripheral neuropathy
Iron Microcytic anemia
Calcium Muscle twitching (tetany)
Selenium Dermatitis

Chart sources: [1,4]

SIBO Complications

A. Impaired digestion or absorption of nutrients:

  • Impaired digestion of lactose (lactose intolerance) [16,17,18,19] and fructose malabsorption [2,18]
  • Protein malabsorption and protein-losing enteropathy due to damage of the small intestinal lining resulting in muscle wasting [1,2,20]
  • Fat malabsorption resulting in greasy stools (steatorrhea). Mechanism: bacteria may inactivate bile acids, which are necessary for the absorption of fats [2]. Severe SIBO with fat malabsorption may be associated with reduced absorption of fat-soluble vitamins:
    • Vitamin A: dry eyes, night blindness
    • Vitamin D: osteomalacy with bone fractures, decreased calcium absorption, resulting in increased oxalate absorption and increased risk of oxalate kidney stones and in muscle cramps (tetany) [1,4]
    • Vitamin E: Neuropathy
    • Vitamin K: Increased bleeding
  • Impaired iron absorption resulting in microcytic anemia with weakness and paleness [1]
  • Impaired vitamin B12 and folate absorption resulting in macrocytic anemia and neuropathy with paleness, tingling or numbness [1,4]
  • Impaired selenium absorption resulting in dermatitis [1]

Other Possible Complications of SIBO

  • Non-alcoholic fatty hepatitis [2]
  • Rosacea. In several studies, acne rosacea was associated with SIBO; when SIBO was eradicated, rosacea was often healed at the same time [21].

In some individuals diagnosed with irritable bowel syndrome (IBS), antibiotics helped relieve symptoms, which suggests their symptoms were more likely caused by SIBO than IBS [22,23,24].

SIBO is a common cause of false positive results of breath tests for fructose malabsorption and lactose intolerance [18].


SIBO can be diagnosed by the hydrogen, methane, bile acid or xylose breath test [25].


Treatment of SIBO can includes [26]:

  • Correction of the underlying disorder
  • Correction of nutrient deficiencies, if necessary
  • Oral antibiotics, such as ciprofloxacin, clindamycin, metronidazole, rifaximin or tetracyclin, depending on the circumstances (causing bacteria, the underlying problem, age); initial treatment may last for 1-2 weeks and, if necessary, may be prolonged or repeated at a later time.

There is INSUFFICIENT EVIDENCE about the effectiveness of probiotics in treatment of SIBO [2].

  1. Syed SZ, Bacterial overgrowth syndrome, clinical presentation Emedicine
  2. Bures J et al, 2010, Small intestinal bacterial overgrowth syndrome PubMed Central
  3. Saltzman JR et al, 1994, Bacterial overgrowth without clinical malabsorption in elderly hypochlorhydric subjects PubMed
  4. Singh VV et al, 2003, Small Bowel Bacterial Overgrowth: Presentation, Diagnosis, and Treatment University of Alberta
  5. Bass NM et al, 2009, Emerging Issues in Gastroenterology and Hepatology PubMed Central
  6. Smith GM et al, 1990, Small intestinal bacterial overgrowth in patients with chronic lymphocytic leukaemia PubMed Central
  7. Klaus J et al, 2009, Small intestinal bacterial overgrowth mimicking acute flare as a pitfall in patients with Crohn’s Disease BMC Gastroenterology
  8. Trspi E et al, 1999, Intestinal bacterial overgrowth during chronic pancreatitis PubMed
  9. Simrén M et al, 2006, Use and abuse of hydrogen breath tests PubMed Central
  10. Resmini E et al, 2013, Evidence of Prolonged Orocecal Transit Time and Small Intestinal Bacterial Overgrowth in Acromegalic Patients Endocrine Society
  11. Lisowska A et al, 2009, Small intestine bacterial overgrowth is frequent in cystic fibrosis: combined hydrogen and methane measurements are required for its detection Acta Biochimica Polonica
  12. Fridge JL et al, 2007, Risk factors for small bowel bacterial overgrowth in cystic fibrosis PubMed
  13. Montgomery RD et al, 1986, Causes of malabsorption in the elderly PubMed
  14. Stephen J et al, 1999, Small bowel bacterial overgrowth in subjects living in residential care homes Age and Ageing
  15. Pimentel M et al, 2004, A link between irritable bowel syndrome and fibromyalgia may be related to findings on lactulose breath testing PubMed Central
  16. Zhao J et al, 2010, Lactose intolerance in patients with chronic functional diarrhoea: the role of small intestinal bacterial overgrowth PubMed
  17. Yakoob J et al, 2011, Small Intestinal Bacterial Overgrowth and Lactose Intolerance Contribute to Irritable Bowel Syndrome Symptomatology in Pakistan PubMed Central
  18. Nucera G et al, 2005, Abnormal breath tests to lactose, fructose and sorbitol in irritable bowel syndrome may be explained by small intestinal bacterial overgrowth Wiley Online Library
  19. Almeida JA et al, 2008, Lactose malabsorption in the elderly: role of small intestinal bacterial overgrowth PubMed
  20. King CE et al, 1981, Protein-losing enteropathy in the human and experimental rat blind-loop syndrome
  21. Parodi A et al, 2008, Small intestinal bacterial overgrowth in rosacea: clinical effectiveness of its eradication
  22. Park H et al, 2010, The Role of Small Intestinal Bacterial Overgrowth in the Pathophysiology of Irritable Bowel Syndrome  PubMed Central
  23. Pimental M et al, 2006, The effect of a nonabsorbed oral antibiotic (rifaximin) on the symptoms of the irritable bowel syndrome: a randomized trial  PubMed
  24. Dear KL et al, 2005, Do interventions which reduce colonic bacterial fermentation improve symptoms of irritable bowel syndrome?  PubMed
  25. Syed SZ, Bacterial overgrowth syndrome, workup  Emedicine
  26. Syed SZ, Bacterial overgrowth syndrome, treatment and management  Emedicine

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