Bacterial Overgrowth Syndrome Workup

Updated: Mar 07, 2023
  • Author: Chinelo N Animalu, MD, MPH, FIDSA; Chief Editor: Michael Stuart Bronze, MD  more...
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Laboratory Studies

Bacterial overgrowth syndrome (BOS) diagnostic testing should include a workup for diarrhea, anemia, and malabsorption. In the past, retrieval of aspirates from the small intestine itself during endoscopy was the diagnostic tool of choice; however, its use was limited due to low specificity.

Standard anemia workup and nutritional evaluation are indicated.

Stool analysis can help detect abnormal stool components. The pH may be acidic, and reducing substance may be present in the stool.

D-lactic acidosis syndrome can result from carbohydrate fermentation. Lactic acid levels may need to be measured and, if elevated, monitored. D-lactic acid levels, measured in the blood or urine, can help differentiate bacterial overgrowth syndrome from other metabolic causes.

Short-chain fatty acid levels may be elevated in the duodenal fluid but not the stool. [12] Abnormal duodenal short-chain fatty acid levels average approximately 1 µmol/mL, with acetic acid, propionic acid, and n -butyric acid representing 61%, 16%, and 8% of the total, respectively. The average short-chain fatty acid level in a healthy patient is 0.27 µmol/mL, with acetic acid representing 84% of the total.

Keto-bile acid concentration in duodenal fluid is increased and correlates with the type of bacterial overgrowth. [13] The molar percent of keto-bile acids in normal duodenal fluid is very close to 0, while gram-negative aerobic and anaerobic overgrowth is associated with levels of 32 µmol/mL and 11 µmol/mL, respectively.

Urine 4-hydroxyphenylacetic acid levels may be elevated. [14] Enteric bacteria that possess L-amino acid decarboxylase produce 4-hydroxyphenylacetic acid from dietary tyrosine. Increased excretion has been demonstrated in adults with bacterial overgrowth syndrome. Creatinine levels that exceed 120 mg/g are typical in children with small-bowel disease or bacterial overgrowth syndrome, including children with chronic Giardia lamblia gastroenteritis. Children with severe pancreatic dysfunction secondary to cystic fibrosis also have significantly high levels of this metabolite. A 2% false-positive rate and no false-negative results are found when this test is used to screen healthy control subjects and hospitalized children.


Imaging Studies

Evaluation for malabsorptive processes should include small-bowel follow-through, which is used to evaluate structure and mobility. Strictures, malrotation, diverticulosis, fistulae, and pseudo-obstruction can be found with this technique.

Imaging and examination of the lower GI tract should be considered if upper GI evaluation is nondiagnostic.



Breath tests are used to measure byproducts of bacterial metabolism to identify malabsorbed substances. [15] Several studies suggest that 3 breath tests are of adequate specificity, but these studies are not in full agreement regarding the exact sensitivity. Studies that compare these tests with duodenal bacterial counts suggest that the xylose breath test yields the highest specificity. [16]

Hydrogen breath test

Hydrogen breath tests are based on the fact that in humans hydrogen is exclusively produced by intestinal bacteria, most notably by anaerobic bacteria in the colon of healthy people and also in the small intestine in the case of bacterial overgrowth syndrome. Preoral glucose or lactulose challenge is given before performing hydrogen breath tests. Bacteria ferment malabsorbed carbohydrates. Fermentation releases hydrogen gas that is absorbed and excreted by the lungs.

Under normal conditions, fermenting bacteria reside in the colon. In bacterial overgrowth syndrome, the exhaled hydrogen concentration rises early, corresponding to small intestinal bacteria fermentation of carbohydrates. Under such conditions, a later rise in exhaled hydrogen may also be detected during large bowel fermentation. Antibiotic administration invalidates this test.

For diagnosis, use 1-2 g/kg of glucose, not to exceed 25-50 g. A rise in exhaled hydrogen to 20 parts per million is diagnostic. For diagnosis, use 10 g lactulose. A rise in 20 parts per million above baseline is diagnostic. The specificity and sensitivity of this test are 62.5% and 82% after glucose and 56% and 86% after lactulose administration. [17]

Bile acid breath test

Give glycocholate tagged with carbon 14 with a light meal, and collect breath samples at 2, 4, and 6 hours. An abnormal rise in radioactive carbon dioxide levels indicates bacterial deconjugation of glycocholate.

The specificity and sensitivity of this test are 60-76% and 33-70%, respectively

False positive results may come from disease or resection of terminal ileum, the site of bile absorption. Carbon 14 carries a risk of radiation, which can be problematic in children and pregnant women. [4]

Xylose breath test

Gram-negative bacteria metabolize xylose, resulting in the release of radioactive carbon dioxide. Administer 1 g of D-xylose tagged with carbon 14, as a liquid, after an overnight fast. Measure radioactive breath carbon dioxide at 30, 60, 90, and 120 minutes. An abnormally high carbon dioxide concentration usually is detected within 30-60 minutes. The specificity and sensitivity of this test are 14.3-95% and 40-94%, respectively. [4]

Combination of hydrogen breath test with simultaneous D-xylose breath test results in increase in sensitivity of noninvasive diagnostics of bacterial overgrowth syndrome. [18, 19]


Histologic Findings

Descending duodenal biopsies performed in a group of elderly individuals with bacterial overgrowth syndrome demonstrated that mean villus height, mean crypt depth, and total mucosal thickness may be reduced. These indices are not significantly different from controls after 6 months of treatment of bacterial overgrowth syndrome. A significant drop in the number of intraepithelial lymphocytes is also seen over this observation period. Mucosal atrophy can result in an 80% reduction of intestinal surface area in infants. Once the offending agent is removed, repair of the small bowel progresses slowly. After 2 months, the villi surface area is 63% normal but the microvillous surface area is only 38% normal.


Other Tests

Quantitative measurement of bacteria from small bowel aspirate culture.

The quantitative measurement of bacteria aspirate obtained from sterial cultures taken from the proximal small bowel can be used in the diagnosis of BOS. Previously, a bacterial colony count of ≥105 colony-forming units per milliliter (CFU/mL) [20]  obtained from a duodenal/jejunal aspirate was considered diagnostic of BOS however, recent guidelines have embraced a bacterial colony count of ≥103 colony-forming units per milliliter (CFU/mL) as diagnostic of BOS according to the North American Consensus. [21]  The use of this technique to establish diagnosis is usually expensive and considered an invasive technique and use of simpler methods should be considered first.