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Bacterial Overgrowth

Jon A. Vanderhoof, MD, Pediatric Gastroenterologist; Rosemary J. Young, MS, BSN, Pediatric Gastroenterology Clinical Nurse Specialist


University of Nebraska Medical Center, Creighton University


A variety of bacteria normally resides in the intestinal tract. Species vary from the small to large bowel and increasing numbers occur over the length of the bowel, with about 1000 bacteria per milliliter of intestinal contents being present in the upper bowel to almost 1 billion per milliliter in the colon (See Figure 1) [1]. There is a lower number of bacteria in the small bowel as compared to the large bowel because of the forward peristalsis of the intestinal tract, bacteriocidal action of gastric acid and bile, reduction by enzymatic digestion and mucus entrapment, low exposure from the environment, and presence of an ileocecal valve [2].


Bacterial overgrowth in the small bowel is often associated with gastrointestinal anomalies such as those that result in short bowel syndrome. The causes of small bowel bacterial overgrowth include:

• Anatomical abnormalities occurring due to congenital (birth) defects and traumatic alterations (injury/surgery),

• Abnormalities of intestinal peristalsis (motility) such as intestinal pseudo-obstruction,

• Defects of intestinal mucosal surface and immune defense mechanisms (Table 1).

Symptoms of small bowel bacterial overgrowth vary depending on the cause of the overgrowth, as well as the location of the excess bacteria, and type of bacteria present [3]. Most often, symptoms include combinations of abdominal pain and cramping, diarrhea (which can sometimes be bloody), dyspepsia, gas, and weight loss.


Diagnosing Overgrowth

Identifying the cause of small bowel bacterial overgrowth, and even diagnosing it as the cause of the patient’s symptoms, is often challenging. Aspirating fluid from the bowel during an upper gastrointestinal endoscopy was once considered the gold standard for diagnosis; however, this method is often not helpful because it may be impossible to aspirate from the area where the overgrowth is occurring and because methods of culturing the fluid are often affected by errors in obtaining and processing the fluid. Glucose breath hydrogen testing is sometimes beneficial in identifying overgrowth. Glucose is used as a substrate for this breath test because it is rapidly metabolized by bacteria in the small bowel (before it can be absorbed) and results in excess hydrogen which is easily detected in the patient’s breath [4]. Other diagnostic tests include quantitative and qualitative evaluation of urine for indicans and detection of an elevated level of serum d-lactic acid, both of which indicate bacterial metabolism [5-6]. At times, d-lactic acidosis can be so severe as to cause seizures and metabolic acidosis with coma. Elevated serum folate levels may also be present with bacterial overgrowth. The presence of a dilated bowel segment on upper GI x-ray may identify the location of overgrowth in advanced cases.


Treating Overgrowth

Treatment of small bowel bacterial overgrowth is varied, depending upon the severity of symptoms. Broad spectrum antibiotics have been utilized with fairly good success. Long-standing cases of bacterial overgrowth or the presence of very pathogenic organisms require more aggressive, and often a combination of, treatments [7].




The simplest method to treat small bowel bacterial overgrowth is to alter the patient’s diet. If chronic low-grade symptoms are present, utilizing a high fat (50-60% of total caloric intake), low carbohydrate diet is beneficial: it reduces the food substrate which most bacteria thrive on, i.e. carbohydrates; and limits bacterial proliferation, which results in symptomatic improvement. If the patient is eating a completely oral diet, achieving a high fat intake is often not difficult; however, reducing concurrent carbohydrate intake is more of a challenge (Table 2). Consultation with a dietitian is helpful in this regard and it is our experience that this diet should be rigidly adhered to on a daily basis. If the person is also receiving enteral formula, modifying the solution by the addition of fat and/or switching to a higher fat formula, such as Pulmocare®, may make a significant difference.




If the dietary therapy is insufficient to control symptoms, it should be continued with the addition of antibiotics. Broad spectrum antibiotics, such as Bactrim and Flagyl, used continuously, at half the usual antibiotic dose, are often very effective. Trials of different antibiotics may be needed to find the right combination. In addition to Bactrim and Flagyl, we have found Augmentum and Keflex to be beneficial. Our most severe case of small bowel bacterial overgrowth was a child with short bowel syndrome who suffered severe d-lactic acidosis with seizures. He went through several treatment regimes before we identified oral Vancomycin, a potent antibiotic, as an effective measure to control his overgrowth. After the acute overgrowth has been controlled, antibiotic therapy may be required only for a few days out of every month or may be so severe as to require prolonged continuous therapy. If symptoms reappear after a few months, switching antibiotics is often necessary. We have seen no development of antibiotic resistant complications utilizing this therapy over prolonged periods of time, probably because of the lower doses utilized.




Probiotic therapy is another potential treatment for small bowel bacterial overgrowth. Probiotics are live, human-derived microorganisms that benefit the person taking them by improving their intestinal microbial balance. There are many probiotics available, but few have undergone rigorous evaluation in clinical studies. Lactobacillus GG has been well studied and found to be beneficial in some mild cases of bacterial overgrowth [8]. One child that we followed seemed to respond to antibiotic therapy initially, but eventually became symptomatic regardless of the antibiotic protocol utilized. He had experienced severe arthritis due to bacterial byproducts from his overgrowth. The addition of Lactobacillus GG, (2 capsules a day,) to Flagyl therapy significantly decreased his arthritic symptoms.


Bowel Flushes


If medication therapy is not effective, or if symptoms are quite severe, daily or weekly bowel flushes may be beneficial. These routines work by mechanically flushing excess bacteria from the bowel. We have found daily use of low dose magnesium citrate or Miralax® (both osmotic laxatives) to be helpful for some of our patients. At times, simply having the patient attempt to pass stool every couple of hours is sufficient to improve their condition. Many patients with short bowel syndrome have learned to avoid stooling in order to control their frequent watery bowel movements, which can be particularly counterproductive when they have bacterial overgrowth.


Avoid Acid Suppression Agents


There have been some reports of bacterial overgrowth being exacerbated by the use of acid suppression agents. These agents are commonly used in patients with short bowel syndrome to help control excess acid production and reduce small bowel fluid losses. Using acid suppression agents can be harmful because they suppress gastric acid which plays a normal role in reducing the bacteria consumed in the diet. Therefore, if possible, these agents should be avoided or reduced in dosage.




Inflammation from bacterial overgrowth can be so severe as to result in a colitis situation with bloody stools. In addition to treating excess bacteria through antibiotic therapy and diet, it may be necessary to use sulfasalazine and/or corticosteroids to reduce the inflammation caused by the excess bacteria. This is only used in extreme cases and on a very short-term basis.




Severe situations of small bowel bacterial overgrowth unresponsive to dietary, medical, or mechanical measures may require surgical therapy. Temporary colostomy placement or an intestinal tapering and lengthening (Bianchi) surgical procedure may be beneficial in these cases [9]. These methods, of course, are not without complications themselves and should only be reserved for the most severe cases (See Figure 2).


Small bowel bacterial overgrowth is a condition which can occur at any time in many consumers of home parenteral and enteral nutrition. If a previously stable homePEN consumer becomes symptomatic with diarrhea, weight loss, abdominal pain, cramping, and an increase in intestinal gas, this condition should be considered. Numerous measures are available as treatment options. Research into this area is ongoing especially in the areas of probiotic therapy, and new surgical measures.




1. Physiology of the Gastrointestinal Tract, 2nd Ed. Johnson LR, ed. New York, NY; Raven Press. 1987.

2. Forstner G, Sherman P, Lichtman S. Bacterial overgrowth. In: Walker W, Durie P, Hamilton J, Walker-Smith J, Watkins J, ed. Pediatric gastrointestinal diseases. St. Louis, MO; Mosby. pp 689-700.

3. Sherman P, Lichtman S. Small bowel bacterial overgrowth syndrome. Dig Dis. 1987;5:154-74.

4. Kerlin P, Wong L. Breath hydrogen testing in bacterial overgrowth of the small intestine. Gastroenterology. 1988;95:982-8.

5. Aarbakke J, Schjonsby H. Value of urinary simple phenol and indican determinations in the diagnosis of the stagnant loop syndrome. Scan J Gastroenterol. 1976;11:409-14.

6. Scully TB, Kraft SC, Carr WC, et al. D-lactate-associated encephalopathy after massive small bowel resection. J Clin Gastroenterol. 1989;11:448-51.

7. Vanderhoof JA, Young RJ, Murray N, Kaufman SS. Treatment strategies for small bowel bacterial overgrowth in short bowel syndrome. J Pediatr Gastroenterol Nutr. 1998;27:155-60.

8. Vanderhoof JA, Young RJ. The role of probiotics in the treatment of intestinal infections and inflammation. Curr Opin Gastroenterol. 2001;17(1):58-62.

9. Warner BW, Vanderhoof JA, Reyes JD. What’s new in the management of short gut syndrome in children. J Am Coll Surg. 2000;190(6):725-36.

This website is an educational resource. It is not intended to provide medical advice or recommend a course of treatment. You should discuss all issues, ideas, suggestions, etc. with your clinician prior to use. Clinicians in a relevant field have reviewed the medical information; however, the Oley Foundation does not guarantee the accuracy of the information presented, and is not liable if information is incorrect or incomplete. If you have questions please contact Oley staff.


Updated in 2015 with a generous grant from Shire, Inc. 


This website was updated in 2015 with a generous grant from Shire, Inc. This website is an educational resource. It is not intended to provide medical advice or recommend a course of treatment. You should discuss all issues, ideas, suggestions, etc. with your clinician prior to use. Clinicians in a relevant field have reviewed the medical information; however, the Oley Foundation does not guarantee the accuracy of the information presented, and is not liable if information is incorrect or incomplete. If you have questions please contact Oley staff.
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