Bacterial Overgrowth Syndrome Treatment & Management

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

Treatment in bacterial overgrowth syndrome (BOS) should include correction of primary underlying disease if any, including antibiotic therapy and nutritional support. The primary approach should be the treatment of any disease or anatomic defect that potentiated bacterial overgrowth. Many of the clinical conditions associated with bacterial overgrowth syndrome are not readily reversible, and management is based on antibiotic therapy aimed at rebalancing enteric flora. Careful consideration must be taken to prevent total eradication of protective microorganisms. The goal should be directed at reducing symptoms. Initial antibiotic therapy usually is empiric and should be broad and cover both aerobic and anaerobic microorganisms. Community resistance patterns should also be considered.

Rifaximin is currently the mainstay of treatment. Tetracycline was the mainstay of therapy, but its use as a single agent has fallen out of favor in adult patients given community increases in bacterial resistance.

Bacterial sensitivities from duodenal intubations with nonidiopathic bacterial overgrowth syndrome support the use of amoxicillin-clavulanate. Amoxicillin-clavulanate appears to be 75% effective in patients with diabetes.

Studies show that rifaximin eradicates bowel overgrowth syndrome in as many as 80% of patients. [22, 23] Higher doses (1200 or 1600 mg/d) are more effective than standard doses (600 or 800 mg/d). [24] Long-term favorable clinical results have been achieved with rifaximin in patients with irritable bowel and bacterial overgrowth syndrome. [25]

Clindamycin and metronidazole are useful in elderly patients with idiopathic bacterial overgrowth syndrome.

Cholestyramine reduces diarrhea in infants and neonates with intractable diarrhea. [26] Infants with 10-25 days of severe persistent diarrhea for which a cause could not be found despite an extensive infectious and immunologic workup were treated with cholestyramine and gentamicin or metronidazole. Cholestyramine and gentamicin significantly reduced stool weight within 4-5 days of therapy but had mild detrimental effects on fat and nitrogen absorption.

Ciprofloxacin and metronidazole result in normalization of hydrogen breath tests in most patients with Crohn disease. [7]

Norfloxacin, cephalexin, trimethoprim-sulfamethoxazole, and levofloxacin have been recommended for the treatment of bacterial overgrowth syndrome. [4, 27]

The exact length of therapy is not clearly defined; length of therapy should be tailored to symptom improvement. A single 7-10 day course of antibiotic may improve symptoms in 46-90% of patients with bacterial overgrowth syndrome. [28]  Recurrence following therapy is not uncommon and is more likely in elder patients, especially those with history of appendectomy and chronic proton pump inhibitor use. Patients with recurrent symptoms may need repeated (eg, the first 5-10 d of every month) or continuous use of cyclical antibiotic therapy. [4]

Probiotic therapy results in bacterial overgrowth syndrome have been inconclusive and generally not recommended for general clinic use. [2, 29]

Therapeutic use of prokinetics in bacterial overgrowth syndrome due to motility disorders have been tried in many studies. Metoclopramide, cisapride, domperidone, erythromycin, tegaserod, and octreotide have been used; however, data suggest long-term effectiveness is limited. [27]

Nutritional support with dietary modifications such as lactose-free diet, vitamin replacement, and correction of deficiencies in nutrients like calcium and magnesium should be an important part of bacterial overgrowth syndrome treatment, if applicable.

Certain potential underlying abnormalities are amenable to treatment, as follows:

The following potential underlying diseases are not amenable to treatment, but prevention of their progression may be therapeutic:

  • Diabetic autonomic neuropathy

  • Scleroderma

  • Pseudoobstruction

  • Amyloidosis

  • Achlorhydria

  • Vagotomy


Surgical Care

In the absence of underlying structural abnormalities that limit normal bowel function, surgery generally is unwarranted.

Repair postoperative strictures and blind loops; for example, a Billroth type II may need conversion to a Billroth type I.

Strictures, fistulae, and diverticula may require surgical correction.



Patients refractory to standard medical or surgical treatment or those who have severe symptoms should be referred to a gastroenterologist/infectious disease specialist for additional workup.



No robust studies have yet properly defined the role of dietary modification in the treatment of bacterial overgrowth syndrome. A low-fiber diet and reduction of fermentable sugars such as sucralose may reduce the occurrence of bacterial overgrowth syndrome, although this potential is extrapolated from results in patients with IBS. There is growing interest in the role of low-FODMAP (fermentable oligo-, di-, mono-saccharides and polyols) diets in bacterial overgrowth syndrome. Studies on the role of FODMAP in patients with IBS found that a low-FODMAP diet was associated with fewer fermentation products, as assessed with a breath test. [30, 31]



Controlling the underlying etiology is an important component of preventing bacterial overgrowth syndrome recurrence. Known underlying medical conditions that predispose to bacterial overgrowth syndrome (eg, diabetes mellitus, scleroderma, alcoholism, cirrhosis, chronic pancreatitis, hypochlorhydria due to atrophic gastritis or medications) need to be optimally controlled. Surgical intervention may be beneficial in patients with anatomic abnormalities such as surgically created blind loops, strictures due to previous surgeries, and conditions such as Crohn disease who continue to have persistent symptoms of bacterial overgrowth syndrome, including unintentional weight loss, diarrhea, and bloating, among others, after adequate treatment. Patients with motility disorders should avoid medications that decrease intestinal motility.

Given the high relapse rate associated with bacterial overgrowth syndrome following antibiotic therapy, some clinicians opt to repeat a second course of antibiotics to reduce the risk for early relapse. A small study suggested that patients who undergo retreatment with antibiotics tend to have a lower relapse rate, although no clear guidelines support this. [32]

Antibiotic prophylaxis usually is reserved for patients who experience multiple relapses (≥4) per year and who are known to have risk factors for recurrence.

The use of probiotics to treat or prevent bacterial overgrowth syndrome has not been well validated. Limited studies support their use. A meta-analysis of small studies found no difference in the incidence of bacterial overgrowth syndrome among the probiotic group versus the control group. [33]


Long-Term Monitoring

Close-interval follow-up is recommended to ensure that therapy is improving symptoms. It is also not clearly defined whether serial testing for increased bacteria burden is warranted.


Further Inpatient Care

Admission criteria for bacterial overgrowth syndrome (BOS) should be based on severity of clinical manifestations at presentation, especially in high-risk individuals.