Answer: E. The best treatment for bacterial overgrowth is dietary changes and antibiotic treatment for up to 6 months. Dietary changes may assist with the treatment of small bowel bacterial overgrowth by providing consistent readily absorbed nutrition to the body. Carbohydrates are the main source of nutrition for the bacteria, and therefore the amount of non-absorbed carbohydrates in the patient’s diet should be reduced. The best diet is high fat, low carbohydrate, and low fiber because fat is less metabolized by the bacteria than carbohydrates, leading to less bloating, gas, and abdominal discomfort. Lactose-containing foods should also be avoided as many of those who test positive for small bowel bacterial overgrowth are lactose intolerant. Nutritional deficits should also be corrected by means of extra vitamin supplementation.

Most patients with small bowel bacterial overgrowth require antibiotic treatment in addition to dietary changes. The goal of antibiotic treatment is to reduce the bacterial flora, leading to improvement of symptoms. Current recommended therapies cover both aerobic and anaerobic bacteria. There are very few randomized controlled trials studying the treatment of small bowel bacterial overgrowth, and data are limited regarding recommended length of treatment, particularly in those who have undergone Roux-en-Y gastric bypass surgery. Current recommendations for treatment include the following:

Continue Reading

  • Rifaximin 
  • Rotation of ciprofloxacin, metronidazole, and doxycycline on a monthly rotation once monthly for a total of 6 months
  • Augmentin


Mrs. M underwent carbohydrate breath test, and results were positive for small bowel bacterial overgrowth. She was started on a 6-month rotation of ciprofloxacin, metronidazole, and doxycycline. At the end of the 6-month course, she returned to the clinic. Her diarrhea had been eliminated and she was having regular stools once daily. She no longer had significant odor to her stools or significant gas. Her laboratory values were all normal or above normal. Her vitamin supplementation was reduced to twice-daily multivitamins, twice-daily calcium, once-daily vitamin D 3000 IU, once-daily Vitron-C, and once-monthly vitamin B12. This is a more standard regimen for those who have undergone Roux-en-Y gastric bypass surgery. 

Julia Jurgensen APRN, CNP, practices at the Mayo Clinic in Rochester, Minnesota, in the department of endocrinology, specializing in diabetes management and obesity.


  1. Pimentel M. Treatment of small intestinal bacterial overgrowth. UpToDate. Updated November 16, 2015. Accessed January 24, 2016.
  2. Pimentel M. Clinical manifestations and diagnosis of small intestinal bacterial overgrowth. UpToDate. Updated January 25, 2016. Accessed April 14, 2016.
  3. Singh VV, Toskes PP. Small bowel bacterial overgrowth: presentation, diagnosis, and treatment. Curr Treat Options Gastroenterol. 2004;7(1):19-28.