Small bacterial overgrowth in children

Publication: 01/07/2021  
Next review: 01/07/2024  
Clinical Guideline
ID: 7053 
Approved By: IAPG 
Copyright© Leeds Teaching Hospitals NHS Trust 2021  


This Clinical Guideline is intended for use by healthcare professionals within Leeds unless otherwise stated.
For healthcare professionals in other trusts, please ensure that you consult relevant local and national guidance.



There are no specific tests are currently available in LTHT for diagnosing Small Intestinal Bacterial Overgrowth (SIBO). Treatment should be initiated if there is strong clinical suggestion of SIBO based on symptoms and risk factors.

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The underlying cause of the bacterial overgrowth should be treated where possible. Ancillary treatments are listed below which may be considered based upon the cause of the bacterial overgrowth:

  • Diet - high fat, low carbohydrate
  • Prebiotics/probiotics
  • Prokinetics for dysmotility
  • Surgery for abnormalities of the GI tract
  • Treatment of nutritional deficits - notably calcium, magnesium, iron and vitamins
  • Stop gastric acid suppressor medication

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Treatment should be only initiated by a Consultant Paediatric Gastroenterologist or Consultant Paediatric gastrointestinal surgeon.

Empirical options for SIBO

Duration: Treatment is to be prescribed as a cyclical course with 2 weeks on and 2 weeks off treatment. Treatment should continue as long as it is effective (e.g. decreased abdominal pain/bloating, reduced flatulence/diarrhoea) but needs regular reviews by the clinical team1.

1st Line:
For patients >2years

Rifaximin electronic Medicines Compendium information on Rifaximin PO

  • 2-5 years: 100mg TDS
  • 6-12 years: 100-200mg TDS
  • >12 years: 200mg TDS

2nd line:
If rifaximin is inappropriate (<2years) or has been ineffective

Metronidazole electronic Medicines Compendium information on Metronidazole PO 7.5mg/kg TDS
Trimethoprim PO 4mg/kg BD

  • If the 1st and 2nd line options have failed reconsider diagnosis of SIBO.
  • Patient should be referred for specialist input2 where there has been failure to both 1st and 2nd line treatments or both are contraindicated.

3rd line:

If SIBO remains most likely/confirmed diagnosis regimen should be decided after discussion with Consultant Gastroenterologist or Microbiologist.


  1. The course can also be given as 1 week on and 1 week off and, for the most difficult cases, Rifaximin can be given continuously. This can be considered if the patient starts to develop symptoms of bacterial overgrowth 5-8 days after stopping antibiotic for week off.
  2. Specialist input = Consultant Paediatric Gastroenterologist


Record: 7053
Clinical condition:

Small bacterial overgrowth (SIBO)

Target patient group: Children
Target professional group(s): Pharmacists
Secondary Care Nurses
Adapted from:

Evidence base

  • Arasaradnam RP, Brown S, Forbes A et al. 2018. Guidelines for the investigation of chronic diarrhoea in adults: British Society of Gastroenterology, 3rd edition Gut;0:1–20.
  • Avelar Rodriguez D et al. 2019. Small Intestinal Bacterial Overgrowth in Children: A State-Of-The-Art Review. Front Pediatr; 7:363.
  • Dulkowicz, A.C., Lacy, B.E. and Levine, G.M. 2007. Small Intestinal Bacterial Overgrowth: A Comprehensive Review. Gastroenterology & Hepatology Volume 3, Issue 2: 112-123. Evidence level A.
  • Gatta L, Scarpignato C. 2017. Systematic review with meta-analysis: rifaximin is effective and safe for the treatment of small intestine bacterial overgrowth. Aliment Pharmacol Ther; 45(5):604-616. doi:10.1111/apt.13928
  • Grace E, Shaw C, Whelan K et al. 2013. Review article: small intestinal bacterial overgrowth – prevalence, clinical features, current and developing diagnostic tests, and treatment. Aliment Pharmacol Ther; 38: 674-688
  • Khalighi et al. 2014. Evaluating the efficacy of probiotic on treatment in patients with small intestinal bacterial overgrowth (SIBO) - A pilot study. Indian J Med Res; 140(5): 604–608.
  • Lauritano EC, Gabrielli M, Scarpellini E, et al. 2008. Small intestinal bacterial overgrowth recurrence after antibiotic therapy. Am J Gastroenterol; 103:2031.
  • Malik BA et al. 2011. Diagnosis and pharmacological management of small intestinal bacterial overgrowth in children with intestinal failure. Can J Gastroenterol; 25(1): 41-45.
  • Planas-Vilaseca, A. et al. 2016. D-lactic acidosis: A rare cause of metabolic acidosis. Endocrinología, Diabetes y Nutrición (English ed.). Vol: 63(8): 433-434
  • Quigley EM & Quera R. 2006. Small intestinal bacterial overgrowth: roles of antibiotics, prebiotics, and probiotics. Gastroenterology; 130 :78–90.
  • Reddy VS, Patole SK and Rao S. 2013. Role of Probiotics in Short Bowel Syndrome in Infants and Children—A Systematic Review. Nutrients; 5: 679-99
  • Rosania R et al. 2013. Effect of probiotic or prebiotic supplementation on antibiotic therapy in the small intestinal bacterial overgrowth: a comparative evaluation. Curr Clin Pharmacol; 8(2):169-72.
  • Shah SC, Day LW, Somsouk M, Sewell JL. 2013. Meta-analysis: Antibiotic therapy for small intestinal bacterial overgrowth. Aliment Pharmacol Ther; 38:925–34.

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