The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome

JPEN J Parenter Enteral Nutr. 2016 Nov;40(8):1106-1113. doi: 10.1177/0148607115591216. Epub 2015 Jun 9.


Background: Changes in the intestinal microbiome of patients with short bowel syndrome (SBS) are thought to significantly affect clinical outcome. These changes may not only delay enteral diet advancement but may also predispose patients to bacterial translocation, bacteremia, and liver disease. Patients with SBS are thought to be more susceptible to changes in gut microbial communities due to intestinal dysmotility and/or lack of anatomic safeguards such as the ileocecal valve.

Materials and methods: We analyzed the bacterial composition of 21 fecal specimens from 9 children with SBS and 8 healthy children ages 4 months to 8 years by 16S ribosomal RNA gene sequencing. The sequences were quality filtered and analyzed using QIIME, the Ribosomal Database Project Classifier, and the randomForest supervised learning algorithm.

Results: The fecal microbiome of patients with SBS is different from that of healthy controls. Stool from patients with SBS had a significantly greater abundance of the bacterial classes Gammaproteobacteria and Bacilli. Stool from patients with SBS who experienced increased stool frequency tended to have increased abundance of Lactobacillus (P = .057) and decreased abundance of Ruminococcus.

Conclusion: This study shows that the fecal microbiome of patients with SBS is significantly different from that of healthy controls when analyzed by 16S metagenomics. Differences in the composition and function of gut microbiomes in children with SBS may affect bowel physiology, and these findings may provide new opportunities for intestinal rehabilitation and clinical management.

Keywords: dysbiosis; gammaproteobacteria; microbiome; short bowel syndrome.

MeSH terms

  • Bacillus / isolation & purification
  • Bacterial Translocation
  • Case-Control Studies
  • Child
  • Child, Preschool
  • DNA, Bacterial / isolation & purification
  • Feces / microbiology*
  • Female
  • Gammaproteobacteria / isolation & purification
  • Gastrointestinal Microbiome*
  • Humans
  • Infant
  • Intestines / microbiology
  • Lactobacillus / isolation & purification
  • Male
  • RNA, Ribosomal, 16S / isolation & purification
  • Ruminococcus / isolation & purification
  • Sequence Analysis, DNA
  • Short Bowel Syndrome / microbiology*
  • Short Bowel Syndrome / therapy
  • Specimen Handling


  • DNA, Bacterial
  • RNA, Ribosomal, 16S