The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome

Abstract

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.

© 2015 American Society for Parenteral and Enteral Nutrition.

Figures

Figure 1

The relative abundances of bacterial phyla (A) and classes (B) in 8 fecal samples from healthy controls and 12 fecal samples from patients with short bowel syndrome (SBS), as detected by sequencing of the 16S ribosomal RNA gene (V3–V5 region). The box plots depict median and interquartile range, their whiskers denote the 10th and 90th percentiles of each group, and dots indicate outlying values. Plots that contain an asterisk (*) are taxa that significantly differ between patients with SBS and controls at P < .05 using a Mann-Whitney test.

Figure 2

Healthy children and patients with short bowel syndrome (SBS) harbored different gut microbiome structures, as detected by 16S ribosomal RNA gene sequencing. The bacterial communities within the 20 fecal samples of control subjects and patients with SBS clustered by group when analyzed by principal coordinates analysis of unweighted UniFrac distances. Blue square = healthy control subjects. Red circle = patients with SBS.

Figure 3

Heatmap of bacterial operational taxonomic units (OTUs) contributing to the differentiation of short bowel syndrome (SBS) stool communities (diarrheal and asymptomatic) from those of healthy controls. Taxa were characterized using 16S ribosomal RNA gene sequencing, and those features that were identified by the randomForest classification algorithm as differentiating the 2 subject groups are highlighted here. The relative abundances of each OTU are scaled by row (blue = enriched relative to the median, pink = depleted relative to the median), and each differed significantly between patients with SBS and healthy controls when analyzed via Mann-Whitney tests. Taxonomic identities associated with each OTU represent the lowest taxonomic depth that could be assigned with >80% confidence by the Ribosomal Database Project Classifier.