A comparison of small bowel and fecal microbiota in children with short bowel syndrome
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Updated: Dec 28, 2025
An Intestinal Gut Organ Culture System for Analyzing Host-Microbiota Interactions
Published on: June 30, 2021
Hannah G Piper1, Laura A Coughlin2, Van Nguyen2
1Department of Surgery, University of British Columbia, Vancouver, BC, Canada.
Insights
Infants with short bowel syndrome (SBS) show altered gut microbiota. Fecal samples, while containing more bacteria, may reflect the small intestinal microbial community in SBS patients.
Area of Science:
- Microbiology
- Pediatric Gastroenterology
- Gut Microbiome Research
Background:
- Short bowel syndrome (SBS) in infants is associated with disruptions in the small intestinal microbial community, affecting gut function.
- Accurate characterization of the infant small bowel microbiota is difficult, and the reliability of using fecal samples for this purpose remains uncertain.
- This study investigates the relationship between fecal and small intestinal microbiota in infants with SBS.
Purpose of the Study:
- To compare the microbial composition of fecal samples with that of the small bowel in infants with short bowel syndrome (SBS).
- To assess the utility of fecal sampling as a proxy for small intestinal microbiota analysis in pediatric SBS patients.
Main Methods:
- Fecal samples were collected from infants with SBS (colon in continuity or small bowel ostomy) and healthy controls.
- 16S rRNA sequencing and quantitative PCR (qPCR) were employed to analyze bacterial abundance and quantity.
- Statistical analysis, including the Kruskal-Wallis test, was used to compare microbial profiles between groups.
Main Results:
- The gut microbiota of infants with SBS significantly differed from that of healthy controls.
- While fecal samples exhibited higher bacterial quantities, no significant differences were observed in the abundance of key bacterial groups (facultative/obligate anaerobes, Clostridia, Enterobacteriaceae, Bifidobacterium) between SBS subgroups (sbSTOMA vs. COLON).
- Demographics and small intestinal length were comparable between the sbSTOMA and COLON groups.
Conclusions:
- Infants diagnosed with SBS exhibit significant disturbances in their intestinal microbiota.
- Direct sampling of the small intestinal lumen presents considerable challenges in this population.
- Fecal sample analysis may offer a viable, less invasive method to infer the composition of the proximal microbial community in infants with SBS.
Background:
Babies with short bowel syndrome (SBS) have small intestinal microbial disturbances that impact gut function. Characterizing the small bowel microbiota is challenging, and the utility of sampling stool is unclear. This study compares the microbiota from fecal samples and the small bowel.
Methods:
Stool samples were collected (2016-2017) from infants with SBS and colon in continuity (COLON) or SBS with small bowel ostomy (sbSTOMA). The abundance and quantity of major bacterial genera was compared between groups and to healthy controls using 16S rRNA sequencing and qPCR. Kruskall-Wallis test was used for analysis with P values <0.05 considered significant.
Results:
Samples (n = 41) were collected from 15 SBS infants (<2 years) (9 sbSTOMA, 6 COLON) and 3 healthy infants. Demographics and small intestinal length did not differ between sbSTOMA and COLON infants. The microbiota of SBS groups differed significantly from healthy controls. Fecal samples contained higher quantities of bacteria, but there were no significant differences between sbSTOMA and COLON groups in the abundance of facultative or obligate anaerobes, anti-inflammatory Clostridia, Enterobacteriaceae, or Bifidobacterium.
Conclusion:
Infants with SBS have disturbances to their intestinal microbiota. Sampling small intestinal effluent is challenging. Stool samples may provide a window into the more proximal microbial community.
Type Of Study:
Diagnostic.
Level Of Evidence:
Level II.
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