Microbial alteration of small bowel stoma effluents and colonic feces in infants with short bowel syndrome

Abstract

Background and aim: Studies about differences in microbial communities between the small intestine and colon in infants with short bowel syndrome (SBS) are rare. We aimed to characterize the bacterial diversity of small bowel stoma effluents and feces of SBS infants.

Methods: Seven SBS infants were enrolled in this study and provided two samples (one from the stoma and the other from the anus) each. Eleven age-matched healthy controls were recruited to provide one fecal sample each. 16S rRNA gene MiSeq sequencing was conducted to characterize the microbiota diversity and composition.

Results: The bacterial diversity of the stoma effluents was significantly higher than that in the feces of SBS infants. Proteobacteria dominated in both the stoma effluents and colonic. Acinetobacter (P = 0.004), Klebsiella (P = 0.015), Citrobacter (P = 0.019), and Lactobacillus (P = 0.030) were more abundant in stoma effluents compared to feces of SBS patients, while Bacteroidetes, Bifidobacterium and Veillonella were less abundant in stoma effluents. Significantly higher levels of Proteobacteria, Enterococcus and lower levels of Blautia, Collinsella, Faecalibacterium, Veillonella were present in the fecal samples of SBS patients than those in the healthy controls. Kyoto Encyclopedia of Genes and Genomes pathways related to metabolism and membrane function were depleted in SBS patients.

Conclusions: The predominant intestinal bacterial groups were different in SBS children before and after the fistula closure. Fecal samples of SBS patients featured overabundant Proteobacteria and less SCFA producing bacteria. Depleted functional profiles of the microbiome were found in fecal samples of SBS patients.

Level of evidence: III.

Keywords: Gut microbiota; Short bowel syndrome; Small bowel stoma effluents.