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. 2019 Jan;68(1):30-36.
doi: 10.1097/MPG.0000000000002140.

Enteric Virome and Bacterial Microbiota in Children With Ulcerative Colitis and Crohn Disease

Melissa A Fernandes  1 , Sofia G Verstraete  1 , Tung G Phan  2 , Xutao Deng  2 , Emily Stekol  1 , Brandon LaMere  3 , Susan V Lynch  3 , Melvin B Heyman  1 , Eric Delwart  2   4
Affiliations

Enteric Virome and Bacterial Microbiota in Children With Ulcerative Colitis and Crohn Disease

Melissa A Fernandes et al. J Pediatr Gastroenterol Nutr. 2019 Jan.

Abstract

Objectives: We examined the fecal virome and bacterial community composition of children with Crohn disease (CD), ulcerative colitis (UC), and healthy controls to test the hypothesis that unique patterns of viral organisms and/or presence of bacterial pathogens may be identified that could contribute to the pathogenesis of pediatric inflammatory bowel disease (IBD).

Methods: Fecal samples from 24 children (mean 12.2 years) with CD (n = 7) or UC (n = 5) and similar aged controls (n = 12) were processed to determine individual viromes. Viral sequences were identified through translated protein sequence similarity search. Bacterial microbiota were determined by sequencing of the V4 region of the 16S rRNA gene.

Results: Only a few human viruses were detected, so virome analyses focused on bacterial viruses. The relative abundance of Caudovirales was greater than that of Microviridae phages in both IBD and healthy controls. Caudovirales phages were more abundant in CD (mean 80.8%) than UC (48.8%) (P = 0.05) but not controls. The richness of viral strains in Microviridae but not Caudovirales was higher in controls than CD (P = 0.05) but not UC cases. No other measure of phage abundance, richness, or Shannon diversity showed significant difference between the 2 IBD and control groups. Bacterial microbiota analysis revealed that IBD diagnosis, albumin, hemoglobin, erythrocyte sedimentation rate, and probiotic supplementation correlated to the composition of gut bacterial microbiota.

Conclusions: Minor patterns in gut virome and bacterial community composition distinguish pediatric IBD patients from healthy controls. Probiotics are associated with bacterial microbiota composition. These exploratory results need confirmation in larger studies.

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Figures

Figure 1:
Figure 1:
Caudovirales relative-abundance is greater in CD compared with UC patients, and Microviridae richness is reduced in CD versus control populations. Box height represents the group mean and error bars signify +/− 1 standard deviation. See text for details.
Figure 2:
Figure 2:
Dominant bacterial family explains a large proportion of variance in pediatric fecal microbiota composition.
See this image and copyright information in PMC

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