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Enteric Virome and Bacterial Microbiota in Children With Ulcerative Colitis and Crohn Disease
Melissa A Fernandes1, Sofia G Verstraete1, Tung G Phan2
1Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco.
Insights
Pediatric inflammatory bowel disease (IBD) patients show minor differences in gut viruses and bacteria compared to healthy children. Probiotic use was linked to gut bacterial composition in this exploratory study.
Area of Science:
- Microbiology
- Gastroenterology
- Virology
Background:
- Pediatric inflammatory bowel disease (IBD), encompassing Crohn disease (CD) and ulcerative colitis (UC), is a complex condition.
- The role of the gut virome and bacterial microbiota in IBD pathogenesis remains incompletely understood.
Purpose of the Study:
- To investigate unique patterns in the fecal virome and bacterial community composition of children with IBD.
- To identify potential viral or bacterial contributors to the pathogenesis of pediatric IBD.
Main Methods:
- Analysis of fecal virome and bacterial microbiota in 24 children (7 CD, 5 UC, 12 controls).
- Viral sequences identified via translated protein similarity; bacterial microbiota analyzed using 16S rRNA gene sequencing.
Main Results:
- Virome analysis focused on bacterial viruses, with Caudovirales phages more abundant in CD patients than UC patients.
- Viral strain richness differed between controls and CD patients for Microviridae phages.
- Bacterial microbiota composition correlated with IBD diagnosis, albumin, hemoglobin, ESR, and probiotic use.
Conclusions:
- Minor differences in gut virome and bacterial communities distinguish pediatric IBD patients from healthy controls.
- Probiotic supplementation is associated with gut bacterial microbiota composition.
- Further validation in larger studies is required for these exploratory findings.
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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