Disease-specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

By J. Norman, S. Handley, Megan T. Baldridge, L. Droit, Catherine Y. Liu, B. Keller, Amal Kambal, Cynthia L. Monaco, Guoyan Zhao, P. Fleshner and 10 more. Cell, 2015

1,135 citations recorded by the source corpus.

SUMMARY Decreases in the diversity of enteric bacterial populations are observed in patients with Crohn’s disease (CD) and ulcerative colitis (UC). Less is known about the virome in these diseases. We show that the enteric virome is abnormal in CD and UC patients. In-depth analysis of preparations enriched for free virions in the intestine revealed that CD and UC were associated with a significant expansion of Caudovirales bacteriophages. The viromes of CD and UC patients were disease- and cohort-specific. Importantly, it did not appear that expansion and diversification of the enteric virome was secondary to changes in bacterial populations. These data support a model in which changes in the virome may contribute to intestinal inflammation and bacterial dysbiosis. We conclude that the virome is a candidate for contributing to, or being a biomarker for, human inflammatory bowel disease and speculate that the enteric virome may play a role in other diseases.

Subfields: Accounting, Economics and Econometrics

View Paper: https://www.semanticscholar.org/paper/ea816c30e0df51a631c56379404b292501a4ca82

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1. Xiaohui S. Xie

Citations in the corpus

• Mechanisms and consequences of intestinal dysbiosis (2017, background): “Bacteriophage richness, as defined by the number of taxa per sample, was increased in these diseases, whereas bacterial richness was concomitantly decreased [174].”
• Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study (2017, background): “Studies looking at the effects of perturbations in the gut from Crohn’s disease in humans [73] and from diet in mice [74] show this response with increased diversity of phage communities paired with decreased diversity of the bacterial community.”
• Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease (2015, background): “A recent report proposed that tailed phages (Caudovirales) were enriched in viral concentrates from stool of IBD patients (Norman et al., 2015).”
• The human gut virome is highly diverse, stable and individual-specific (2019, background): “Illustrating this 329 point, many previous studies only looked at a fraction of identifiable sequences (14-30%), 330 effectively ignoring the rest of the virome (D’arc et al., 2018; Norman et al., 2015).”
• Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights (2016, background): “More recently, shotgun metagenomics [19] provided expanded resolution to the level of microbial species [20-22] and strain [23], to the fungal and viral kingdoms [24], and to the level of individual genes across the metagenome [25,26].”
• Identifying viruses from metagenomic data using deep learning (2020, methodology): “sequenced virome in the human gut sample from IBD patients using Illumina sequencing technology [1].”
• GENETICS AND PATHOGENESIS OF INFLAMMATORY BOWEL DISEASE (2016, background): “The virome appears to be CD and UC disease and cohort specific, and importantly, the changes were not associated with bacterial population changes (98).”
• VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences (2020, background): “In human systems, viruses have been implicated in contributing to dysbiosis that can lead to various diseases, such as inflammatory bowel diseases, or even have a symbiotic role with the immune system [11 – 13].”
• Bacteriophages of the Human Gut: The "Known Unknown" of the Microbiome. (2019, methodology): “To obtain more concentrated samples of VLPs, ultracentrifugation at 120,000 g, precipitation with polyethylene glycol and NaCl or ZnCl2, or tangential flow filtration can be employed (Castro-Mejı́a et al., 2015).”
• VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data (2017, background): “For example, viruses in the human gut microbiome have been found to profoundly influence inflammatory bowel disease and severe acute malnutrition [3, 4].”