PreprintCited by 935Bacteriophages and microbial interactionsGut microbiota and healthViral gastroenteritis research and epidemiology

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The human gut virome: Inter-individual variation and dynamic response to diet

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Minot, Samuel, Sinha, Rohini, Chen, Jun, Li, Hongzhe, Keilbaugh, Sue A., Wu, Gary D., Lewis, James D., Bushman, Frederic D.·2011·Genome Research

DOI 10.1101/gr.122705.111PMC PMC3202279

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Abstract

Immense populations of viruses are present in the human gut and other body sites. Understanding the role of these populations (the human "virome") in health and disease requires a much deeper understanding of their composition and dynamics in the face of environmental perturbation. Here, we investigate viromes from human subjects on a controlled feeding regimen. Longitudinal fecal samples were analyzed by metagenomic sequencing of DNA from virus-like particles (VLP) and total microbial communities. Assembly of 336 Mb of VLP sequence yielded 7175 contigs, many identifiable as complete or partial bacteriophage genomes. Contigs were rich in viral functions required in lytic and lysogenic growth, as well as unexpected functions such as viral CRISPR arrays and genes for antibiotic resistance. The largest source of variance among virome samples was interpersonal variation. Parallel deep-sequencing analysis of bacterial populations showed covaration of the virome with the larger microbiome. The dietary intervention was associated with a change in the virome community to a new state, in which individuals on the same diet converged. Thus these data provide an overview of the composition of the human gut virome and associate virome structure with diet.

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Additional file 7 of Common antibiotics, azithromycin and amoxicillin, affect gut metagenomics within a household
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Authors: Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S. A., Wu, G. D., Lewis, J. D., & Bushman, F. D.
Affiliations: University of Pennsylvania (US)
ORCID: Minot, Samuel
Li, Hongzhe
Wu, Gary D.
Lewis, James D.
Bushman, Frederic D.
Venue: Genome Research
Publisher: Cold Spring Harbor Laboratory
Published: 2011-08-31
Volume: 21
Issue: 10
Pages: 1616-1625
ISSN: 1088-9051 (ISSN-L)
DOI: 10.1101/gr.122705.111
PMC: PMC3202279
OpenAlex: W2097146199
Cited by: 935
References: 58
Citations by year: 2026: 28 · 2025: 37 · 2024: 57 · 2023: 71 · 2022: 52 · 2021: 85 · 2020: 71 · 2019: 92 · 2018: 78 · 2017: 84 · 2016: 68 · 2015: 63 · 2014: 59 · 2013: 54 · 2012: 33
Type: posted content
Language: en
Open access: bronze
doi.org
Locations: Genome Research (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: Crohn's and Colitis Foundation of America
Pennsylvania Department of Health
University of Pennsylvania (UL1 RR024134)
Crohn's and Colitis Foundation
Georgia Clinical and Translational Science Alliance
National Institutes of Health (DK050306)
National Institute of Allergy and Infectious Diseases (R01AI039368, AI39368)
National Institute of Diabetes and Digestive and Kidney Diseases (UH2DK083981, P30DK050306)
National Center for Research Resources (UL1RR024134, S10RR024525)
Topics: Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Health Sciences › Medicine › Infectious Diseases › Viral gastroenteritis research and epidemiology
Keywords: gut virome, bacteriophages, virus-like particles, diet, dietary intervention, interindividual variability, gut microbiota, antibiotic resistance genes, viral metagenomics, viral community dynamics
MeSH terms: Adolescent, Adult, Bacteria, Bacteriophages, Feces, Genes, Bacterial, Genes, Viral, Humans, Repetitive Sequences, Nucleic Acid, RNA, Ribosomal, 16S, Virion, Open Reading Frames, Sequence Analysis, DNA, Diet, Fat-Restricted, Contig Mapping, Drug Resistance, Bacterial, Gastrointestinal Tract, Metagenome, Young Adult, High-Throughput Nucleotide Sequencing, Diet, High-Fat

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The human gut virome: Inter-individual variation and dynamic response to diet

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