The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific
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Abstract
The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterized, and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. We performed longitudinal metagenomic analysis of fecal viruses in healthy adults that reveal high temporal stability, individual specificity, and correlation with the bacterial microbiome. Using a database-independent approach that uses most of the sequencing data, we uncovered the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of viral genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella, and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.
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Results obtained from the small number of studies performed using shotgun metagenomic sequencing suggest that the oral virome may be as significant in disease pathogenesis as the oral bacteriome.
“Results obtained from the small number of studies performed using shotgun metagenomic sequencing suggest that the oral virome may be as significant in disease pathogenesis as the oral bacteriome.87, 88”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [87]
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- Authors
- Shkoporov, A. N., Clooney, A. G., Sutton, T. D. S., Ryan, F. J., Daly, K. M., Nolan, J. A., McDonnell, S. A., Khokhlova, E. V., Draper, L. A., Forde, A., Guerin, E., Velayudhan, V., Ross, R. P., & Hill, C.
- Affiliations
- University College Cork (IE)
- Corresponding author
- Shkoporov, Andrey N.
- Hill, Colin
- ORCID
- Venue
- Cell Host & Microbe
- Publisher
- Elsevier BV
- Published
- 2019-10
- Volume
- 26
- Issue
- 4
- Pages
- 527-541.e5
- ISSN
- 1931-3128 (ISSN-L)
- OpenAlex
- W2979358136
- Cited by
- 737
- References
- 78
- Citations by year
- 2026: 82 · 2025: 113 · 2024: 113 · 2023: 107 · 2022: 111 · 2021: 135 · 2020: 65 · 2019: 7
- FWCI
- 51.61
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell Host & Microbe (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- European Regional Development Fund
- Science Foundation Ireland
- Janssen Biotech
- Topics
- Physical Sciences › Environmental Science › Ecology › 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, viral metagenomics, temporal stability, crAss-like phages, Microviridae, gut microbiota, Bacteroides, Prevotella, Faecalibacterium, viral community structure
- MeSH terms
- Gastrointestinal Microbiome, Faecalibacterium, Bacteroides, Humans, Longitudinal Studies, Microviridae, Prevotella, Viral Load, Metagenome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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