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The human gut virome is highly diverse, stable and individual-specific

View ORCID ProfileAndrey N. Shkoporov, View ORCID ProfileAdam G. Clooney, View ORCID ProfileThomas D.S. Sutton, View ORCID ProfileFeargal J. Ryan, View ORCID ProfileKaren M. Daly, James A. Nolan, View ORCID ProfileSiobhan A. McDonnell, Ekaterina V. Khokhlova, View ORCID ProfileLorraine A. Draper, View ORCID ProfileAmanda Forde, View ORCID ProfileEmma Guerin, Vimalkumar Velayudhan, R. Paul Ross, View ORCID ProfileColin Hill
doi: https://doi.org/10.1101/657528
Andrey N. Shkoporov
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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  • ORCID record for Andrey N. Shkoporov
  • For correspondence: andrey.shkoporov@ucc.ie c.hill@ucc.ie
Adam G. Clooney
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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  • ORCID record for Adam G. Clooney
Thomas D.S. Sutton
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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  • ORCID record for Thomas D.S. Sutton
Feargal J. Ryan
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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  • ORCID record for Feargal J. Ryan
Karen M. Daly
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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  • ORCID record for Karen M. Daly
James A. Nolan
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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Siobhan A. McDonnell
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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  • ORCID record for Siobhan A. McDonnell
Ekaterina V. Khokhlova
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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Lorraine A. Draper
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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  • ORCID record for Lorraine A. Draper
Amanda Forde
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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  • ORCID record for Amanda Forde
Emma Guerin
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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  • ORCID record for Emma Guerin
Vimalkumar Velayudhan
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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R. Paul Ross
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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Colin Hill
APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12 YT20, Ireland
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  • ORCID record for Colin Hill
  • For correspondence: andrey.shkoporov@ucc.ie c.hill@ucc.ie
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Summary

The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterised and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. Here we performed a longitudinal focused metagenomic study of faecal bacteriophage populations in healthy adults. Our results reveal high temporal stability and individual specificity of bacteriophage consortia which correlates with the bacterial microbiome. We report the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of bacteriophage 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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 03, 2019.
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The human gut virome is highly diverse, stable and individual-specific
Andrey N. Shkoporov, Adam G. Clooney, Thomas D.S. Sutton, Feargal J. Ryan, Karen M. Daly, James A. Nolan, Siobhan A. McDonnell, Ekaterina V. Khokhlova, Lorraine A. Draper, Amanda Forde, Emma Guerin, Vimalkumar Velayudhan, R. Paul Ross, Colin Hill
bioRxiv 657528; doi: https://doi.org/10.1101/657528
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The human gut virome is highly diverse, stable and individual-specific
Andrey N. Shkoporov, Adam G. Clooney, Thomas D.S. Sutton, Feargal J. Ryan, Karen M. Daly, James A. Nolan, Siobhan A. McDonnell, Ekaterina V. Khokhlova, Lorraine A. Draper, Amanda Forde, Emma Guerin, Vimalkumar Velayudhan, R. Paul Ross, Colin Hill
bioRxiv 657528; doi: https://doi.org/10.1101/657528

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