Stability of the human gut virome and effect of gluten-free diet
Garmaeva, Sanzhima; Gulyaeva, Anastasia; Sinha, Trishla; Shkoporov, Andrey N; Clooney, Adam G; Stockdale, Stephen R; Spreckels, Johanne E; Sutton, Thomas D S; Draper, Lorraine A; Dutilh, Bas E; Wijmenga, Cisca; Kurilshikov, Alexander; Fu, Jingyuan; Hill, Colin; Zhernakova, Alexandra
(2021) Cell Reports, volume 35, issue 7, pp. 1 - 21
(Article)
Abstract
The human gut microbiome consists of bacteria, archaea, eukaryotes, and viruses. The gut viruses are relatively underexplored. Here, we longitudinally analyzed the gut virome composition in 11 healthy adults: its stability, variation, and the effect of a gluten-free diet. Using viral enrichment and a de novo assembly-based approach, we demonstrate
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the quantitative dynamics of the gut virome, including dsDNA, ssDNA, dsRNA, and ssRNA viruses. We observe highly divergent individual viral communities, carrying on an average 2,143 viral genomes, 13.1% of which were present at all 3 time points. In contrast to previous reports, the Siphoviridae family dominates over Microviridae in studied individual viromes. We also show individual viromes to be stable at the family level but to vary substantially at the genera and species levels. Finally, we demonstrate that lower initial diversity of the human gut virome leads to a more pronounced effect of the dietary intervention on its composition.
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Keywords: RNA viruses, bacteriophage, diversity, ecosystem resilience, gluten, gut, microbiome, viral-like particles, virome, General Biochemistry,Genetics and Molecular Biology
ISSN: 2211-1247
Publisher: Elsevier Saunders
Note: Funding Information: We thank all of the participants for their collaboration, Gosia Trynka for initiating the GFD study, and Kate McIntyre for editing the manuscript. We thank Karen M. Daly and Olivia Connolly for the help with the extraction of VLP DNA/RNA from the samples and theoretical support in genomic library preparation. We thank Dianne H. Jansen for help with the extraction of total community DNA from the samples and Stella Ilchenko for help with the graphic design of the figures. S.G. and T.S. hold scholarships from the Graduate School of Medical Sciences, University of Groningen and the Junior Scientific Masterclass, University of Groningen , respectively. A.Z. holds a NWO - Dutch Research Council (NWO Dutch: Nederlandse Organisatie voor Wetenschappelijk Onderzoek) Vidi grant ( NWO-VIDI 016.178.056 ), an ERC starting grant (ERC Starting Grant 715772 ), and an NWO Gravitation grant Exposome-NL ( 024.004.017 ). J.F. is supported by the ERC Consolidator grant 101001678 , NWO-VICI grant VI.C.202.022 , NWO-VIDI 864.13.013, and the Netherlands Organ-on-Chip Initiative, an NWO Gravitation project 024.003.001. This work is also supported by a CardioVasculair Onderzoek Nederland grant ( CVON 2018–27 ) to A.Z. and J.F. C.W. is supported by an ERC advanced grant ( FP/2007–2013/ERC grant 2012–322698 ), an NWO Spinoza prize ( NWO SPI 92–266 ), and the NWO Gravitation Netherlands Organ-on-Chip Initiative ( 024.003.001 ). B.E.D. is supported by NWO Vidi grant 864.14.004 and ERC Consolidator grant 865694: DiversiPHI . A.N.S. holds SFI-HRB-Wellcome Trust Research Career Development Fellowship #220646/Z/20/Z. A.N.S., A.G.C., S.R.S., T.D.S.S., L.A.D., and C.H. are supported by Science Foundation Ireland under grant number SFI/12/RC/2273 . Funding Information: We thank all of the participants for their collaboration, Gosia Trynka for initiating the GFD study, and Kate McIntyre for editing the manuscript. We thank Karen M. Daly and Olivia Connolly for the help with the extraction of VLP DNA/RNA from the samples and theoretical support in genomic library preparation. We thank Dianne H. Jansen for help with the extraction of total community DNA from the samples and Stella Ilchenko for help with the graphic design of the figures. S.G. and T.S. hold scholarships from the Graduate School of Medical Sciences, University of Groningen and the Junior Scientific Masterclass, University of Groningen, respectively. A.Z. holds a NWO - Dutch Research Council (NWO Dutch: Nederlandse Organisatie voor Wetenschappelijk Onderzoek) Vidi grant (NWO-VIDI 016.178.056), an ERC starting grant (ERC Starting Grant 715772), and an NWO Gravitation grant Exposome-NL (024.004.017). J.F. is supported by the ERC Consolidator grant 101001678, NWO-VICI grant VI.C.202.022, NWO-VIDI 864.13.013, and the Netherlands Organ-on-Chip Initiative, an NWO Gravitation project 024.003.001. This work is also supported by a CardioVasculair Onderzoek Nederland grant (CVON 2018?27) to A.Z. and J.F. C.W. is supported by an ERC advanced grant (FP/2007?2013/ERC grant 2012?322698), an NWO Spinoza prize (NWO SPI 92?266), and the NWO Gravitation Netherlands Organ-on-Chip Initiative (024.003.001). B.E.D. is supported by NWO Vidi grant 864.14.004 and ERC Consolidator grant 865694: DiversiPHI. A.N.S. holds SFI-HRB-Wellcome Trust Research Career Development Fellowship #220646/Z/20/Z. A.N.S. A.G.C. S.R.S. T.D.S.S. L.A.D. and C.H. are supported by Science Foundation Ireland under grant number SFI/12/RC/2273. A.Z. C.W. and C.H. conceptualized and managed the study. S.G. A.G. T.S. and J.E.S. generated the data. A.N.S. L.A.D. and C.H. provided technical and theoretical support in the data generation. S.G. and A.G. analyzed the data. A.N.S. A.G.C. S.R.S. T.D.S.S. L.A.D. B.E.D. A.K. and C.H. provided technical and theoretical expertise in analyzing the data. S.G. A.G. T.S. and A.Z. drafted the manuscript. S.G. A.G. T.S. A.N.S. A.G.C. S.R.S. J.E.S. T.D.S.S. L.A.D. B.E.D. C.W. A.K. J.F. C.H. and A.Z. reviewed and edited the manuscript. The authors declare no competing interests. Publisher Copyright: © 2021 The Author(s)
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