Stability of the human gut virome and effect of gluten-free diet
Sanzhima Garmaeva,
Anastasia Gulyaeva,
Trishla Sinha,
Andrey N. Shkoporov,
Adam G. Clooney,
Stephen R. Stockdale,
Johanne E. Spreckels,
Thomas D.S. Sutton,
Lorraine A. Draper,
Bas E. Dutilh,
Cisca Wijmenga,
Alexander Kurilshikov,
Jingyuan Fu,
Colin Hill,
Alexandra Zhernakova
Affiliations
Sanzhima Garmaeva
Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
Anastasia Gulyaeva
Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
Trishla Sinha
Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
Andrey N. Shkoporov
APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
Adam G. Clooney
APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
Stephen R. Stockdale
APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
Johanne E. Spreckels
Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
Thomas D.S. Sutton
APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
Lorraine A. Draper
APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
Bas E. Dutilh
Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht 3584 CH, the Netherlands
Cisca Wijmenga
Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
Alexander Kurilshikov
Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
Jingyuan Fu
Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
Colin Hill
APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
Alexandra Zhernakova
Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Corresponding author
Summary: 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 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.
