The human gut virome: Inter-individual variation and dynamic response to diet
Samuel S. Minot,Rohini Sinha,Jun Chen,Hongzhe Li,Sue A. Keilbaugh,Gary D. Wu,James D. Lewis,Frederic D. Bushman +7 more
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TLDR
An overview of the composition of the human gut virome is provided and the dietary intervention was associated with a change in the virome community to a new state, in which individuals on the same diet converged.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.read more
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The impact of the gut microbiota on human health: an integrative view.
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Christian Milani,Sabrina Duranti,Francesca Bottacini,Eoghan Casey,Francesca Turroni,Jennifer Mahony,Clara Belzer,Susana Delgado Palacio,Silvia Arboleya Montes,Leonardo Mancabelli,Gabriele Andrea Lugli,Juan M. Rodríguez,Lars Bode,Willem M. de Vos,Willem M. de Vos,Miguel Gueimonde,Abelardo Margolles,Douwe van Sinderen,Marco Ventura +18 more
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Jason M. Norman,Scott A. Handley,Megan T. Baldridge,Lindsay Droit,Catherine Y. Liu,Brian C. Keller,Amal Kambal,Cynthia L. Monaco,Guoyan Zhao,Phillip Fleshner,Thaddeus S. Stappenbeck,Dermot P.B. McGovern,Ali Keshavarzian,Ece Mutlu,Jenny Sauk,Dirk Gevers,Ramnik J. Xavier,Ramnik J. Xavier,David Wang,Miles Parkes,Herbert W. Virgin +20 more
TL;DR: It is concluded that the virome is a candidate for contributing to, or being a biomarker for, human inflammatory bowel disease and speculate that the enteric virome may play a role in other diseases.
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