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Insights into the Human Virome Using CRISPR Spacers from Microbiomes

Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Campus BOX 7624, Raleigh, NC 27695, USA
Author to whom correspondence should be addressed.
Viruses 2018, 10(9), 479;
Received: 8 August 2018 / Revised: 31 August 2018 / Accepted: 3 September 2018 / Published: 7 September 2018
(This article belongs to the Special Issue Phage-Host Interactions)
Due to recent advances in next-generation sequencing over the past decade, our understanding of the human microbiome and its relationship to health and disease has increased dramatically. Yet, our insights into the human virome, and its interplay with important microbes that impact human health, is relatively limited. Prokaryotic and eukaryotic viruses are present throughout the human body, comprising a large and diverse population which influences several niches and impacts our health at various body sites. The presence of prokaryotic viruses like phages, has been documented at many different body sites, with the human gut being the richest ecological niche. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated proteins constitute the adaptive immune system of bacteria, which prevents attack by invasive nucleic acid. CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing. View Full-Text
Keywords: CRISPR-Cas systems; CRISPR spacers; virome; phages; microbiome CRISPR-Cas systems; CRISPR spacers; virome; phages; microbiome
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MDPI and ACS Style

Hidalgo-Cantabrana, C.; Sanozky-Dawes, R.; Barrangou, R. Insights into the Human Virome Using CRISPR Spacers from Microbiomes. Viruses 2018, 10, 479.

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