Insights into the Human Virome Using CRISPR Spacers from Microbiomes
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...
Main Authors: | , , |
---|---|
Format: | Article |
Language: | English |
Published: |
MDPI AG
2018-09-01
|
Series: | Viruses |
Subjects: | |
Online Access: | http://www.mdpi.com/1999-4915/10/9/479 |
id |
doaj-688d52cfb1b94466b24d1f3c52ba9073 |
---|---|
record_format |
Article |
spelling |
doaj-688d52cfb1b94466b24d1f3c52ba90732020-11-24T22:57:24ZengMDPI AGViruses1999-49152018-09-0110947910.3390/v10090479v10090479Insights into the Human Virome Using CRISPR Spacers from MicrobiomesClaudio Hidalgo-Cantabrana0Rosemary Sanozky-Dawes1Rodolphe Barrangou2Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Campus BOX 7624, Raleigh, NC 27695, USADepartment of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Campus BOX 7624, Raleigh, NC 27695, USADepartment of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Campus BOX 7624, Raleigh, NC 27695, USADue 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.http://www.mdpi.com/1999-4915/10/9/479CRISPR-Cas systemsCRISPR spacersviromephagesmicrobiome |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Claudio Hidalgo-Cantabrana Rosemary Sanozky-Dawes Rodolphe Barrangou |
spellingShingle |
Claudio Hidalgo-Cantabrana Rosemary Sanozky-Dawes Rodolphe Barrangou Insights into the Human Virome Using CRISPR Spacers from Microbiomes Viruses CRISPR-Cas systems CRISPR spacers virome phages microbiome |
author_facet |
Claudio Hidalgo-Cantabrana Rosemary Sanozky-Dawes Rodolphe Barrangou |
author_sort |
Claudio Hidalgo-Cantabrana |
title |
Insights into the Human Virome Using CRISPR Spacers from Microbiomes |
title_short |
Insights into the Human Virome Using CRISPR Spacers from Microbiomes |
title_full |
Insights into the Human Virome Using CRISPR Spacers from Microbiomes |
title_fullStr |
Insights into the Human Virome Using CRISPR Spacers from Microbiomes |
title_full_unstemmed |
Insights into the Human Virome Using CRISPR Spacers from Microbiomes |
title_sort |
insights into the human virome using crispr spacers from microbiomes |
publisher |
MDPI AG |
series |
Viruses |
issn |
1999-4915 |
publishDate |
2018-09-01 |
description |
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. |
topic |
CRISPR-Cas systems CRISPR spacers virome phages microbiome |
url |
http://www.mdpi.com/1999-4915/10/9/479 |
work_keys_str_mv |
AT claudiohidalgocantabrana insightsintothehumanviromeusingcrisprspacersfrommicrobiomes AT rosemarysanozkydawes insightsintothehumanviromeusingcrisprspacersfrommicrobiomes AT rodolphebarrangou insightsintothehumanviromeusingcrisprspacersfrommicrobiomes |
_version_ |
1725650870034497536 |