Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome

13 Pág.

Detalles Bibliográficos
Autores: López-Beltrán, Adrián, Botelho, João, Iranzo, Jaime
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/369561
Acceso en línea:http://hdl.handle.net/10261/369561
https://api.elsevier.com/content/abstract/scopus_id/85201029316
Access Level:acceso abierto
Palabra clave:CRISPR
Gut microbiome
Lysogeny
Metagenomics
Microbial community
Microbial defense system
Virome
Virus–bacteria interaction
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spelling Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiomeLópez-Beltrán, AdriánBotelho, JoãoIranzo, JaimeCRISPRGut microbiomeLysogenyMetagenomicsMicrobial communityMicrobial defense systemViromeVirus–bacteria interaction13 Pág.Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals to study how the interplay of genetic parasites and CRISPR-Cas immunity reflects on the dynamics and composition of the human gut microbiome. Based on the coordinated study of 80 000 CRISPR-Cas loci and their targets, we show that CRISPR-Cas immunity effectively modulates bacteriophage abundances in the gut. Acquisition of CRISPR-Cas immunity typically leads to a decrease in the abundance of lytic phages but does not necessarily cause their complete disappearance. Much smaller effects are observed for lysogenic phages and plasmids. Conversely, phage-CRISPR interactions shape bacterial microdiversity by producing weak selective sweeps that benefit immune host lineages. We also show that distal (and chronologically older) regions of CRISPR arrays are enriched in spacers that are potentially functional and target crass-like phages and local prophages. This suggests that exposure to reactivated prophages and other endemic viruses is a major selective pressure in the gut microbiome that drives the maintenance of long-lasting immune memory.A.L-B. is supported by the Agencia Estatal de Investigación of Spain (Grant No. PRE2020-092935). J.B. is supported by the Maria Zambrano grant of the Spanish Ministry of Universities (Grant No. UP2021-035), and the Severo Ochoa Program for Centres of Excellence in R&D of the Agencia Estatal de Investigación of Spain (Grant No. CEX2020-000999-S (2022–2025) to the CBGP). J.I is supported by the Ramón y Cajal Programme of the Spanish Ministry of Science (Grant No. RYC-2017–22524); the Agencia Estatal de Investigación of Spain (Grant No. PID2019-106618GA-I00), the Severo Ochoa Programme for Centres of Excellence in R&D of the Agencia Estatal de Investigación of Spain (Grant No. SEV-2016–0672 (2017–2021) to the CBGP); and the Comunidad de Madrid (through the call Research Grants for Young Investigators from Universidad Politécnica de Madrid, Grant No. M190020074JIIS).Peer reviewedOxford University PressAgencia Estatal de Investigación (España)Ministerio de Universidades (España)Ministerio de Ciencia e Innovación (España)Comunidad de MadridLópez-Beltrán, Adrián [0000-0002-0111-0741]Iranzo, Jaime [0000-0002-4538-7726]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202420242024info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/369561https://api.elsevier.com/content/abstract/scopus_id/85201029316reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-106618GA-I00Centro de Biotecnología y Genómica de Plantas (CBGP)https://doi.org/10.1093/ismejo/wrae134Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3695612026-05-22T06:33:51Z
dc.title.none.fl_str_mv Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome
title Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome
spellingShingle Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome
López-Beltrán, Adrián
CRISPR
Gut microbiome
Lysogeny
Metagenomics
Microbial community
Microbial defense system
Virome
Virus–bacteria interaction
title_short Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome
title_full Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome
title_fullStr Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome
title_full_unstemmed Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome
title_sort Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome
dc.creator.none.fl_str_mv López-Beltrán, Adrián
Botelho, João
Iranzo, Jaime
author López-Beltrán, Adrián
author_facet López-Beltrán, Adrián
Botelho, João
Iranzo, Jaime
author_role author
author2 Botelho, João
Iranzo, Jaime
author2_role author
author
dc.contributor.none.fl_str_mv Agencia Estatal de Investigación (España)
Ministerio de Universidades (España)
Ministerio de Ciencia e Innovación (España)
Comunidad de Madrid
López-Beltrán, Adrián [0000-0002-0111-0741]
Iranzo, Jaime [0000-0002-4538-7726]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv CRISPR
Gut microbiome
Lysogeny
Metagenomics
Microbial community
Microbial defense system
Virome
Virus–bacteria interaction
topic CRISPR
Gut microbiome
Lysogeny
Metagenomics
Microbial community
Microbial defense system
Virome
Virus–bacteria interaction
description 13 Pág.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/369561
https://api.elsevier.com/content/abstract/scopus_id/85201029316
url http://hdl.handle.net/10261/369561
https://api.elsevier.com/content/abstract/scopus_id/85201029316
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-106618GA-I00
Centro de Biotecnología y Genómica de Plantas (CBGP)
https://doi.org/10.1093/ismejo/wrae134
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,198674

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