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Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project

2024-08-12Clinical study Open access
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dc.contributor.authorVale, Filipa
dc.contributor.authorHpGP Research Network
dc.contributor.authorRoberts, Richard
dc.contributor.authorKobayashi, Ichizo
dc.contributor.authorCamargo, Constanza
dc.contributor.authorRabkin, Charles
dc.contributor.authorHpGP Research Network
dc.date.accessioned2025-04-02T14:43:11Z
dc.date.available2025-04-02T14:43:11Z
dc.date.issued2024-08-12
dc.descriptionHpGP Research Network Collaborators: Mónica Oleastro, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
dc.description.abstractProphages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (HpGP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the HpGP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the HpGP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages.por
dc.description.sponsorshipIntramural Research Program from the US National Cancer Institute (NCI), National Institutes of Health (NIH) FCT: PTDC/BTM-TEC/3238/2020 and CPCA-IAC/AV/478719/2022, FCT projects UIDB/04138/ 2020, UIDP/04138/2020, and UIDB/04046/2020
dc.identifier.citationGut Microbes. 2024 Jan-Dec;16(1):2379440. doi: 10.1080/19490976.2024.2379440. Epub 2024 Aug 12
dc.identifier.issn1949-0976
dc.identifier.pmid39132840
dc.identifier.urihttp://hdl.handle.net/10400.18/10469
dc.language.isoeng
dc.peerreviewedyes
dc.publisherTaylor & Francis Group
dc.relationPTDC/BTM-TEC/3238/2020
dc.relationResearch Institute for Medicines
dc.relationBiosystems and Integrative Sciences Institute
dc.relation.hasversionhttps://www.tandfonline.com/doi/full/10.1080/19490976.2024.2379440#d1e1801
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.subjectHelicobacter pylori
dc.subjectH. pylori
dc.subjectProphages
dc.subjectGenomics
dc.subjectBacterial Adaptation
dc.subjectHpGP
dc.subjectGenome Rearrangement
dc.subjectMobile Elements
dc.subjectPhage Cycle
dc.subjectInfecções Gastrointestinais
dc.titleGene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Projectpor
dc.typeclinical study
dspace.entity.typePublication
oaire.awardTitleResearch Institute for Medicines
oaire.awardTitleBiosystems and Integrative Sciences Institute
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBTM-TEC%2F3238%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F04138%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F04046%2F2020/PT
oaire.citation.issue1
oaire.citation.startPage2379440
oaire.citation.titleGut Microbes
oaire.citation.volume16
oaire.fundingStream3599-PPCDT
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream6817 - DCRRNI ID
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
relation.isProjectOfPublication896b5212-8f95-4c91-bdf9-070f1654cb5e
relation.isProjectOfPublicationfe981d64-0f63-4bb3-9872-613e531ce02d
relation.isProjectOfPublicationdc433369-36fd-4935-bd52-c56aa49c72e1
relation.isProjectOfPublication.latestForDiscovery896b5212-8f95-4c91-bdf9-070f1654cb5e

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