Diversity of human-associated bifidobacterial prophage sequences

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dc.contributor.authorBuckley, Darrenen
dc.contributor.authorOdamaki, Toshitakaen
dc.contributor.authorXiao, Jin-zhongen
dc.contributor.authorMahony, Jenniferen
dc.contributor.authorvan Sinderen, Douween
dc.contributor.authorBottacini, Francescaen
dc.contributor.funderScience Foundation Irelanden
dc.date.accessioned2023-11-21T10:18:17Z
dc.date.available2023-11-21T10:18:17Z
dc.date.issued2021en
dc.description.abstractMembers of Bifidobacterium play an important role in the development of the immature gut and are associated with positive long-term health outcomes for their human host. It has previously been shown that intestinal bacteriophages are detected within hours of birth, and that induced prophages constitute a significant source of such gut phages. The gut phageome can be vertically transmitted from mother to newborn and is believed to exert considerable selective pressure on target prokaryotic hosts affecting abundance levels, microbiota composition, and host characteristics. The objective of the current study was to investigate prophage-like elements and predicted CRISPR-Cas viral immune systems present in publicly available, human-associated Bifidobacterium genomes. Analysis of 585 fully sequenced bifidobacterial genomes identified 480 prophage-like elements with an occurrence of 0.82 prophages per genome. Interestingly, we also detected the presence of very similar bifidobacterial prophages and corresponding CRISPR spacers across different strains and species, thus providing an initial exploration of the human-associated bifidobacterial phageome. Our analyses show that closely related and likely functional prophages are commonly present across four different species of human-associated Bifidobacterium. Further comparative analysis of the CRISPR-Cas spacer arrays against the predicted prophages provided evidence of historical interactions between prophages and different strains at an intra- and inter-species level. Clear evidence of CRISPR-Cas acquired immunity against infection by bifidobacterial prophages across several bifidobacterial strains and species was obtained. Notably, a spacer representing a putative major capsid head protein was found on different genomes representing multiple strains across B. adolescentis, B. breve, and B. bifidum, suggesting that this gene is a preferred target to provide bifidobacterial phage immunity.en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid2559en
dc.identifier.citationBuckley, D., Odamaki, T., Xiao, J., Mahony, J., Van Sinderen, D. and Bottacini, F. (2021) ‘Diversity of human-associated bifidobacterial prophage sequences’, Microorganisms, 9(12), 2559 (16pp). doi: 10.3390/microorganisms9122559en
dc.identifier.doi10.3390/microorganisms9122559en
dc.identifier.endpage16en
dc.identifier.issn2076-2607en
dc.identifier.issued12en
dc.identifier.journaltitleMicroorganismsen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/15244
dc.identifier.volume9en
dc.language.isoenen
dc.publisherMDPIen
dc.relation.ispartofMicroorganismsen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/en
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Starting Investigator Research Grant (SIRG)/15/SIRG/3430/IE/Phage-host interactome of the dairy bacterium Streptococcus thermophilus (PHIST)/en
dc.rights© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectGut microbiotaen
dc.subjectBifidobacteriumen
dc.subjectPhageomeen
dc.subjectBifidobacteriaen
dc.subjectProphageen
dc.subjectCRISPR-Casen
dc.titleDiversity of human-associated bifidobacterial prophage sequencesen
dc.typeArticle (peer-reviewed)en
dc.typejournal-articleen
oaire.citation.issue12en
oaire.citation.volume9en
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