Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve

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dc.contributor.authorBottacini, Francesca
dc.contributor.authorMorrissey, Ruth
dc.contributor.authorRoberts, Richard John
dc.contributor.authorJames, Kieran
dc.contributor.authorvan Breen, Justin
dc.contributor.authorEgan, Muireann
dc.contributor.authorLambert, Jolanda
dc.contributor.authorvan Limpt, Kees
dc.contributor.authorKnol, Jan
dc.contributor.authorO'Connell Motherway, Mary
dc.contributor.authorvan Sinderen, Douwe
dc.contributor.funderNutricia Research Foundation
dc.contributor.funderScience Foundation Ireland
dc.contributor.funderFederation of European Microbiological Societies
dc.contributor.funderHealth Research Board
dc.date.accessioned2018-06-15T11:47:19Z
dc.date.available2018-06-15T11:47:19Z
dc.date.issued2018
dc.description.abstractBifidobacterium breve represents one of the most abundant bifidobacterial species in the gastrointestinal tract of breast-fed infants, where their presence is believed to exert beneficial effects. In the present study whole genome sequencing, employing the PacBio Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. Our findings demonstrate that genes encoding Restriction/Modification (R/M) systems constitute a substantial part of the B. breve variable gene content (or variome). Using the methylome data generated by SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BS-seq) and comparative genome analysis, we were able to detect methylation recognition motifs and assign these to identified B. breve R/M systems, where in several cases such assignments were confirmed by restriction analysis. Furthermore, we show that R/M systems typically impose a very significant barrier to genetic accessibility of B. breve strains, and that cloning of a methyltransferase-encoding gene may overcome such a barrier, thus allowing future functional investigations of members of this species.en
dc.description.sponsorshipFederation of European Microbiological Societies (FEMS-RG-2016-0103); Health Research Board (513 PDTM/20011/9)en
dc.description.statusPeer reviewed
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBottacini, F., Morrissey, R., Roberts, Richard J., James, K., van Breen, J., Egan, M., Lambert, J., van Limpt, K., Knol, J., O'Connell Motherway, M. and van Sinderen, D. (2018) 'Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve', Nucleic Acids Research, 46(4), pp. 1860-1877. doi: 10.1093/nar/gkx1289en
dc.identifier.doi10.1093/nar/gkx1289
dc.identifier.endpage1877
dc.identifier.issn0305-1048
dc.identifier.issued4
dc.identifier.journaltitleNucleic Acids Researchen
dc.identifier.startpage1860
dc.identifier.urihttps://hdl.handle.net/10468/6353
dc.identifier.volume46
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/
dc.relation.urihttps://academic.oup.com/nar/article/46/4/1860/4780163
dc.rights© 2017, the Authors. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.subjectRestriction-modification systemsen
dc.subjectDNA-microarray dataen
dc.subjectGene-expressionen
dc.subjectMethyltransferasesen
dc.subjectUCC2003en
dc.subjectEnzymesen
dc.subjectEndonucleasesen
dc.subjectMutagenesisen
dc.subjectMicrobiotaen
dc.subjectAlgorithmen
dc.titleComparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breveen
dc.typeArticle (peer-reviewed)en
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