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

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dc.contributor.author Bottacini, Francesca
dc.contributor.author Morrissey, Ruth
dc.contributor.author Roberts, Richard John
dc.contributor.author James, Kieran
dc.contributor.author van Breen, Justin
dc.contributor.author Egan, Muireann
dc.contributor.author Lambert, Jolanda
dc.contributor.author van Limpt, Kees
dc.contributor.author Knol, Jan
dc.contributor.author O'Connell Motherway, Mary
dc.contributor.author van Sinderen, Douwe
dc.date.accessioned 2018-06-15T11:47:19Z
dc.date.available 2018-06-15T11:47:19Z
dc.date.issued 2018
dc.identifier.citation Bottacini, 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/gkx1289 en
dc.identifier.volume 46
dc.identifier.issued 4
dc.identifier.startpage 1860
dc.identifier.endpage 1877
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10468/6353
dc.identifier.doi 10.1093/nar/gkx1289
dc.description.abstract Bifidobacterium 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.sponsorship Federation of European Microbiological Societies (FEMS-RG-2016-0103); Health Research Board (513 PDTM/20011/9) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Oxford University Press en
dc.relation.uri https://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.com en
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
dc.subject Restriction-modification systems en
dc.subject DNA-microarray data en
dc.subject Gene-expression en
dc.subject Methyltransferases en
dc.subject UCC2003 en
dc.subject Enzymes en
dc.subject Endonucleases en
dc.subject Mutagenesis en
dc.subject Microbiota en
dc.subject Algorithm en
dc.title Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Douwe Van Sinderen, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: d.vansinderen@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Nutricia Research Foundation
dc.contributor.funder Science Foundation Ireland
dc.contributor.funder Federation of European Microbiological Societies
dc.contributor.funder Health Research Board
dc.description.status Peer reviewed
dc.identifier.journaltitle Nucleic Acids Research en
dc.internal.IRISemailaddress d.vansinderen@ucc.ie en
dc.internal.IRISemailaddress kieran.james@ucc.ie en
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/


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© 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.com Except where otherwise noted, this item's license is described as © 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.com
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