Comparative and functional genomic analysis of dairy lactococci

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dc.check.opt-outNot applicableen
dc.check.reasonThis thesis is due for publication or the author is actively seeking to publish this materialen
dc.contributor.advisorvan Sinderen, Douween
dc.contributor.authorKelleher, Philip
dc.contributor.funderDepartment of Agriculture, Food and the Marineen
dc.date.accessioned2017-08-24T10:27:04Z
dc.date.issued2017
dc.date.submitted2017
dc.description.abstractLactococcus lactis has been exploited for thousands of years for the production of fermented dairy products, and from an economic perspective has become one of the most valuable bacteria. L. lactis is used predominantly as a starter culture for the production of various cheeses. The constant threat of (bacterio)phage infection combined with consumerdriven diversification of product ranges have created an increased need to improve technologies for the rational selection of novel starter culture blends. Whole genome sequencing, spurred on by recent advances in next-generation sequencing platforms, is a promising approach to facilitate the rapid identification and selection of such strains based on gene-trait matching. In this thesis the most up-to-date sequencing methodologies were applied to sequence sixteen L. lactis isolates to facilitate an in-depth comparative and functional genome analysis of the taxon with particular emphasis placed on dairy traits. The research presented in this thesis has significantly advanced our understanding of L. lactis in several ways. Firstly, the genomes of sixteen lactococcal dairy strains were sequenced to completion, doubling the number of fully sequenced L. lactis genomes available from the National Centre for Biotechnology Information. This has significantly expanded the number of complete lactococcal genomes available for comparative and functional genome analyses, while it has thoroughly scrutinized chromosomal versus plasmid diversity, including the elucidation of both the pan/core genome and the pan-plasmidome. Secondly, the identification of the first lactococcal megaplasmids and undertaking of the first methylome analysis of the L. lactis taxon has greatly increased our understanding of hostencoded phage defence systems, with particular emphasis on the role of restriction modification systems. Finally, the frequency of lactococcal prophages within the chromosomes of L. lactis has been thoroughly investigated concomitantly with the risk of prophage excision. Altogether these yield a complete overview of the genetic diversity of this taxon.en
dc.description.sponsorshipDepartment of Agriculture, Food and the Marine (Food Institutional Research Measure (FIRM) Ref: 10/RD/TMFRC/704)en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Version
dc.format.mimetypeapplication/pdfen
dc.identifier.citationKelleher, P. 2017. Comparative and functional genomic analysis of dairy lactococci. PhD Thesis, University College Cork.en
dc.identifier.endpage340en
dc.identifier.urihttps://hdl.handle.net/10468/4522
dc.language.isoenen
dc.publisherUniversity College Corken
dc.rights© 2017, Philip Kelleher.en
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/en
dc.subjectLactococcus lactisen
dc.subjectComparative genomicsen
dc.subjectProphageen
dc.subjectDairyen
dc.subjectMethylomeen
dc.subjectSequencingen
dc.subjectStarter culturesen
dc.subjectPlasmidsen
dc.thesis.opt-outfalse
dc.titleComparative and functional genomic analysis of dairy lactococcien
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD (Science)en
ucc.workflow.supervisord.vansinderen@ucc.ie
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