Comparative and functional genomic analysis of dairy lactococci

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dc.contributor.advisor van Sinderen, Douwe en Kelleher, Philip 2017-08-24T10:27:04Z 2017 2017
dc.identifier.citation Kelleher, P. 2017. Comparative and functional genomic analysis of dairy lactococci. PhD Thesis, University College Cork. en
dc.identifier.endpage 340 en
dc.description.abstract Lactococcus 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.sponsorship Department of Agriculture, Food and the Marine (Food Institutional Research Measure (FIRM) Ref: 10/RD/TMFRC/704) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher University College Cork en
dc.rights © 2017, Philip Kelleher. en
dc.rights.uri en
dc.subject Lactococcus lactis en
dc.subject Comparative genomics en
dc.subject Prophage en
dc.subject Dairy en
dc.subject Methylome en
dc.subject Sequencing en
dc.subject Starter cultures en
dc.subject Plasmids en
dc.title Comparative and functional genomic analysis of dairy lactococci en
dc.type Doctoral thesis en
dc.type.qualificationlevel Doctoral en
dc.type.qualificationname PhD (Science) en
dc.internal.availability Full text available en
dc.description.version Accepted Version
dc.contributor.funder Department of Agriculture, Food and the Marine en
dc.description.status Not peer reviewed en Microbiology en
dc.check.reason This thesis is due for publication or the author is actively seeking to publish this material en
dc.check.opt-out Not applicable en
dc.thesis.opt-out false
dc.internal.conferring Summer 2017 en

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© 2017, Philip Kelleher. Except where otherwise noted, this item's license is described as © 2017, Philip Kelleher.
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