Comparative and functional genomic analysis of dairy lactococci

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