Comparative microbial genome analysis of lactobacilli

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dc.contributor.advisor O'Toole, Paul W. en
dc.contributor.advisor Claesson, Marcus en
dc.contributor.author Harris, Hugh
dc.date.accessioned 2018-05-11T13:25:13Z
dc.date.available 2018-05-11T13:25:13Z
dc.date.issued 2017
dc.date.submitted 2017
dc.identifier.citation Harris, H. 2017. Comparative microbial genome analysis of lactobacilli. PhD Thesis, University College Cork. en
dc.identifier.endpage 194 en
dc.identifier.uri http://hdl.handle.net/10468/6086
dc.description.abstract The genus Lactobacillus is a diverse group with a combined species count of over 200. They are the largest group within the lactic acid bacteria and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. Comparative Genomics is becoming increasingly important as a method of investigating the diversity of function and phylogeny of all microbial taxa, including Lactobacillus. In Chapter 1, I give an overview of relevant concepts in comparative microbial genomics, focusing on relevant literature for lactobacilli and related genera. In Chapter 2, we (Sun et al. 2015) carried out comparative genomic analyses of type strains of 213 Lactobacillus strains and associated genera, describing their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe a broad and diverse presence of CRISPR-Cas immune systems, host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species. In Chapter 3, we (Harris et al. 2017) we carried out comparative genomic analyses of the functional and phylogenomic diversity of 42 genomes of strains of L. salivarius. We found that multiple phylogenomic and non-phylogenomic methods used for reconstructing trees all converge on similar tree topologies, showing that different metrics largely agree on the evolutionary history of the species. The greatest genomic variation lies on the small plasmids, followed by the repA-type circular megaplasmid, with the chromosome varying least of all. Glycosyl hydrolases, bacteriocins and proteases vary considerably on all replicons while two exopolysaccharide clusters show a lot of variation on the chromosome. In Chapter 4, I focussed on the evolutionary rates of lactobacilli, divided into 10 phylogenetic sub-clades based on an ongoing study (Salvetti et al; in prep). Several multiple alignment strategies were compared, and I showed that conclusions about purifying versus directional selection across subclades was influenced by alignment strategy. In Chapter 5, I give a general discussion of how my thesis contributes to current literature, including future perspectives in the comparative genomics of lactobacilli. en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher University College Cork en
dc.rights © 2017, Hugh Harris. en
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/3.0/ en
dc.subject Comparative genomics en
dc.subject Lactobacillus en
dc.subject Lactobacilli en
dc.title Comparative microbial genome analysis of lactobacilli en
dc.type Doctoral thesis en
dc.type.qualificationlevel Doctoral en
dc.type.qualificationname PhD en
dc.internal.availability Full text available en
dc.check.info Not applicable en
dc.description.version Accepted Version
dc.contributor.funder Health Research Board en
dc.description.status Not peer reviewed en
dc.internal.school Microbiology en
dc.check.type No Embargo Required
dc.check.reason Not applicable en
dc.check.opt-out No en
dc.thesis.opt-out false
dc.check.embargoformat Embargo not applicable (If you have not submitted an e-thesis or do not want to request an embargo) en
ucc.workflow.supervisor pwotoole@ucc.ie
dc.internal.conferring Summer 2018 en


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