Comparative microbial genome analysis of lactobacilli

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Harris, Hugh
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University College Cork
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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.
Comparative genomics , Lactobacillus , Lactobacilli
Harris, H. 2017. Comparative microbial genome analysis of lactobacilli. PhD Thesis, University College Cork.
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