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An investigation into antimicrobial production in the Lactobacillus genus and the fish microbiome
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Date
2019
Authors
Collins, Fergus W. J.
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Publisher
University College Cork
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Abstract
This thesis outlines a study of the identification and characterisation of antimicrobials from two primary sources; the Lactobacillus genus and the microbiome of fish. Through the incorporation of a wide variety of techniques, this study successfully demonstrates how a variety of methods can be used for the identification and production of novel antimicrobials. Chapter 1 gives an overview of the variety of different antimicrobials which can be produced by the lactic acid bacteria (LAB) which can play an important role in a number of processes, such as the preservation of fermented foods. These antimicrobials can vary from organic acids, such as lactic and acetic acid, to antimicrobial peptides known as ‘bacteriocins’. Chapter 2 outlines the identification of a novel bacteriocin known as ‘formicin’ through traditional colony isolation and screening methods. Formicin was identified from Bacillus paralicheniformis APC1576, an antimicrobial producing strain isolated from the intestine of a fish. Using a combination of mass spectrometry and genomic screening, formicin was found to be a two-peptide lantibiotic, displaying antimicrobial activity against a broad range of Gram positive microbes. In Chapter 3, through a combination of in silico and lab-based screening of the Lactobacillus pangenome, it was possible to determine the extent and diversity of bacteriocins encoded and produced by the genus. This study shows that bacteriocin production may not be as prevalent as previously believed, however of the bacteriocins which were identified from within the genomes, many were found to be novel. By screening the strains identified as harbouring bacteriocin-related genes, five novel active bacteriocins were identified. Many strains of lactobacilli were found to encode bacteriocins, however upon analysis, these failed to display in vitro antimicrobial activity. Often the regulation of bacteriocin operons, or the loss of key bacteriocin-associated genes, results in the failure of these strains to produce bacteriocins when tested in vitro. Chapter 4 outlines a method for the heterologous expression of a particular class of bacteriocins, the Class IIa ‘pediocin-like’ bacteriocins. Here, using an expression designed for Class IIa bacteriocins, it was possible to produce eight novel bacteriocins identified from genomic data. In Chapter 5 shotgun metagenomic sequencing is used to characterise the compositional and functional properties of the intestinal microbiome of deep sea fish. Here it can be seen how bacteria have adapted to live in this environment by encoding systems to relieve the stress associated with life at higher pressures. The study also outlines the diversity of the potential antimicrobials which may be produced within the microbiome of such fish whilst also highlighting an apparent lack of genes associated with known mechanisms of antibiotic resistance. Overall, the results of this work demonstrate the effectiveness of a variety of methods for identifying novel antimicrobials from a range of bacterial sources.
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Keywords
Bacteriocin , Deep-sea , Antimicrobial
Citation
Collins, F. W. J. 2019. An investigation into antimicrobial production in the Lactobacillus genus and the fish microbiome. PhD Thesis, University College Cork.