The application of next generation sequencing to profile microbe related cheese quality defects

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dc.contributor.advisorGiblin, Lindaen
dc.contributor.advisorMcSweeney, Paul L. H.en
dc.contributor.advisorCotter, Paul D.en
dc.contributor.advisorSheehan, Diarmuiden
dc.contributor.authorO'Sullivan, Daniel
dc.contributor.funderDepartment of Agriculture, Food and the Marine, Irelanden
dc.description.abstractHigh throughput next generation sequencing, together with advanced molecular methods, has considerably enhanced the field of food microbiology. By overcoming biases associated with culture dependant approaches, it has become possible to achieve novel insights into the nature of food-borne microbial communities. In this thesis, several different sequencing-based approaches were applied with a view to better understanding microbe associated quality defects in cheese. Initially, a literature review provides an overview of microbe-associated cheese quality defects as well as molecular methods for profiling complex microbial communities. Following this, 16S rRNA sequencing revealed temporal and spatial differences in microbial composition due to the time during the production day that specific commercial cheeses were manufactured. A novel Ion PGM sequencing approach, focusing on decarboxylase genes rather than 16S rRNA genes, was then successfully employed to profile the biogenic amine producing cohort of a series of artisanal cheeses. Investigations into the phenomenon of cheese pinking formed the basis of a joint 16S rRNA and whole genome shotgun sequencing approach, leading to the identification of Thermus species and, more specifically, the pathway involved in production of lycopene, a red coloured carotenoid. Finally, using a more traditional approach, the effect of addition of a facultatively heterofermentative Lactobacillus (Lactobacillus casei) to a Swiss-type cheese, in which starter activity was compromised, was investigated from the perspective of its ability to promote gas defects and irregular eye formation. X-ray computed tomography was used to visualise, using a non-destructive method, the consequences of the undesirable gas formation that resulted. Ultimately this thesis has demonstrated that the application of molecular techniques, such as next generation sequencing, can provide a detailed insight into defect-causing microbial populations present and thereby may underpin approaches to optimise the quality and consistency of a wide variety of cheeses.en
dc.description.sponsorshipTeagasc (Walsh Fellowship Program); Department of Agriculture, Food and the Marine, Ireland (Food Institutional Research Measure)en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Version
dc.identifier.citationO'Sullivan, D. 2015. The application of next generation sequencing to profile microbe related cheese quality defects. PhD Thesis, University College Cork.en
dc.publisherUniversity College Corken
dc.rights© 2015, Daniel O'Sullivan.en
dc.subjectNext generation sequencingen
dc.subjectCheese defectsen
dc.titleThe application of next generation sequencing to profile microbe related cheese quality defectsen
dc.typeDoctoral thesisen
dc.type.qualificationnamePhD (Food Science and Technology)en
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