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

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dc.contributor.advisor Giblin, Linda en
dc.contributor.advisor McSweeney, Paul L. H. en
dc.contributor.advisor Cotter, Paul D. en
dc.contributor.advisor Sheehan, Diarmuid en
dc.contributor.author O'Sullivan, Daniel
dc.date.accessioned 2016-06-29T11:25:20Z
dc.date.available 2016-06-29T11:25:20Z
dc.date.issued 2015
dc.date.submitted 2015
dc.identifier.citation O'Sullivan, D. 2015. The application of next generation sequencing to profile microbe related cheese quality defects. PhD Thesis, University College Cork. en
dc.identifier.endpage 285 en
dc.identifier.uri http://hdl.handle.net/10468/2809
dc.description.abstract High 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.sponsorship Teagasc (Walsh Fellowship Program); Department of Agriculture, Food and the Marine, Ireland (Food Institutional Research Measure) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher University College Cork en
dc.rights © 2015, Daniel O'Sullivan. en
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/3.0/ en
dc.subject Microbiology en
dc.subject Next generation sequencing en
dc.subject Cheese defects en
dc.title The application of next generation sequencing to profile microbe related cheese quality defects en
dc.type Doctoral thesis en
dc.type.qualificationlevel Doctoral en
dc.type.qualificationname PhD (Food Science and Technology) en
dc.internal.availability Full text available en
dc.check.info No embargo required en
dc.description.version Accepted Version
dc.contributor.funder Teagasc en
dc.contributor.funder Department of Agriculture, Food and the Marine, Ireland en
dc.description.status Not peer reviewed en
dc.internal.school Food and Nutritional Sciences en
dc.internal.school Teagasc en
dc.check.type No Embargo Required
dc.check.reason No embargo required en
dc.check.opt-out No en
dc.thesis.opt-out false
dc.check.embargoformat Not applicable en
ucc.workflow.supervisor p.mcsweeney@ucc.ie
dc.internal.conferring Summer 2016 en


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© 2015, Daniel O'Sullivan. Except where otherwise noted, this item's license is described as © 2015, Daniel O'Sullivan.
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