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The Application of Next Generation Sequencing to Profile Microbe Related Cheese Quality Defects
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2015
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O'Sullivan, Daniel. The Application of Next Generation Sequencing to Profile Microbe Related Cheese Quality Defects. Thesis, National University of Ireland, Cork (UCC), 2015
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 sequencingbased
approaches were applied with a view to better understanding microbe associated
quality defects in cheese. Initially, a literature review provides an overview of microbeassociated
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.