Novel sequencing-based methods to characterise microbiomes, and in particular spore-forming bacteria, in the dairy processing chain

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dc.contributor.advisor Cotter, Paul en
dc.contributor.advisor Hill, Colin en McHugh, Aoife J. 2020-06-04T10:26:50Z 2020-03 2020-03
dc.identifier.citation McHugh, A. J. 2020. Novel sequencing-based methods to characterise microbiomes, and in particular spore-forming bacteria, in the dairy processing chain. PhD Thesis, University College Cork. en
dc.identifier.endpage 323 en
dc.description.abstract Spore-forming bacteria are a concern to dairy processors as a consequence of their potential to be pathogenic or to cause spoilage. Strict customer enforced limits are applied in the case of some sporeformers, but the traditional agar-based detection methods used to assess compliance have limits with respect to sensitivity and specificity. In this thesis, novel sequencing-based methods are applied to characterise microbiomes in the dairy processing chain with an emphasis on spore-forming bacteria. An initial 16S sequencing-based investigation of ultra-high temperature processing on the relative composition of thermophilic sporeformers in a dairy powder revealed that different temperatures impacted on the proportions of genera present. Shotgun metagenomic sequencing was subsequently used to identify the mesophilic sporeformers present in a specific type of dairy powder, produced monthly over one year, and investigate the functional potential of strains present to determine associated risks. A further study, tracking of the dairy microbiota from farm bulk tank milk to skimmed milk powder using 16S amplicon sequencing and shotgun metagenomic sequencing, highlighted the enrichment of spore-forming bacteria in the latter stages of dairy powder production. Finally, Oxford Nanopore’s MinION sequencer was used for environmental monitoring in a dairy processing facility. Results from the long-read sequencer were comparable to those from Illumina-based sequencing and culture-based analysis. Overall this thesis highlights that sequencing-based methods could be used to provide a more in-depth understanding of the microbiota of dairy and the dairy processing environment. Such an improved understanding could allow dairy processors to make timely, informed decisions to reduce the risk of microbial contamination. en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher University College Cork en
dc.rights © 2020, Aoife J. McHugh. en
dc.rights.uri en
dc.subject Dairy en
dc.subject Microbiota en
dc.subject Spore en
dc.subject Metagenomics en
dc.subject Dairy powder en
dc.subject Dairy processing en
dc.title Novel sequencing-based methods to characterise microbiomes, and in particular spore-forming bacteria, in the dairy processing chain en
dc.type Doctoral thesis en
dc.type.qualificationlevel Doctoral en
dc.type.qualificationname PhD - Doctor of Philosophy en
dc.internal.availability Full text available en
dc.description.version Accepted Version en
dc.contributor.funder Food Institutional Research Measure en
dc.description.status Not peer reviewed en Microbiology en
dc.internal.conferring Summer 2020 en
dc.relation.project Food Institutional Research Measure (Grant no. 14/F/883 SACCP) en
dc.contributor.advisorexternal Feehily, Conor en
dc.availability.bitstream GC. 06.07.21 email from author to remove embargo. Chapter 2 pages 69-97, Chapter 4 pages 146-207, Chapter 5 pages 208-280. each for 5 years. Appendix-publications pages 294-323, indefinitely. en
dc.availability.bitstream openaccess 2025-03-12

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© 2020, Aoife J. McHugh. Except where otherwise noted, this item's license is described as © 2020, Aoife J. McHugh.
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