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

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dc.availability.bitstreamopenaccess
dc.check.date2025-03-12
dc.contributor.advisorCotter, Paulen
dc.contributor.advisorHill, Colinen
dc.contributor.advisorexternalFeehily, Conoren
dc.contributor.authorMcHugh, Aoife J.
dc.contributor.funderFood Institutional Research Measureen
dc.date.accessioned2020-06-04T10:26:50Z
dc.date.issued2020-03
dc.date.submitted2020-03
dc.description.abstractSpore-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.description.statusNot peer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationMcHugh, 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.endpage323en
dc.identifier.urihttps://hdl.handle.net/10468/10127
dc.language.isoenen
dc.publisherUniversity College Corken
dc.relation.projectFood Institutional Research Measure (Grant no. 14/F/883 SACCP)en
dc.rights© 2020, Aoife J. McHugh.en
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectDairyen
dc.subjectMicrobiotaen
dc.subjectSporeen
dc.subjectMetagenomicsen
dc.subjectDairy powderen
dc.subjectDairy processingen
dc.titleNovel sequencing-based methods to characterise microbiomes, and in particular spore-forming bacteria, in the dairy processing chainen
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD - Doctor of Philosophyen
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