Outsmarting phages to generate better dairy products

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dc.check.date2026-09-30
dc.contributor.advisorvan Sinderen, Douwe
dc.contributor.advisorMahony, Jennifer
dc.contributor.authorWhite, Kelseyen
dc.contributor.funderIrish Research Councilen
dc.date.accessioned2025-02-12T16:31:16Z
dc.date.available2025-02-12T16:31:16Z
dc.date.issued2024en
dc.date.submitted2024
dc.description.abstractThe dairy fermentation industry relies on the activity of various lactic acid bacteria in starter cultures to acidify milk and produce a variety of fermented dairy products. Undefined mesophilic starter cultures are predominantly composed of many strains (in an unknown composition) belonging to species such as Lactococcus lactis and Lactococcus cremoris. Bacteriophage infection of the bacterial strains within these starter cultures are one of the most significant and persistent threats to successful dairy fermentations. Delayed or disrupted fermentations, as a result of phage attacks, may cause costly disruptions resulting in unnecessary waste and a loss of product. One of the most problematic and abundant lactococcal phage genera is Skunavirus. Most lactococcal phages, including skunaviruses, commence infection with the binding of a phage-encoded receptor binding protein (RBP) to a surface-exposed host receptor, which in the case of skunaviruses is a cell wall polysaccharide (CWPS). To ensure the manufacture of consistent and high-quality fermentation end products, it is essential that the composition and integrity of starter cultures is maintained. Therefore, this thesis aims to investigate phage-host interactions between skunaviruses and their lactococcal hosts pertinent to dairy fermentation facilities utilising undefined mesophilic starter cultures. Chapter 2 of this thesis outlines a combined culture-based analysis and metagenomics investigation to evaluate the composition of two mesophilic undefined starter cultures. A novel qPCR-based genotype detection assay, capable of discerning nine distinct lactococcal genotypes, was devised and used to examine compositional changes of an undefined starter culture. These analytical approaches facilitated a multifaceted assessment of starter culture compositional stability during milk fermentation, which has become an important quality control aspect due to increasing demand for reliable and high-quality dairy products. In Chapter 3, a phageome analysis of whey samples originating from dairy fermentation factories employing mesophilic undefined starter cultures was conducted to investigate the phage prevalence and diversity in the samples. Particular focus was placed on investigating the range of Skunavirus RBP genotypes and associated RBP-CWPS binding abilities present in these whey phageomes. These findings allowed for the refinement and expansion of the Skunavirus RBP grouping systems thereby vastly expanding our knowledge on lactococcal Skunavirus RBP diversity and CWPS specificity. Chapter 4 of this thesis details the diversity of skunaviruses present in the same whey samples used for the phageome analysis described in Chapter 3 through culture-dependent phage screening, targeted isolation based on RBP specificity, and phage RBP-activated cell sorting (PhRACS). Through this investigation, the genomes of 26 newly isolated Skunavirus members were sequenced and analysed, with a specific focus placed on surveying genes encoding auxiliary carbohydrate binding module-containing proteins. Host range analysis of the skunaviruses revealed a clear correlation between the encoded RBP phylogroups and cwps genotypes of corresponding host strains. In addition, phageome-derived Skunavirus contigs were analysed to further determine the diversity of phages present in the dairy fermentation facilities. Chapter 5 assesses the strain-level diversity of lactococcal strains originating from mesophilic undefined starter cultures. Culture-dependent approaches were used to assess the technological attributes, such as acidification, proteolytic activity, and phage sensitivity, of these isolates. Genomic analysis of sequenced lactococcal strains was focused on industrially relevant genomic elements such as cwps biosynthesis gene clusters, plasmids, and phage-defense systems. In addition, a genomic analysis of strains belonging to the emerging dairy-associated species Lactococcus laudensis was carried out. In summation, both the bacterial composition of starter cultures as well as the phage diversity of corresponding whey samples were thoroughly investigated, generating comprehensive insights into the complex microbial community of these mesophilic fermentation systems. Understanding the intricate phage-host interactions occurring in the environment in which mesophilic fermentation systems are extensively applied will aid in efforts to development and maintain robust dairy starter culture systems for sustainable food production practices.en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationWhite, K. E. 2024. Outsmarting phages to generate better dairy products. PhD Thesis, University College Cork.
dc.identifier.endpage336
dc.identifier.urihttps://hdl.handle.net/10468/17033
dc.language.isoenen
dc.publisherUniversity College Corken
dc.relation.projectIrish Research Council (Grant no. EPSPG/2020/12)
dc.rights© 2024, Kelsey White.
dc.rights.urihttps://creativecommons.org/licenses/by-nc-sa/4.0/
dc.subjectBacteriophageen
dc.subjectLactic acid bacteriaen
dc.subjectLactococcus cremorisen
dc.subjectReceptor binding proteinen
dc.subjectCell wall polysaccharidesen
dc.subjectUndefined starter cultureen
dc.subjectMetagenomicsen
dc.subjectCarbohydrate bindingen
dc.titleOutsmarting phages to generate better dairy productsen
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD - Doctor of Philosophyen
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