Leveraging community-based sequencing approaches to characterise the dairy microbiome
type: CreativeWork
description: Microorganisms exist in communities along the food chain and contribute, positively and negatively, to the safety and quality of food products downstream. While traditional culture-based methods usually investigate specific groups of microorganisms, advances in high-throughput DNA sequencing have enabled the study of entire microbial communities in food or food-related samples. In this thesis, shotgun metagenomic sequencing was employed to investigate microbial communities in bulk tank milk. First, shotgun sequencing was used to determine the impact of farm cleaning methods on the microbiome. The results revealed that seasonality and geography significantly impacted the bulk tank milk microbiota but that the use of chlorine-based relative to chlorine-free cleaning methods did not result in differences. Next, further sampling was performed to determine if interactions exist between the bulk tank milk microbiota, raw milk chemical composition and climatic variables. Analysis of shotgun sequencing data from bulk tank milk over 12-months revealed a stable core microbiota and showed a significant and obvious influence of season and location on the raw milk microbiota. Associations were detected between pathogenic and mastitis-related taxa and chemical composition and climate/environmental variables. The interconnected nature of these variables suggests there is merit in considering the use of chemical and/or climate variables as markers for food safety and spoilage threats in bulk tank milk. While useful information can be obtained through shotgun metagenomic sequencing, the untargeted nature of this approach involves the sequencing of all DNA present in samples, including host-derived reads that are present in high proportions in milk (~90%), as well as both live and dead cells, which could alter inferred community structure or diversity. To overcome these challenges, two studies were completed to improve current shotgun metagenomic sequencing methodology. First, three …
abstract: Microorganisms exist in communities along the food chain and contribute, positively and negatively, to the safety and quality of food products downstream. While traditional culture-based methods usually investigate specific groups of microorganisms, advances in high-throughput DNA sequencing have enabled the study of entire microbial communities in food or food-related samples. In this thesis, shotgun metagenomic sequencing was employed to investigate microbial communities in bulk tank milk. First, shotgun sequencing was used to determine the impact of farm cleaning methods on the microbiome. The results revealed that seasonality and geography significantly impacted the bulk tank milk microbiota but that the use of chlorine-based relative to chlorine-free cleaning methods did not result in differences. Next, further sampling was performed to determine if interactions exist between the bulk tank milk microbiota, raw milk chemical composition and climatic variables. Analysis of shotgun sequencing data from bulk tank milk over 12-months revealed a stable core microbiota and showed a significant and obvious influence of season and location on the raw milk microbiota. Associations were detected between pathogenic and mastitis-related taxa and chemical composition and climate/environmental variables. The interconnected nature of these variables suggests there is merit in considering the use of chemical and/or climate variables as markers for food safety and spoilage threats in bulk tank milk. While useful information can be obtained through shotgun metagenomic sequencing, the untargeted nature of this approach involves the sequencing of all DNA present in samples, including host-derived reads that are present in high proportions in milk (~90%), as well as both live and dead cells, which could alter inferred community structure or diversity. To overcome these challenges, two studies were completed to improve current shotgun metagenomic sequencing methodology. First, three …
author: Yap, Min
language: en
keywords: Dairy, Microbiota, Metagenomics, High-throughput sequencing
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
date published: 2022
date modified: 2026-07-24T01:47:43Z
provider: University College Cork
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University College Cork

PropertyValue
property ID: Handle
value: https://hdl.handle.net/10468/14131