High-throughput sequencing-based characterisation of fermented foods and their impacts on host gut microbiota

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Walsh, Aaron M.
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University College Cork
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Fermentation has been practised worldwide for millennia as a method to preserve or enhance foods, and, today, fermented foods remain a significant component in the human diet. Additionally, these foods are becoming increasingly popular since numerous health benefits have been ascribed to them, and thus it is necessary to (1) optimise their production, (2) assess their safety, and (3) determine the mechanisms by which they confer these effects. In this thesis, we examine if high-throughput sequencing technologies, particularly shotgun metagenomics, can address these needs. In Chapters 3 and 4, we show that shotgun metagenomics, when used alongside metabolomics, can be applied to understand the ways in which the microbiota influences flavour development in fermented foods. In Chapter 5, we report that shotgun metagenomics can accurately, and rapidly, detect pathogenic strains in fermented foods. In Chapter 6, we demonstrate that the choice of bioinformatics tools has a significant impact on shotgun metagenomic analysis of fermented foods. Finally, in Chapter 7, we provide evidence that a traditional fermented food modulates the gut microbiota in mice, while simultaneously reducing anxious-like behaviours in the animals. Overall, this thesis highlights that high-throughput sequencing is an invaluable tool for studying fermented foods. We illustrate that the technology not only expands our knowledge on the roles played by microorganisms during food fermentations, but it can also be used to ensure food safety or even investigate the ways in which these foods affect the host. Thus, high-throughput sequencing can bridge the gap between traditional food microbiology and health.
Fermented foods , Microbiota , High-throughput sequencing , Shotgun metagenomics , Bioinformatics
Walsh, A. M. 2018. High-throughput sequencing-based characterisation of fermented foods and their impacts on host gut microbiota. PhD Thesis, University College Cork.