Shotgun metagenomics exploration of fermented food microbiomes

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Leech, John
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University College Cork
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Fermentation is among the worlds oldest forms of food preservation. Study into these foods began in earnest with Lois Pasteur over 150 years ago. Although much information has been gathered since, we have entered a new era of next generation sequencing where an unprecedented amount of information can be extracted from these food microbiomes. This thesis explores the utility of this technology on a wide variety of these foods. In chapter 1, we review the combination of omic technologies to understand the role of the fermenting microbes on various attributes of the food products, such as flavour and health-enhancing components of the food. Chapter 2 explores 58 fermented foods from various parts of the world using shotgun metagenomics. These 58 foods consist of a wide range of products, many of which have seen a recent resurgence in popularity, due to the emerging importance of the human microbiome and health. Many of these foods have not been investigated using shotgun metagenomics previously. The chapter also highlights the role food substrate plays in determining the microbial composition of these foods. Chapters 3 & 4 investigate kombucha specifically, a fermented beverage that has enjoyed a massive growth in commercial value over recent years. These chapters also combine targeted metabolomics, and with the combination of shotgun metagenomics, examines the interplay between microorganisms, kombucha chemistry, and oxygen transfer rate. Chapter 5 explores the microbiomes of 91 fermented foods from Africa. African fermented foods in particular, have lacked in-depth examination via next generation sequencing. Similarly to Chapter 2, Chapter 5 reveals that African fermented food microbiomes are also determined by the ingredients used to produce these foods. Finally, chapter 6 investigates the effect of read depth on the recovery of Metagenome Assembled Genomes (MAGs), revealing that specific genome coverage is the most important factor in terms of the likelihood of recovering a particular MAG.
Metagenomics , Fermented foods
Leech, J. 2021. Shotgun metagenomics exploration of fermented food microbiomes. PhD Thesis, University College Cork.