Nutrifermentics: Microbial epigenetics for innovation in fermentation : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University

Abstract

Microbial epigenetics presents a novel and efficient approach for manipulating microorganisms without altering their genetic information. This present study focuses on harnessing the potential of microbial epigenetics to transform and revolutionise fermented product development, a concept termed "nutrifermentics." The dynamic interplay between microbial epigenetics and dietary factors were investigated in both eukaryotic (Saccharomyces cerevisiae) and prokaryotic (Lactobacillus acidophilus) strains, with a specific focus on the capacity of nutrifermentics to drive innovations in fermentation, particularly within the food industry. In this study, benzoic acid, a common food additive and a recognised histone deacetylase inhibitor (HDACi), was shown to alter the formation of epigenetic histone marks (H3K4Me2, H3K27Me2, H3K18ac, and H3Ser10p) in S. cerevisiae yeast. Consequently, the phenotypic behaviour of the yeast was altered, with increased production of phenylethyl alcohol and ester compounds during alcoholic fermentation observed. Subsequently, the relationship between short-term and long-term stress induced by benzoic acid in yeast and their effects on aging was explored. Through comprehensive transcriptomic and metabolomic analyses, it was established that short-term stress fosters longevity, while long-term stress diminishes lifespan. Interestingly, cells under long-term stress (LT) demonstrate the activation of genes associated with epigenetic regulatory enzymes and secondary stress response genes, including heat shock proteins (HSPs). Paradoxically, despite this heightened cellular stress response activity, these cells exhibit shorter lifespans when compared to their short-term stressed counterparts (ST). These findings indicate there is a potential evolutionary advantage, specifically an enhanced short-term survival, associated with aging markers like HSPs. Additionally, these results imply potential applications for aging interventions through the use of inhibitors targeting heat shock proteins. To determine the impact of a diverse range of epigenetically active compounds, such as genistein, in bacteria, the epigenetic responses of L. acidophilus, a well-known probiotic bacterium widely used in yoghurt production, were evaluated. Epigenetics, transcriptomics, and metabolomics were used to demonstrate the potential to alter individual gene or loci expression without genetic modification. The production of both primary and secondary metabolites, such as melibiose, were altered in response to different epigentically active compounds, which provides insight into the role these dietary compounds can play in enhancing bacterial fermentative capability in a sustainable and genetic modification-free way. In conclusion, this present study unveils the potential of microbial epigenetics and dietary compounds to enhance fermentation processes. It offers valuable insights and practical applications for researchers and industries in the field of fermented product development and biotechnology applications.