Nutrifermentics: Pioneering next generation fermented products

Abstract

Nutrifermentics” is a new concept we have developed to describe an approach to fermentation focused on understanding how specific dietary compounds impact on the epigenetic regulation of microbial strains. We use this knowledge to develop microbial strains for food and beverage production without resorting to genetic modification. Our innovative approach, rooted in epigenetics, allows us to modify the metabolomic profile of fermented products without directly altering the DNA of the involved microbes. This cutting-edge technique has already shown promising results in alcohol fermentation and wine production. Here, we investigated the epigenetic responses (changes in DNA methylation levels) of the probiotic gut bacteria Lactobacillus acidophilus, which is widely used in yogurt making, to dietary epigenetically-active compounds such as genistein. These epigenetic changes altered the metabolomic profile and produced beneficial primary and secondary metabolites, including antimicrobial compounds like 3-phenyllactic acid and health-promoting substances like trehalose. Moreover, this study demonstrated that individual genes or loci, such as those responsible for melibiose production which was upregulated 8 fold, can be altered without resorting to genetic modification methods such as CRISPR, thus highlighting the plethora of biotechnology applications for this technology. This in-depth multiomic analysis of the effect of certain dietary compounds on epigenetics, transcriptomics, and metabolomics in the probiotic gut bacteria Lactobacillus acidophilus, provides useful insights into the role of dietary compounds on the fermentative capability of bacteria. Furthermore, this study has shown that dietary epigenetic compounds can be used to alter the microbes used in the fermentation process, ultimately leading to the development of sustainable and non-GMO fermented products.