Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota

Abstract

Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.

Keywords: fermented food; microbiome; multi-omics.

Figure 1

Common fermentation substrates and produced fermented foods and beverages.

Figure 2

An illustration of the metabolic interplay and functional compatibility of kombucha fermentation microbiota, representing a model for the adaptation and symbiosis of the microbiota in the fermentation ecosystem.

Figure 3

CRISPR-Cas9-mediated gene editing and its possible applications in food fermentation. The precise gene editing can be utilised for improving of the starter culture by deletion of undesirable traits or insertion of desirable traits. CRISPR-Cas9 technology could be utilised for microbiome engineering by targeting unique sequences and selectively eliminate spoilage and undesirable microbes from the community.

Figure 4

Evolution of the process of fermentation throughout the history, starting from relying on the natural indigenous microbes reaching to the innovative approach of microbiome engineering using advanced technological tools.

Figure 5

The different tools of the multi-omics analysis and their roles in understanding the food fermentation process, microbiome structure and functional activity profiling.