Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food

Water Kefir is a plant-based fermented beverage, traditionally produced on a small scale by fermenting a sucrose solution with fresh or dried fruits, using water kefir grains as inoculum. The grains are relatively simple communities that consist of both eukaryotes and prokaryotes, rendering them a paradigm for studying microbial ecology and interspecies interactions. Recently, water kefir has attracted growing research and industrial interest due to its potential and perceived health benefits. Owing to its increasing popularity, there is a growing demand for controlled and standardised production on an industrial scale. However, industrial-scale production remains a challenge due to the limited knowledge of the biological interactions of the microbial consortia and the lack of defined starter cultures. This review examines the current understanding of microbial and metabolic complexity of water kefir obtained from various omics studies. It further investigates the potential of an integrated multi-omics approach to elucidate mechanisms of microbial interactions and provides a roadmap for conducting multi-omics studies on fermented foods using water kefir as an example. This review also explores the potential application of genome-scale metabolic modelling in the development of functional and defined microbial communities for food fermentation. It identifies key challenges associated with such modelling and provides perspectives to address them. Finally, this review briefly discusses the regulatory challenges associated with the use of defined communities in food systems.