Simplifying complex microbial communities for food and beverage fermentations

Fermentation of foods and beverages has occurred in human societies for many thousands of years. In our modern world, food systems have dramatically changed and as our understanding of microbiology progressed, food production has shifted to using defined fermentations, inoculated by single yeast strains or defined assemblage of bacteria. Food and beverage substrates are rarely sterile before inoculation, so the single strains often co-exist with resident microflora. Flavours, functions and processes are affected by using a single strain, but the vast metabolic repository given by other microbes present in the food system can provide important inputs. Here, I provide a review of the new approaches being used to fully realise the metabolic potential of un-inoculated fermentations for food production. Kombucha, bread, and chocolate are considered. These new approaches use flavour as the starting point for distinctive foods and we work backwards to describe the appropriate microbial community. I discuss how new methods driven by metagenomic sequencing and integration of sensitive metabolomics have given us new models to consider how a ‘core’ microbial community can provide effective fermentation and enjoyable flavour.