The wine and cheese making industries are built upon strikingly similar commercial microbial culture foundations. During cheese making, milk is acidified with starter cultures, then undergoes a maturing phase in which flavor is formed by either commercial adjunct (flavor forming) cultures or by the naturally occurring bacteria in the milk. In winemaking alcohol fermentation is performed by Saccharomyces cerevisae followed by the malolactic fermentation, where bacteria degrade the malic acid. Flavor formation is a complex interplay between non-saccharomyces yeasts and the complex mixture of bacteria present in the must.
For both wine and cheese making, the fermentation processes are a complex interplay between starter cultures and naturally occurring microorganisms. Sometimes this interplay enters a wrong direction leading to off-flavors, stuck fermentation or other defects in the production such as slits or cracks in cheddar cheese. These defects pose a major economic risk for dairies and winemakers globally, especially in areas with poor hygiene. Remarkably, current methods utilized in the development of new cultures within both industries have changed little in the past century – largely relying on simple trial and error of potential new microbes of interest. Today, with the recent advances within the fields of genomics, transcriptomics and metabolomics, we are poised to enter an era in which a radically new approach can be taken – deconstruction of not only the complexities of the microbial communities involved in the process, but more importantly reconstruction of the actual gene pathways and interactions that underpin the eventual flavor profiles of the product – ultimately the most relevant end product of the industries. Furthermore this approach will also enable development of improved starter cultures capable of controlling the diverse microflora present in the fermentations.