For many foods and beverages, a comprehensive understanding of mixed microbial fermentations plays a major role in the production of safe, high-quality products. Also, for the production of spontane- ously fermented cash crops such as cocoa and coffee, understanding the complex interplay between different groups of microorganisms and the continuously changing microenvironment is of major impor- tance to control the process and its impact on product quality and value. Within the last decades, the technologies to study mixed fer- mentations have been developed extensively including the application of advanced microscopic and molecular techniques, with the latter
including advanced technologies such as high throughput sequenc- ing of either DNA or RNA. By using microscopic techniques, new insights have been gained regarding population. By the use of molecu- lar techniques, various methods have been developed to study micro- bial successions including nonculturable microorganisms and, by targeting mRNA either by microarray analyses, qPCR, or HTS, new insights can be gained on the metabolic potential and activity of dif- ferent groups of microorganisms during mixed fermentations. Future prospects will be to combine all these new techniques, thereby allow- ing us to understand both the physiological and molecular changes taking place in the matrix of the fermented product at both the popu- lation and single cell level. Knowledge from more well-characterized solid, mixed fermented foods such as cheese should be transferred to less characterized mixed fermentations such as those seen for cocoa and coffee. Increased understanding of the complex nature of mixed fermentations should allow us to develop and implement measures for their control in order to optimize product quality, safety and value and to optimize process efficiency.
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