High-throughput microbiome profiling of fermented grain drinks: quality, consistency and risk insights

Fermentation has played a vital role in the production of food and beverages throughout human history. In recent years, growing interest in its potential health benefits - particularly in relation to immune function and gastrointestinal health - has surged. The microbial communities responsible for fermentation are central to both food safety and the probiotic properties often promoted by producers as supporting a healthy gut microbiome. However, the composition and quality of these microbial populations vary significantly across manufacturers and remain largely uncharacterized due to a lack of standardized industry protocols. This study aims to enhance our understanding of microbial diversity in fermented products by comparing bacterial and fungal communities present in grain-based fermented beverages produced by seven different European manufacturers. Samples were collected at two distinct time points, representing separate production batches. Using metabarcoding approaches - targeting mitochondrial 16S rRNA for bacteria and the internal transcribed spacer region (ITS2) for fungi - we identified considerable variation in microbial genera across both batches and manufacturers. These findings underscore the need for standardized microbial characterization and quality control measures in the fermented food industry ensure product consistency, optimize potential health benefits, and safeguard consumer well-being.