Microbial communities of artisanal ciders in Slovenia and their role in fermentation

Traditional cider production relies on spontaneous fermentation driven by complex microbial communities. In this study, we investigated the microbial communities, chemical compositions, and functional interactions underlying artisanal cider production in Carinthia, a subalpine region of northern Slovenia. Samples of spontaneously fermented ciders and swabs from wooden cellar equipment were collected from 11 remote farms using traditional practices to identify potential microbial reservoirs. Yeasts and bacteria were isolated, enumerated, dereplicated, and identified using sequencing of barcoding regions. Chemical parameters, organic acids, and volatile phenols were quantified, and their associations with microbiota were assessed. Despite differences in farm elevation, apple varieties, and equipment, all ciders shared a stable, technologically relevant core microbiota consisting of pellicle-forming yeasts, a diverse Saccharomyces complex dominated by Saccharomyces uvarum, Brettanomyces species, lactic acid bacteria primarily represented by Oenococcus oeni, and acetic acid bacteria. The microbial profiles found on wooden equipment largely overlapped with those in the ciders, indicating that resident microbiota contribute to inoculation and product consistency. Controlled fermentation trials showed that S. uvarum drives alcoholic fermentation, and that O. oeni contributes to lactic acid production. Growth of O. oeni was enhanced by the presence of B. bruxellensis, suggesting metabolic interdependencies. Overall, this study highlights the importance of indigenous microbial communities in determining the composition and characteristics of traditional cider and provides a foundation for preserving and managing distinctive fermentations across regions.