Microbial Communities of Artisanal Ciders in Slovenia and their Role in Fermentation

In this manuscript, we report the sampling and identification of complex microbiota associated with an artisanal cider from remote farms in the pre-Alpine region of Slovenia. The aim of the study was to determine the microbial community composition using culturomics and its effects on the chemical characteristics of ciders. The composition of the main microbial species was generally consistent across distant farms at different elevations, despite the use of various apple varieties and cellar equipment. Further, in order to investigate potential microbial reservoirs, we also sampled processing equipment in cellars and showed that resident microbiota actively participate in fermentation and contribute to the unique profiles of artisanal ciders. Functional analysis of the dominant microbial species in fermentation trials revealed that Saccharomyces uvarum drives primary fermentative dynamics, while Oenococcus oeni contributes to lactic acid production regardless of its growth level. In mixed cider fermentations, pellicle-forming yeasts and Brettanomyces species are also one of the major contributors to the characteristics of artisanal ciders.