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Abstract Wine is a complex matrix resulting from a fermentation process carried out by specific microbial communities. These communities can be in competition and the development of some microorganisms, as the yeast Brettanomyces bruxellensis , can impact the fermentation process and lead to organoleptic alterations of wine. To manage this risk, microbiological diagnostic methods as microscopic observations, qPCR or flow cytometry are already used in oenology, but remain either not specific enough, or tedious. In this context, IAGE (Ingénierie et Analyses en Génétique Environnementale) has developed the first digital-PCR system enabling the detection and quantification of B. bruxellensis during the whole winemaking process. Furthermore, wine DNA extraction was optimized to enable a representative and sensitive analysis of B. bruxellensis intact cells, as well as an easy-to-implement protocol to cope with the increasing number of samples to analyze. The IAGE workflow for B. bruxellensis quantification has been proven to be successful when analyzing naturally-contaminated samples during the different steps of the winemaking process and offers a robust method to oenologists for appropriate treatments and risk management in wine cellars. Highlights Development of a dPCR method led to a highly-specific analysis of B. bruxellensis intact cells in different steps of the winemaking process. DNA extraction method has been optimized to be robust across various types of wine with varying concentrations of inhibitors, as well as throughout different stages of the wine making process. The complete process was proven successful in analyzing a large number of naturally-contaminated samples, giving results in less than 48 hours.
Gruet et al. (Tue,) studied this question.