Exploring yeast interactions through metabolic profiling

Abstract

As a complex microbial ecosystem, wine is a particularly interesting model for studying interactions between microorganisms as fermentation can be done by microbial consortia, a unique strain or mixed culture. The effect of a specific yeast strain on its environments is unique and characterized by its metabolites and their concentration. With its great resolution and excellent mass accuracy, ultrahigh resolution mass spectrometry (uHRMS) is the perfect tool to analyze the yeast metabolome at the end of alcoholic fermentation. this work reports the change in wine chemical composition from pure and mixed culture fermentation with Lachancea thermotolerans, Starmerella bacillaris, Metschnikowia pulcherrima and S. cerevisiae. We could clearly differentiate wines according to the yeast strain used in single cultures and markers, which reflect important differences between the yeast species, were extracted and annotated. Moreover, uHRMS revealed underlining intra species metabolomics differences, showing differences at the strain level between the two Starmerella bacillaris. non volatile metabolomics analysis of single and sequential fermentations confirmed that mixed fermentations lead to a different composition. Distinct metabolites appeared in wines from sequential fermentation compared to single fermentation. this suggests that interactions between yeasts are not neutral.Microorganisms coexist in most environments and interact with each other. These interactions happen in nearly every niche on the planet and in numerous processes such as bioremediation of pollutants, farming, biotechnology, medicine or food-processing 1,2 . Under oenological conditions, when yeasts grow simultaneously during alcoholic fermentation, they often do not coexist passively, and in most cases, physiological and metabolic interactions are established between them. The interactions between the different strains of Saccharomyces and non-Saccharomyces yeast can be direct or indirect, through the physicochemical changes in the environment caused by one strain reacting to the other. In oenology, the effect of these interactions is characterized as being positive, negative or neutral 3 . Genomics and proteomics provide an understanding of the interaction 3-5 but none of them could yet provide significant progress on the microbial interaction mechanisms. Recently, high resolution mass spectrometry has been used to elucidate interactions between yeasts and bacteria in the malolactic fermentation by comparison of extracellular metabolic profiles 6 . Even more recently, ultrahigh resolution mass spectrometry (uHRMS) confirmed that cell-cell contact influences the metabolism of L. thermotolerans and S. cerevisiae 7 . Therefore, metabolomics seems to be a suitable tool to better understand the microbial interactome in order to control fermentation by multi-starters. Metabolomics is defined as the study of all metabolites given in a biological system under particular physiological conditions 8 . The analytical techniques developed for metabolomics studi...

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