Expression data from yeast strain VIN13 in pure-culture fermentations and in mixed fermentations with co-inoculated Oenococcus oeni strain S6

The yeast Saccharomyces cerevisiae is an important component of the wine fermentation process and determines various attributes of the final product. However, lactic acid bacteria (LAB) are also an integral part of the microflora of any fermenting must. Various wine microorganism engineering projects have been endeavoured in the past in order to change certain wine characteristics, namely aroma compound composition, ethanol concentration, levels of toxic/ allergenic compounds etc. Most of these projects focus on a specific gene or pathway, whereas our approach aims to understand the genetically complex traits responsible for these phenotypes in a systematic manner by implementing a transcriptomic analysis of yeast in mixed fermentations with the LAB O. oeni. Our aim is to investigate interactions between yeast and LAB on a gene expression level to identify targets for modification of yeast and O. oeni in a directed manner. Our goal was to identify the impact that the common wine microorganism O. oeni (malolactic bacteria) has on fermenting yeast cells on a gene expression level. To this end we co-inoculated the yeast and bacteria at the start of fermentation in a synthetic wine must, using yeast-only fermentations witout O. oeni as a control. Fermentations were carried out in synthetic wine must in triplicate for both the control S. cerevisiae VIN13 strain and the mixed fermentation of VIN13 and O. oeni (strain S5). Sampling of yeast for RNA extractions were performed at day 3 of fermentation, during the exponential growth phase of the yeast cells, and again at day 7 of fermentation, during the early stationary growth phase.

酿酒酵母（Saccharomyces cerevisiae）是葡萄酒发酵过程中的关键组成部分，可决定最终成品的多项品质属性。然而，乳酸菌（Lactic Acid Bacteria, LAB）同样是所有发酵葡萄汁微生物群落中不可或缺的组成部分。过往已有多项葡萄酒微生物工程研究，旨在调控葡萄酒的多项特性，具体包括香气物质组成、乙醇浓度、有毒/致敏物质含量等。此类研究大多聚焦于单个基因或代谢通路（metabolic pathway），而本研究则采用系统研究思路，通过对与LAB酒酒球菌（Oenococcus oeni, O. oeni）共发酵的酿酒酵母进行转录组分析（transcriptomic analysis），解析调控上述表型（phenotype）的遗传复杂性状。本研究旨在从基因表达层面解析酿酒酵母与LAB的互作机制，从而定向筛选可对酿酒酵母及酒酒球菌进行遗传改造的靶标位点。本研究的核心目标是从基因表达层面，明确常见葡萄酒微生物酒酒球菌（O. oeni，苹果酸乳酸菌）对发酵中酿酒酵母细胞的影响。为此，我们在合成葡萄酒葡萄汁中于发酵起始时共接种酿酒酵母与酒酒球菌，并以仅接种酿酒酵母、不添加酒酒球菌的发酵体系作为对照组。本实验针对对照酿酒酵母VIN13菌株体系，以及VIN13与酒酒球菌S5菌株的共发酵体系，均在合成葡萄酒葡萄汁中进行三次生物学重复。我们分别于发酵第3天（酿酒酵母处于指数生长期（exponential growth phase））及第7天（酿酒酵母处于早期稳定生长期（early stationary growth phase））采集酵母样本用于RNA提取（RNA extraction）。