Stage-Resolved Transcriptional Regulation and Metabolic Interplay during Wine Fermentation with Saccharomyces cerevisiae and Oenococcus oeni

Wine fermentation and flavor development are mediated
by complex
microbial interactions. Previous studies have shown that coinoculation
with Oenococcus oeni can alter acid
composition and aroma, yet the underlying transcriptional responses
of S. cerevisiae and the metabolic
strategies adopted by both species remain poorly understood. In this
study, we performed mixed fermentation of S. cerevisiae and O. oeni, dividing the process
into 6 representative stages for stage-specific analysis. Comparative
evaluation with pure S. cerevisiae fermentation
revealed that the presence of O. oeni reshaped both the acid profile and aromatic complexity of wine,
while also influencing the growth kinetics of S. cerevisiae. Time-resolved transcriptomics demonstrated that O. oeni markedly altered the transcriptional dynamics
of S. cerevisiae through changing the
magnitude of transcriptional level while incurring opposite regulatory
patterns in a small set of genes involved in stress responses and
sulfur metabolism. Through the integration of a community genome-scale
metabolic model with stage-resolved transcriptomic constraints, we
resolved dynamic flux distributions of the mixed fermentation (MF)
system and further revealed the metabolic impact of O. oeni on S. cerevisiae and MF. O. oeni exhibited low competitiveness
for glucose but actively utilized fructose to generate energy through
the phosphoketolase pathway. Also, it showed reversible reaction fluxes
of two reactions involved in acetate formation (ACKr/PTAr), thereby
impacting acetate levels. In addition, metabolic interactions including
amino acid (e.g., arginine, serine, threonine) and mannitol exchange
were identified, reflecting both cooperative and competitive features
of mixed fermentation. Collectively, this work provides the first
comprehensive depiction of the transcriptional and metabolic interplay
between S. cerevisiae and O. oeni during mixed fermentation, offering mechanistic
insights into microbial cooperation and strategies for the rational
design of wine fermentation and flavor quality.