Defined synthetic microbial communities improve process controllability and inter-site reproducibility in high-temperature Daqu production.

High-temperature Daqu (HTD), the core starter for sauce-flavor Baijiu, is highly susceptible to quality fluctuations because it is produced through open solid-state fermentation and depends on heterogeneous Muqu. Here, we evaluated whether defined synthetic microbial communities (SynMCs) could improve process controllability and inter-site reproducibility during HTD production. SynMC biofortification reduced physicochemical variability and reshaped microbial community succession in a stage- and composition-dependent manner. Among the tested designs, inter-kingdom community, particularlySynMC4 and SynMC6, showed comparatively stable physicochemical performance and higher pyrazine accumulation. Integrated multi-omics analysis associated pyrazine enrichment with coordinated shifts in specific low-abundance taxa, suggesting that rare members may participate in VOC differentiation under SynMC regulation. Ecological analyses further indicated that SynMCs altered the balance between stochastic and deterministic assembly and reorganized co-occurrence networks by modifying connectivity and modularity, although these effects varied across fermentation stages and subcommunities. Cross-site validation showed that SynMC6 exerted partially consistent regulatory effects on bacterial communities across geographically independent production systems, while the magnitude and specific metabolic outcomes remained site-dependent. These findings provided an application-oriented basis for improving HTD standardization and highlight the need to incorporate both abundant and rare taxa into further SynMC design.