Abstract: Lactic acid bacteria dominate the bacterial community in Nongxiangxing Baijiu Daqu, which play an important role in maintaining microecological balance and synthesizing flavor precursors, thereby shaping the quality of baijiu. This study analyzed the bacterial community structure in Nongxiangxing Baijiu Daqu via amplicon sequencing and isolated its dominant strains. Furthermore, by integrating genomic and pan-genomic analyses, we elucidated the physiological metabolism and genetic evolution characteristics of these strains. The results showed that Weissella confusa was the dominant species in the late stage of Daqu fermentation. W. confusa DQM2 was successfully isolated as a representative strain. This strain displayed robust thermotolerance (growth at 48 ℃) and could utilize 15 carbon sources. Under pure culture conditions, it produced (14.80 ± 0.49) g/L of L-lactic acid and (4.80 ± 0.61) g/L of acetic acid via heterolactic fermentation after 72 hours. DQM2 had a genome size of 2.22 Mb with a GC relative content of 44.64%. In addition, the genome harbored a complete HSP70 heat shock protein system (DnaK-DnaJ-GrpE), 8 core heat shock genes, 3 antioxidant-related genes, and 261 genes associated with environmental stress tolerance. These genes might collectively assist the strain in resisting high-temperature stress in Daqu by maintaining cellular homeostasis, enhancing antioxidant capacity, utilizing multiple carbon sources, and regulating cell membrane composition. Further pan-genomic analysis of 112 high-quality W. confusa genomes indicated that this species had an open pangenome, with DQM2 harboring 36 unique gene families, including glutathione amide reductase and pantothenate transport protein. These gene families may contribute to heat adaptation through antioxidant activity, enhanced metabolism, and unique regulatory networks. Genomic island analysis suggested that DQM2 possessed a heat stress response network regulated by CtsR and harbored a prophage fragment encoding partial structural proteins and possessing lytic functions, providing a genetic basis for its ecological competitive advantage in the stressful Daqu environment. This study provides theoretical support for exploring dominant microbial resources from Baijiu brewing and studying the ecological adaptability of lactic acid bacteria during Daqu fermentation.

Key words: Weissella confusa; Daqu; whole-genome sequencing; pan-genome; heat tolerance mechanism