Integrated microbiome and metabolome analyses reveal spatial heterogeneity of medium-temperature Daqu and its potential impact on simulated strong-flavor baijiu fermentation

Medium-temperature Daqu (MTD) exhibits pronounced spatial heterogeneity between its surface (QS) and inner (QI) portions, yet their functional differences remain poorly understood. This study compared physicochemical properties, metabolites, and species-level microbial communities of QS and QI and evaluated their impacts on simulated strong-flavor Baijiu (SFB) fermentation. QS exhibited higher saccharification and liquefaction activities and higher counts of lactic acid bacteria and yeasts, whereas QI was enriched in thermophilic molds and volatile compounds. Thirty-two microbial biomarkers differentiated QS and QI, and QS showed a more complex microbial co-occurrence pattern. Simulated fermentation revealed early bacterial divergence followed by convergence to Acetilactobacillus jinshanensis. During mid-to-late fermentation, QI showed higher levels of acids and esters than QS. Collectively, QS was mainly associated with substrate conversion and early fermentation initiation, whereas QI was more closely associated with flavor development during later fermentation stages. These findings provide valuable insights into MTD optimization and SFB quality control.