The changes of microbial community structure and biomass of different layers of Daqu for the production of special-flavor Baijiu (Te-Daqu) and its correction with flavor compounds are not well understood. In this study, the absolute quantitative and relative quantitative amplification sequencing techniques were used to determine the microbial compositions as well as their changes of different layers of Te-Daqu. Moreover, microbial source tracking was used to analyze the origins of dominant bacteria and fungi. Headspace solid phase micro-extraction combined with gas chromatography-mass spectrometry was used to analyze the content of flavor compounds in different layers of Te-Daqu. The results showed that the total bacterial biomass in core of Te-Daqu was significantly lower than that of surface-layer and middle-layer, i.e, was 55% of that of surface-layer and 53% of that of middle-layer. Weissella, Lactobacillus, and Enterobacter were the dominant bacteria within the surface-layer. Thermoactinomyces was the specific bacteria of the core-layer, whereas Saccharopolyspora only dominated in the middle- and core-layer rather the surface-layer. Isatchenkia and Pichia were the main yeasts within the surface-layer, while Aspergillus was the dominant mold within the core-layer. The total contents of alcohols, aldehydes and ketones, pyrazines, ethers, and phenols in the core-layer were higher than that in the surface- and the middle-layers, while the total contents of esters in the surface-layer were higher than that in the core-layer. These results provided an essential reference to optimize the Te-Daqu making process and to improve the quality of Te-Daqu by using ecological fermentation technology.
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