The fermentation of sauce-flavor Baijiu requires high-temperature Daqu as the starter, which is classified into three types: white, yellow, and black. Recent studies highlighted the variability of the microbiota and metabolome profiles of these three types of Daqu, however, what functions they precisely provide in the sauce-flavor Baijiu brewing process remains unclear. In this study, white, yellow, and black Daqu in five different proportions were utilized as starters in field-scale Baijiu fermentation, with the control group lacking Daqu inoculation. Fermented grains inoculated with 100% white Daqu (47.7 °C) had the highest temperature during stacking fermentation, while 100% black Daqu and control groups were lower than 45 °C. Lactic acid (12.6–22.0 mg/g) was the most abundant organic acid, followed by acetic acid (0.7–5.0 mg/g). qPCR analysis revealed that bacterial biomass decreased during fermentation, while fungal biomass increased. A comparison with the control revealed that Daqu contributed high-temperature resistant microorganisms to the stacking fermentation process, primarily Kroppenstedtia, Virgibacillus, Byssochlamys, Thermoascus, and Thermomyces. Meanwhile, stacking fermentation promoted the enrichment of Acetobacter, Kazachstania, and Leiothecium. Mantel test and co-occurrence network analysis revealed that utilizing different fermentation starters could vary the biotic and abiotic factors that drive microbial community succession. We investigated the flavor of Baijiu further, and found that fermentation with white Daqu enhanced the accumulation of ethyl acetate, isoamyl alcohol, and isobutanol, whereas black Daqu increased the accumulation of ethyl lactate, lactic acid, and furfural. This study contributes to the rational usage of different types of Daqu in the manufacturing of Baijiu.
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