The initial composition and structure of microbial community determined the yield and quality of Baijiu during the spontaneous fermentation

The microbiota during pit mud fermentation is one of the most important factors in Baijiu brewing since it determines the yield and quality. However, the effects of the microbial community at the initial stage of Baijiu fermentation remain unknown. Herein, we used high-throughput sequencing to explore the microbial diversity and distribution at the initial and late stages of Baijiu fermentation in individual pit mud workshops. At the initial fermentation stage, the bacterial community had a more significant effect on Baijiu quality than the fungal community. The richness and evenness of the bacterial community in the high-yield pit mud workshop were lower, as well as the Bray–Curtis dissimilarity, during Baijiu fermentation. Lactobacillus was the dominant genus and the biomarker in high-yield pit mud and the only genus composing the association network. For the high Baijiu yield rate, the fungal community tended to maintain a simple association network with a few species as the core microbiota. Rhizopus and Trichosporon were the biomarkers according to the association network during Baijiu fermentation. Finally, Lactobacillus and Rhizopus might be used as bio-indicators for Baijiu quality in the initial fermentation stage. Therefore, we provided new insights into microbiota interactions during fermentation and the effects of the initial microbiota on the final Baijiu quality.