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 a crucial factor in Baijiu brewing since it determines the yield and flavor. However, the impact of the microbial community during the initial fermentation stage on Baijiu quality remains uncertain. Herein, high-throughput sequencing was employed to investigate the microbial diversities and distribution during Baijiu fermentation in individual pit mud workshops at both initial and late stages. During the initial fermentation stage, the bacterial community exerted a more pronounced effect on Baijiu quality than the fungal community. And the high-yield pit mud workshop exhibited lower richness and evenness, as well as greater Bray-Curtis dissimilarity during Baijiu fermentation. Lactobacillus was the dominant genus and biomarker in high-yield pit mud, and it constituted the only genus within the bacterial association network during the late fermentation stage. Fungal communities tended to maintain a simple association network with selected core species. Based on the correlation network, Rhizopus and Trichosporon were identified as biomarkers in Baijiu fermentation process. Together, Lactobacillus and Rhizopus could serve as bio-indicators for Baijiu quality during the initial fermentation stage. Therefore, these findings provided novel insights into microbiota interactions during fermentation and the impact of initial microbiota on final Baijiu quality.