Microbiome dynamics and environment driving factors throughout pit fermentation of Jiang-flavor Baijiu: a multi-omics study

Pit fermentation process has a significant impact on Baijiu production. However, the dynamics patterns and environmental driving mechanisms in Jiang-flavor Baijiu pit fermentation remain unclear. Here, we present a multi-omics study on 180 Jiang-flavor Baijiu fermentation samples across the pit fermentation process. We revealed and validated the dynamics and metabolic functions of the core species employing both culture-independent (i.e., metagenomics and metatranscriptomics) and culture-dependent tools. Our findings delineate the fermentation into three distinct stages, each characterized by a unique microbial community, functional profile, and accumulation of flavor compounds. In stage I, Bacillus subtilis, Pichia kudriavzevii, and Saccharomyces cerevisiae were the most abundant species, while Acetilactobacillus jinshanensis, S. cerevisiae, P. kudriavzevii, Schizosaccharomyces pombe, and Zygosaccharomyces bailii had the highest transcriptional activity. In stage II, A. jinshanensis emerged as the most abundant and metabolically active species in stage II, reaching a proportion of 45.69%±20.21%, and maintained a leading role in stage III with a proportion of 65.75%±6.56%, a period marked by minimal microbial diversity and significant accumulation of key flavor substances, notably esters and acids. In addition, A. jinshanensis was isolated and its core acid-producing microbial status confirmed based on culture-dependent tools. Structural equation modeling indicated that A. jinshanensis plays crucial roles in the heterogeneous succession of alcohol-producing microorganisms, with spatial differences in acidity being a key factor. This work not only provides a robust analytical framework for understanding the Baijiu fermentation microbiome but also lays the groundwork for technological innovation in the fermentation industry.