Unveiling microgeographical and seasonal variation in the microbiome and proteome of Fen-flavored Daqu

Abstract

Fen-flavored Daqu (FFD) serves as a pivotal fermentation starter in producing Fen-flavored Baijiu, yet the impacts of geography and season on its microbiome and functional potential remain incompletely understood. In this study, we conducted integrated metagenomic and metaproteomic analyses of FFD samples from distinct locations and seasons. Our findings revealed that both factors significantly influenced microbial community composition: fungal genera (Lichtheimia, Rhizopus, and Pichia) often predominated, whereas Streptomyces and Lactobacillus were among the major bacterial contributors. Differential protein-expression analyses showed that carbohydrate transport and metabolism contained the largest number of significantly changing proteins in both the microgeographical and seasonal comparisons, underscoring the vital roles of glycolytic and polysaccharide-degrading enzymes. Seasonal shifts—particularly from summer to winter—altered key enzymes such as alpha-glucosidase, beta-glucosidase, and glucoamylase. Cross-kingdom comparisons revealed that genera abundant in metagenomic data do not always mirror those in metaproteomic profiles, pointing to functional complexity and complementarity between datasets. Our results highlight how microgeographical and seasonal factors modulate FFD's microbial ecosystem and drive the expression of crucial enzymes, ultimately affecting the quality and flavor of Fen-flavored Baijiu.