Decoding species-level microbial diversity in low-temperature Daqu via cultureomics and genomic characterization of functionally promising strains

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Low-temperature Daqu (LT- Daqu ) serves as the starter for light-flavor Baijiu , but its species-level microbial composition and functional roles are poorly characterized. Here, high-throughput amplicon sequencing, large-scale cultureomics and whole-genome sequencing were combined to comprehensively profile the cultivable microbiota and predict metabolic functions. Results showed Bacillus , Streptomyces, and Saccharomycopsis dominated genus-level communities, with >98 % of bacterial and >40 % of fungal sequences unassigned to known species. Cultureomics recovered 295 bacterial and 97 fungal isolates, including 45 bacteria and 19 fungi undetected by amplicon sequencing. Comparative genomics of eight dominant isolates (four Staphylococcus species and four fungal species) revealed yeasts harbored richer carbohydrate-active enzyme repertoires (294–315 CAZyme genes), while staphylococci possessed abundant secondary-metabolite biosynthetic gene clusters. KEGG enrichment analysis predicted a rich supply of flavor-relevant metabolites (alcohols, amino acids, organic acids and terpenoids) from both bacterial and fungal guilds. Notably, S. gallinarum encoded >1000 genes linked to catalytic activity and harbored terpenoid biosynthetic pathways, suggesting an under-appreciated role in aroma formation. These findings demonstrate that cultureomics markedly extends the known species diversity of LT- Daqu and identifies key taxa whose unique metabolic traits likely shape the microbial consortium and flavor chemistry of light-flavor Baijiu fermentation.