Variations in Bacterial and Archaeal Communities and Baijiu Metabolites by Distillery and Pit Age

Pit mud (PM) harbors abundant bacteria and archaea, shaping Baijiu’s flavor and adapting to high-ethanol and acidic conditions. This study integrated 16S rRNA sequencing, physicochemical analysis, and non-targeted metabolomics. The results showed that the 30-year-old Zhuyechun PM had higher levels of humic acid, while the 20-year-old Fengchun and Bitanchun PM exhibited near-neutral pH, which is favorable for Clostridia and methanogens. Canonical correspondence analysis revealed Rummeliibacillus and Caproiciproducen positively correlated with organic carbon, humic acid, and available phosphorus, whereas Methanosarcina showed negative correlations. In Baijiu, 1206 non-volatile signals were identified, with unsaturated fatty acid biosynthesis as a key flavor pathway. Methanogens significantly associated with key metabolites (p < 0.05). These findings reveal the correlation between the PM microecosystem and Baijiu quality, providing insights for the development of high-quality Baijiu.