Combined microbiome and metabolome analysis of Dacha and Ercha fermented grains of Fen-flavor Baijiu

Fen-flavor Baijiu is produced via two fermentation rounds (Dacha and Ercha), and quality is shaped by microbes in fermented grains. We hypothesized that the two rounds select distinct lactic acid bacteria (LAB) consortia with different metabolic potentials that associate with stage-specific metabolites and flavor compounds. We profiled 24 fermented-grain samples using shotgun metagenomics and untargeted metabolomics. Ercha showed lower alpha-diversity and a composition distinct from Dacha. Lactobacillus acetotolerans dominated Dacha, whereas Acetilactobacillus jinshanensis dominated Ercha. We detected 225 differential metabolites; 12 involved in flavonoid biosynthesis were higher in Dacha, while pyrimidine metabolism was more prominent in Ercha. Several LAB species—including L. acetotolerans, Lentilactobacillus hilgardii, Lactobacillus amylovorus, and Lactobacillus amylolyticus—showed positive correlations with these flavonoids. Genes encoding L-lactate dehydrogenase and acetate kinase were mainly carried by L. acetotolerans and associated with acetic acid and ethyl acetate in fermented grains. These outcomes supported our hypothesis and suggested actionable levers for production: stage-targeted monitoring of marker taxa/genes and rational starter design to steer flavor formation in Fen-flavor Baijiu.