Multiomics Insights into Microbiome Succession throughout Medium-Temperature Daqu Fermentation

Abstract

The production of traditional medium-temperature Daqu (MT-Daqu) relies heavily on manual adjustments of fermentation parameters, which regulate microbiota to influence Daqu’s functional properties and metabolites. However, the mechanisms underlying the effects of these parameters remain poorly understood. First, the fermentation process was divided into 5 distinct stages based on physicochemical and sensory characteristics, particularly temperature and acidity. Second, multiomics approaches (metagenomics, metatranscriptomics, and metaproteomics) were employed to investigate microbial succession, functional dynamics, and key enzyme activity across metabolic pathways. Our findings demonstrated that Daqu fermentation progressed through 3 functional phases: microbial proliferation (days 0–8), microbiota restructuring (days 8–12), and aroma synthesis (days 12–32). Notably, lactic acid, primarily synthesized by lactic acid bacteria, dominated the organic acid profile initially, accounting for 67.427 ± 0.128% on day 2. By day 17, fungal-derived acids (succinic acid, malic acid, and acetic acid), mainly synthesized by Lichtheimia, became predominant, constituting 60.370 ± 0.641% of the total organic acids. This transition in acid dominance mirrored a microbial community shift from bacterial to fungal predominance. Collectively, this study establishes a multidimensional analytical framework for deciphering the MT-Daqu fermentation microbiome.