This study employed high-throughput sequencing technology to determine the microbial diversity in the brewing workshop environment, Daqu, pit mud, and fermented grains (Jiupei) at different fermentation stages for Nongxiangxing Baijiu. The results showed that the microbial community in the brewing workshop environment had the highest richness and diversity, which was significantly different from that in Jiupei during the fermentation process (P < 0.05). The traceability results indicated that in terms of bacterial communities, the environmental microorganisms contributed the most to Jiupei (64.6%, in the middle and late stages of fermentation), followed by the Daqu microbial community (35.2%, in the early stage of fermentation). In terms of fungal communities, the pit mud microbial community contributed the most to Jiupei (50.2%). The dominant microorganisms in the fermentation process of Jiupei included Lactobacillus, Acetobacter, and Debaryomyces, mainly originated from the environment; Thermoactinomyces, Bacillus, Kroppenstedtia, Weissella, and Thermoascus, mainly originated from Daqu; Kazachstania, Saccharomyces, and Pichia, mainly originated from pit mud. The non-volatile metabolic substances in the fermentation process of the fermented Jiupei were mainly concentrated in organic acids and derivatives, lipids and lipid-like molecules, and organic heterocyclic compounds. The metabolic networks of the microbial communities during the fermentation process were closely connected and interacted strongly. According to the classification of Zi-Pi nodes in the metabolic network, 15 metabolic substances such as 1-nitrosopiperazine, methylfuranol, 4-oxo-2-propyl-pentanoic acid, catechin-7-xyloside, 3-isopropylmalic acid, and 4-vinylcyclohexene were identified as key nodes in the metabolic network. The dominant bacterial communities in the fermentation process of Jiupei were more closely related to the key flavors and had a stronger connection with them than did the fungal communities. This study provides solid theoretical support and practical guidelines for the optimization of Nongxiangxing Baijiu production, helping promote the sustainable development of the Baijiu industry.

This study employed high-throughput sequencing technology to determine the microbial diversity during the fermentation process of Nongxiangxing Baijiu Jiupei. The results showed that based on the succession patterns of the microbial communities, the fermentation process could be divided into three stages: early (days 0–12), middle (days 15–40), and late (days 50–90). The major biomarkers at the early stage were Thermoactinomyces, Bacillus, Kroppenstedtia, Weissella, Saccharopolyspora, Thermomyces, Thermoascus and Rhizopus. The biomarkers at the middle stage were Saccharomyces and Wickerhamiella. The major biomarkers at the late stage were Lactobacillus, Kazachstania, Saccharomycopsis, Aspergillus and Wickerhamomyces. Compared with the middle and late stages, the ecological network connection of the microbial communities at the early stage was more compact, and the interaction was stronger. Starch, reducing sugar and moisture contents were the most important physicochemical factors for explaining the phased succession of the microbial communities. This study provides solid theoretical support and practical guidelines for the production of Nongxiangxing Baijiu, promoting the sustainable development of the Baijiu industry.