Improving the quality of Cuqu is one of the necessary strategies increasing the quality and yield of fresh vinegar. Enhancing the consistency and characteristics of Cuqu is currently a prominent area of research. Here, we investigated the impact of fortified Muqu (FM) consisting of Bacillus velezensis and Bacillus subtilis on enhancing the quality of Cuqu compared to conventional Muqu (CM). Our results demonstrated that FM significantly increased the abundance of Bacillus by 1.85 to 8.19 times, as well as substantially elevated Kroppenstedtia abundance in Cuqu. Source Tracker analysis revealed a higher proportion of bacteria originating from FM in Cuqu compared to those derived from CM, indicating superior environmental adaptability for bacteria in the FM. Additionally, upregulation in expression levels of pyrazine-related key enzymes within Cuqu microbial communities was observed due to FM, resulting in a remarkable 39.70-fold increase in pyrazine compounds production. Multiphase detection technology confirmed that FM improved similarity in microbial community structure and function at different spatial positions within Cuqu. These results elucidated the regulatory function of FM in forming microbial communities and metabolic mechanisms within Cuqu, providing valuable insights for optimizing and predicting traditional fermentation processes in industrial production.

The quality and aroma of strong-flavor Baijiu are mainly dependent on Daqu, pit mud (PM), and the interaction of both. However, little is known about how their combination patterns affect the microbiome and metabolome of Zaopei, especially the metabolic function of rare taxa. Here, an experiment on industrial size was designed to assess the effects of 6 combinations (3 kinds of Daqu × 2 kinds of PM) on the composition and assembly of different taxa, as well as the flavor profile. The results showed that Zaopei’s microbiota was composed of a few abundant taxa and enormous rare taxa, and rare bacterial and abundant fungal subcommunities were significantly affected by combination patterns. The assembly processes of abundant/rare taxa and bacterial/fungal communities were distinct, and environmental changes mediated the balance between stochastic and deterministic processes in rare bacteria assembly. Furthermore, specific combination patterns improved the f lavor quality of Zaopei by enhancing the interspecies interaction, which was closely related to rare taxa, especially rare bacteria. These findings highlighted that rare bacteria might be the keystone in involving community interaction and maintaining metabolic function, which provided a scientific foundation for better understanding and regulating the brewing microbiota from the viewpoint of microbial ecology.