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Purpose The microbial community in the pit mud correlated closely with the quality of the final product of Chinese strong-flavored Baijiu (CSFB). However, environmental conditions and brewing processes can vary by region and distilleries. This may lead to differences in microbial composition and function in pit mud. Therefore, revealing the features of the pit mud microbial community structure and functions of different distilleries will provide key information for understanding the diversity and difference of microbes in the brewing of CSFB, which will be beneficial for the improvement of the quality of pit mud and CSFB in the future. Methods and results Illumina MiSeq sequencing of 16S rRNA gene amplicons was used to analyze the similarities and differences in microbial community structure and function in pit muds of different distilleries located in Shihezi (Xinjiang), Xiangyang (Hubei), and Yibin (Sichuan). At the genus level,  Clostridium ,  Lactobacillus ,  Aminobacterium ,  Petrimonas ,  Syntrophomonas ,  Methanoculleus ,  Syntrophaceticus ,  Sedimentibacter ,  Caloramator ,  Ruminococcus ,  Bacillus ,  Methanosarcina , and  Garciella  were the dominated genera of pit muds. There were great differences in the composition of microorganisms in pit muds used by different distilleries. The significantly enriched prokaryotic microbiotas of pit muds collected in the distilleries of Xiangyang were mainly affiliated with  Bacillus ,  Lactobacillus , and  Croceifilum , and the relative abundance of methanogens, such as  Methanomicrobia  and  Methanobacteria , were only significantly enriched in the pit mud collected from the distilleries of Yibin ( P  &lt; 0.05). Functional analysis indicated that the difference of microbial composition in pit mud will further lead to significant differences in various metabolic functions. Conclusion The compositions and functions of dominant microorganisms in pit mud used for the production of CSFB by different enterprises across regions in China were greatly different, and there was a close relationship between the compositions and functions of microorganisms in pit mud. Therefore, it may be an effective method to improve CSFB fermentation processes by directionally regulating the microbial community functions of pit mud using specific strains.

Deep sequencing reveals changes in prokaryotic taxonomy and functional diversity of pit muds in different distilleries of China