In this study, the influence and relationship between the microbial structure composition at different spatial locations during soy sauce fermentation and the quality of soy sauce were investigated. Within 3–7 days of fermentation, the abundance of Chromohalobacter in the surface and upper layers of moromi was initially high but subsequently decreased. In contrast, Tetragenococcus exhibited low abundance on the surface of moromi at the beginning of fermentation but emerged as the absolute dominant bacteria by the end of the fermentation process. Throughout the fermentation period of 3–42 days, Staphylococcus and Bacillus were the predominant bacterial genera observed at the bottom of the moromi. In addition, Halanaerobium was the dominant bacterial genus in the crude soy sauce layer throughout the fermentation process. Tetragenococcus and Zygosaccharomyces were strongly positively correlated with total acid and ammonia nitrogen. Bacillus and Staphylococcus were significantly negatively correlated with the salt content.
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