Metagenomic Profiling of the Bacterial Community Changes from Koji to Mash Stage in the Brewing of Soy Sauce

Abstract

The improvement of soy sauce fermentation is restricted by the insufficient information on bacterial community. In this study, bacterial communities in the koji and mash stage were compared based on next-generation sequencing technology. A total of 29 genera were identified in the koji stage, while 34 in the mash stage. After koji stage, 7 genera disappeared and 12 new genera appeared in the mash stage. The dominant bacteria were Kurthia, Weissella and Staphylococcus in the koji stage and Staphylococcus, Kurthia, Enterococcus and Leuconostoc in the mash stage. The results provided insights into the microbial communities involved in soy sauce fermentation.

Deciphering microbial community dynamics along the fermentation course of soy sauce under different temperatures using metagenomic analysis

“…In contrast, almost all bacteria in the mash stage were already present in koji. The sharp difference between our study and that of the previous research [ 11 ] may be simply due to a lower threshold for filtering taxa of a certain abundance in our study (0.002% in our study vs. 1.0% in the previous study), especially given the approximate sequencing depths.…”

“…Interestingly, previous research [ 11 ] detected seven genera missing from koji and 12 genera newly appearing in mash using metagenomic analysis. Such a “gain and loss” scenario was also present in our study, with 25 and 29 genera exclusive to the koji stage in the RT and CT experiments, respectively.…”

“…One genus was exclusive to the mash stage in the CT experiment, and there were no genera exclusive to the mash stage in the RT experiment. The higher number of taxa in koji may be attributable to the black soybeans, which provide much more organic material for fermentation than the defatted regular soybeans used in the previous study [ 11 ]. Nevertheless, many bacteria disappeared when shifting to the mash stage.…”

“…Through culture-dependent and culture-independent methods, such as polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis, the microbiota involved in different stages of soy sauce fermentation has been explored [ 8 ]. Most studies were conducted for a single stage fermentation, such as koji making or mash fermentation [ 9 , 10 ], or compared the presence/absence of bacteria between stages [ 11 ]. Moreover, different fermentation temperatures tend to generate products with different flavors [ 12 ].…”

The microbiome of Chinese rice wine (Huangjiu)

“…Therefore, the metagenomic method can be used to reveal microbial diversity and provide a deeper understanding of the metabolic capacity of the microbiome ( Liu et al, 2019 ; Wei et al, 2018 ). Generally, after extracting the total DNA from the samples, sequencing and bioinformatics analysis are performed ( Wei et al, 2018 ) and metagenomic sequencing has been widely used to study microbial populations and functions in fermented foods ( De Filippis, Parente and Ercolini, 2017 ; Liu et al, 2019 ), such as Huangjiu ( Wang et al, 2014a ), soy sauce ( Wang et al, 2017 ), dry sausages ( Hu et al, 2021 ), traditional Korean bean paste and kimchi ( Jeong et al, 2014 ; Jung et al, 2011 ), and traditional fermented fish sauce ( Shen et al, 2021 ). These studies used metagenomic sequencing to provide a theoretical basis for analyzing the relationship between microbial populations and specific flavors in these fermented foods.…”