## 3 Results  
### Temporal Profile of Microbial Community Composition  
The temporal profile of microbial community composition in fermented grains was investigated by high-throughput sequencing. A total of 6,516,245 high-quality bacterial sequences and 6,727,486 high-quality fungal sequences were obtained from the samples, with 328 bacterial OTUs and 508 fungal OTUs. The rarefaction curves based on OTUs identified from samples gradually flattened as the number of samples increased, indicating that the sequencing depth was sufficient and most phylotypes were captured from a sufficient amount of data (Figures S1 and S2). The Shannon and Chao1 indexes of the bacterial community, which indicated the diversity and richness of the bacterial community, gradually increased during the heap fermentation process, reaching the highest levels at the end of heap fermentation, and then they gradually decreased with the extension of pit fermentation. The results showed that during the third round of fermentation, the diversity and richness of the bacterial community showed a trend of firstly an increase and then a decrease (Table S1). The Shannon index of the fungal community gradually decreased during heap fermentation and increased during the pit fermentation, ultimately reaching its highest level. The Chao1 index of the fungal community decreased during heap fermentation and fluctuated between 50.17 and 80.50 during pit fermentation, ultimately reaching the lowest level. These results indicated that the diversity of the fungal community increased while the richness decreased during the third round of the fermentation process (Table S2). The results of the principal coordinate analysis based on the profile of the microbial community showed that the bacterial and fungal community structure during heap fermentation was significantly different from that during pit fermentation (Figure 1). The SILVA rRNA and greengene databases were used for the classification and identification of the microorganisms [16]. In the third round of the fermentation process, 141 genera of bacteria were identified. There were 10 genera with relative abundances greater than 1%. The dominant bacteria genera included _Lactobacillus_, _Virgibacillus_, _Oceanobacillus_, _Kroppenstedtia_, _unclassified_c_Bacillus_, and _Bacillus_ (Figure 2A). With the extension of time, the relative abundance of _Lactobacillus_ showed an increasing trend, reaching a maximum of 98.77% at 21 days of pit fermentation. In contrast, the relative abundance of _Virgibacillus_, _Oceanobacillus_, _Kroppenstedtia_, and _unclassified_c_Bacillus_ gradually decreased with time. By using [PERSON]'s correlation coefficient, the correlations between the top bacterial genera in terms of relative abundance were analyzed (Figure 3A). _Lactobacillus_, as the genus with the largest average relative abundance, was negatively correlated with all the other genera. _Virgibacillus_, _Oceanobacillus_, _Kroppenstedtia_, and _Bacillus_ were positive correlated not only with each other but also with several genera (Figure 3A). For fungi, a total of 209 genera were found in the samples, of which, _Byssochlamys_ and _Issatchenkia_ were the predominant genera, and _Monascus_, _Thernococcus_, _Aspergillus_, _Thermomyces_, _Leiothecium_, _Saccharomyces_, and _Pichia_ were the subdominant genera (Figure 2B). The relative abundance of _Byssochlamys_ reached a maximum of 95.16% at 3 days of heap fermentation and gradually decreased with time, reaching a minimum of 7.16% at the end of the pit fermentation. In contrast, the relative abundance of _Issatchenkia_ showed an increasing trend with the increase in fermentation time, reaching a maximum at the end of the pit fermentation. Correlation analyses showed that _Byssochlamys_ was negatively correlated with _Issatchenkia_, _Thermoscus_, _Aspergillus_, _Thermomyces_, _Leiothecium_, _Pichia_, _Hypophichia_, _Rasamsonia_, _Wickerhamomyces_, and _unclassified_Dipodascaceae_.