## 3 Results and Discussion  
### Changes in Microbial Diversity during Fermentation  
#### 3.1.1 Bacterial Diversity  
A comprehensive analysis of the microbial communities in Jerusalem artichoke juice before (CK group) and after fermentation (JASF group) revealed significant shifts in microbial diversity (Figure 1A). The Chao1, observed species, and post-fermentation Faith_PD indices showed a marked reduction in diversity. Specifically, Chao1 decreased from approximately 483 to 314, observed species dropped from 443 to 307, and Faith_PD fell from 35 to 19. This suggests a dominance of certain microbial taxa during fermentation, resulting in decreased species richness. In contrast, the Simpson and Shannon indices, which reflect diversity and evenness, displayed an increase, with the Simpson index rising from 0.26 to 0.57 and the Shannon index from 1.5 to 2.3, indicating that, despite the reduction in species richness, the microbial community in the JASF group exhibited greater evenness, likely due to a more balanced distribution of dominant species. This observation was further supported by the Pielou_e index, which showed improved species evenness in the JASF group (0.28) compared to the CK group (0.17). Additionally, the Good's coverage index, approaching 1.000 in both groups, confirmed that the sequencing depth was sufficient to capture the microbial diversity present. These findings suggest that, while fermentation reduced overall species richness, it promoted a more balanced and even microbial community structure, likely driven by changes in substrate availability and microbial competition, indicating a shift in the microbial ecosystem dynamics throughout the fermentation process. Heatmap analysis (Figure 1B) further highlighted significant differences in microbial community structures between the CK and JASF groups. During the natural fermentation of Jerusalem artichoke tuber juice, the microbial community structure underwent substantial changes. Prior to fermentation, environmental bacteria, such as _Flavobacterium_, _Sphingomonas_, and _Luteomonas_, predominated, participating in the initial degradation of organic matter in the tuber juice. After fermentation, beneficial bacteria like _Lactobacillus_ and _Pediococcus_ increased significantly, promoting lactic acid production, lowering pH,and thereby inhibiting the growth of harmful bacteria and stabilizing the fermentation environment [46]. _Enterobacter_ and _Bacillus_ also proliferated during fermentation, and while the former includes some potential pathogens, the latter are mostly beneficial, although certain species like _Bacillus cereus_ may cause food poisoning. Therefore, understanding the dynamic changes of beneficial and pathogenic bacteria during fermentation is crucial for ensuring the safety of the fermented product and optimizing the process. Figure 1: _Cont._  
The species diversity and abundance of bacteria at the phylum and genus levels during the spontaneous fermentation of Jerusalem archokte tubers are displayed in Figure 1C. CK and JASF represent unique bacterial communities specific to each fermentation stage, while CK-JASF represents the bacterial species shared between both groups, highlighting overlapping metabolic activities during fermentation. The microbial community is highly diverse, involving multiple phyla and genera, which is essential for a balanced fermentation process, contributing to the development of flavors, textures, and possibly health benefits of the fermented product. _Proteobacteria_ was the dominant phylum in the CK group, indicating its significant role before fermentation, while _Frimicutes_ became more prominent in the JASF group, suggesting their increased activity during fermentation. However, _Proteobacteria_ in the CK group might include potential pathogens that start to decrease as fermentation progresses, suggesting the need to control such pathogens during natural fermentation.