## 3 Results and Discussion
### Changes in Microbial Diversity during Fermentation
#### 3.1.2 Fungal Diversity  
The \(\alpha\)-diversity index analysis of fungi (Figure 2A) shows significant changes in fungal community structure during fermentation. The Chao1 index indicates a significant decrease in fungal richness, from approximately 150 in the CK group to about 32 in the JASF group (\(p\) = 0.0039). The Shannon index reveals a decrease in diversity and evenness, dropping from about 4.0 in the CK group to 3.3 in the JASF group (\(p\) = 0.0039), while [PERSON]'s evenness index increases from 0.56 to 0.68 (\(p\) = 0.0039). The Simpson index remains similar between groups at around 0.86 (\(p\) = 0.87), suggesting little change in the dominance of fungal communities. The number of observed species decreases significantly from about 148 to 30 (\(p\) = 0.0039), consistent with the Chao1 results. The Good's coverage index, nearly 1.000 for both groups (\(p\) = 0.52), indicates sufficient sequencing depth. Overall, while fungal richness decreases after fermentation, evenness increases, leading to a more uniform community structure. Figure 1: Composition and diversity of bacterial communities during spontaneous fermentation. \(\alpha\)-diversity index analysis of bacteria (**A**). Heatmap of genus-level species composition for co-clustering (**B**). Species diversity and abundance of bacteria at the phylum and genus levels (**C**). Statistical significance is indicated by **(\(p\) < 0.01). Figure 2: Composition and diversity of fungal communities during spontaneous fermentation. \(\alpha\)-diversity index analysis of fungi (**A**). Heatmap of genus-level species composition for co-clustering (**B**). Species diversity and abundance of fungi at the phylum and genus levels (**C**). Statistical significance is indicated by **(**\(p<0.01\)). Heatmap analysis reveals distinct fungal community structures before (CK group) and after (JASF group) fermentation (Figure 2B). During the natural fermentation of Jerusalem aritchoke tuber juice, significant changes in the fungal community structure were observed. Before fermentation (CK group), environmental fungi such as _Geosmithia_, _Paecilomyces_, _Brunneochlamydosporium_, _Alternaria_, and _Cladosporium_ dominated, participating in the initial degradation of organic matter. After fermentation, there was a notable increase in _Pichia_ and _Penicillium_. _Pichia_ proliferated significantly during fermentation, contributing to the stability and flavor development of the product. However, the increase in _Penicillium_ raises potential safety concerns due to possible mycotoxin production, which warrants further investigation to ensure product safety [50; 51]. Given that certain _Penicillium_ species can produce mycotoxins, it is essential to monitor and control their presence during fermentation to ensure the safety of the final product. The fermentation process, characterized by lower pH, organic acid production, and reduced oxygen levels, favored the growth of specific yeasts and molds while inhibiting plant pathogens like _Fusarium_ and _Alternaria_. This dynamic shift not only ensures the safety of the fermented product, but also enhances its flavor and quality. Figure 2C shows the species diversity and abundance of fungi at both the phylum and genus levels across two main groups, CK and JASF, with CK-JASF representing the shared fungal species between both groups. At the phylum level, _Ascomycota_ was dominant in all conditions, particularly in CK and CK-JASF, highlighting its critical role during fermentation. This phylum is known for its ability to produce enzymes and secondary metabolites that break down complex carbohydrates and contribute to flavor development [52]. _Basidiumycota_ was more abundant in CK but showed a significant reduction in JASF, possibly due to competition from _Ascomycota_ species that thrive in acidic fermentation environments. _Morietellomycota_ was present in trace amounts, suggesting a minimal role in the fermentation process.