## 3 Results and Discussion
### Bacterial Community Analysis in CTS and Fermented Dough  
Bacterial communities were analyzed by high-throughput sequencing of 16S rRNA gene. The sequencing and diversity results for bacterial communities are shown in Table S2 and Figure 2C,D. The number of sequences for each sample was between 34,143 and 55,287, and the rarefaction curves indicated adequate sequencing depth. The Shannon and Chao1 indexes of the CTS group were higher than those of the AFD and FD groups, suggesting that CTS had higher species abundance and richness than fermented dough. The phylum Firmicutes was dominant (Figure S1B), with relative abundance of 79.8% in the CTS group, and higher abundance in the AFD and FD groups. The subdominant phylum was Proteobacteria, with relative abundance of 20.6% in the CTS group, but this phylum almost disappeared from the AFD and FD groups. Nine bacterial genera (Figure 3C,D) were identified in CTSs and fermented doughs, namely _Pediococcus_, _Companilactobacillus_, _Weissella_, _Fruticlactobacillus_, _Levilactobacillus_, _Latilactobacillus_, _Acetobacter_, _Limosiactobacillus_, and _Gluconobacter_[23; 24]. Among them, _Pediococcus_, _Companilactobacillus_, _Weissella_, _Fruticlactobacillus_, _Levilactobacillus_, _Latilactobacillus_, and _Limosiactobacillus_ were common LAB and always found in fermented food. The predominant genus of bacteria in CTS group was _Pediococcus_, and its relative abundance was higher in the FD and AFD groups than in the CTS group, revealing that _Pediococcus_ was enriched during dough fermentation. Adding alkali increased the relative abundance of _Pediococcus_ from 37.8% in the FD group to 41.1% in the AFD group. _Companilactobacillus_ was the sub-abundant genus in the CTS group, and adding alkali decreased its relative abundance in the AFD group. The third abundant genus was _Weissella_ in the CTS group. Notably, _Acetobacter_ and _Gluconobacter_ were detected in the CTS group, but almost none of them was observed in the AFD and FD groups. This could be explained by the following reason: _Acetobacter_ and _Gluconobacter_ were originated from the raw materials (e.g., _Cucumis melo_) of CTSs, and they could not survive in dough. DNA from dead cells of _Acetobacter_ and _Gluconobacter_ in CTSs were detected by high-throughput sequencing. In the fermentation process, addition of wheat flour and water led this DNA to greatly diluting, and DNA was also degraded during the leavening process [12]. Figure 3: Relative abundance of microbial communities in CTS, FD, and AFD. (**A**) Fungal communities in three groups (CTSs, FDs, and AFDs from eight regions of China) at the genus level. (**B**) Fungal communities in 24 samples (CTSs, FDs, and AFDs from eight regions of China) at the species level. (**C**) Bacterial communities in three groups at the genus level. (**D**) Bacterial communities in three groups at the species level. (**E**) Bacterial communities in three groups at the species level. (**F**) Bacterial communities in 24 samples at the species level. Samples are indicated using the following codes: CTS samples (WW-S, WN-S, YC-S, LY-S, LK-S, HZ-S, BZ-S, WH-S); FD samples (WW-F, WN-F, YC-F, LY-F, LK-F, HZ-F, BZ-F, WH-F); and AFD samples (WW-A, WN-A, YC-A, LY-A, LK-A, HZ-A, BZ-A, WH-A). A Venn plot was used to analyze the similarity and specificity of bacterial species among the CTS, FD, and AFD groups (Figure 4A), indicating that the microorganisms in fermented doughs were almost all derived from CTSs and that adding alkali caused changes between the FD and AFD groups in the types of species originated from CTSs. Co-occurrence network analysis (Figure 4B) of bacterial communities in all CTSs and fermented doughs reflected the dominant species types and coexistence relationships among these samples. The dominant species in CTS, AFD, and FD samples from a given region were the same, indicating alkali addition did not change the types of dominant bacteria derived from CTSs. Ten species (Figure 3E,F) were identified in CTSs and fermented doughs: _P. pentosaceus_, _C.