## 3 Results and Discussion
### Amplicon Metagenomic Sequencing After Storage of BSG and SCG
coagulans_), especially in tray 2. In drums, _Acetobacter_ also generally dominate the bacterial microbiome, followed by LAB. The only exception is the drum 2 bottom, with low _Acetobacter_ but high _Ligilatchocillus_ (_L. acidipiscis_) and _Bacillus_ (_B. coagulans_). The bacterial dynamics are similar to those described for BSG stored in drums, with the co-existence of AAB and LAB under aerobic conditions, while this dynamic likely broke down in drum 2 due to anaerobic conditions, as evidenced by the proliferation of anaerobes. The anaerobes _Lentilatchocillus__buchneri, Roseburia intestinalis_, and _Ruminococcus bicirculans_ are present in low abundance in drum bottom samples as seen in Figure 4c. For SCG, there is less difference between the tray and drum microbiome at the genus level, possibly due to the ability of SCG to better retain moisture during storage in trays, consistent with a lower reported effective moisture diffusivity for SCG than BSG [38; 64]. The bacterial microbiome is generally dominated by synergistic AAB and LAB, while the fungal microbiome is dominated by _Pichia_ in both trays and drums, with relative abundance ranging from about 50% to 90%. The most common species is _P. kudriavzii_, classified under the genus _Issatchenkia_ (with the heterotypic synonym _I. orientalis_) in Figure 4. In addition to the metagenomic results reported here, a taxonomic heatmap for the top 35 bacterial species identified can also be found in Figure S12 in the Supplementary Materials. The results reported here complement those of [PERSON] et al., who investigated the microbiome and storage of BSG at different temperatures under aerobic conditions, but without environmental exposure [18]. They found bacteria TPC to reach approximately 8 log\({}_{10}\) CFU/g for mesophilic bacteria and 6 log\({}_{10}\) CFU/g for thermophilic bacteria by day 16 at 20 \({}^{\circ}\)C, with most of the growth happening before day 3 and stabilizing by day 7 [18]. [PERSON] et al. previously identified the presence of microaerobic bacteria (presumably LAB), anaerobic bacteria (presumably _Clostridia_), yeast, and mold at the site of production [16], but they evidently did not proliferate or were not culturable upon aerobic storage. Metagenomic sequencing provides deeper insight into the microbial ecology,  
Figure 4: Amplicon metagenomic sequencing of SCG-2 and SCG-3 as received and after 14 days of storage in trays (SCG-2) and drums (SCG-3): (**a**) top 10 genera; (**b**) top 10 genera of fungi; (**c**) top 10 species of bacteria; (**d**) top 10 species of fungi identified by 16S rRNA and ITS amplicon sequencing. Note that SCG-1 was not analyzed by metagenomic sequencing due to difficulties in extracting high-quality DNA. identifying the dominant genera and key species both at the time of production and after storage. Mesophilic aerobic bacterial genera such as _Bacillus_ and _Paenibacillus_, as well as the facultative anaerobes _Weisella_ and _Enterococcus_, proliferate in aerobic storage, while AAB and LAB proliferate in anaerobic and microaerobic storage. The most prevalent bacterial species in BSG, but also found in SCG, is the thermophilic facultative anaerbe _B. coagul_, recently reclassified as _Heyndrickxia coagul_s [61]. Extensive growth of the yeast genera _Kluyveromyces_, _Pichia_, _Diutta_, and _Candida_ and molds _Aspergillus_ and _Mucor_ occurs in aerobic storage. The bacterial microbiome of SCG on storage shows similarities with BSG at the genus level, with AAB and LAB prevalent in both aerobic and anaerobic storage conditions, and _Bacillus_ present in conditions, but with differences in identified species. The yeast genus _Pichia_ is extensive in all storage conditions, while _Candida_ proliferate in anaerobic conditions, and the molds _Neurospora_ and _Aspergillus_ are found especially in aerobic storage.