# Characterization of Quality Properties in Spoiled Mianning Ham
## 3 Results and Discussion
### Bacterial Diversity Analysis  
The bacterial \(\alpha\)-diversity indices of normal and spoiled Mianning ham are shown in Table 2. There are nine samples in the project. The data volume of clean tags after quality control is distributed between 71,152-78,043, and the data volume of clean tags after removing chimeras to obtain valid tags (the final data for analysis) is distributed between 60,485-74,897. The average length of valid tags was 402.4-418.22 bp, and the number of OTUs in each sample was distributed between 542-1176. OTU classification of quality sequence valid tags obtained from QC according to 97% similarity was performed using Vsearch (version 2.4.2) software (an open source tool for microbiome analysis) [35]. Based on the results of OTUs clustering analysis and research needs, the number of OTUs shared and unique among different samples was analyzed and plotted as a Venn diagram (Figure 1). The three ham samples had a total of 661 bacterial OTUs. \begin{table}
\begin{tabular}{c c c c c c c} \hline \hline
**Samples** & **Valid Tags** & **OUT Counts** & \
\begin{tabular}{c} **Observed** \\ **Species** \\ \end{tabular} & **Chao1** & **Shannon** & **Simpson** &
\begin{tabular}{c} **Good’s** \\ **Coverage** \\ \end{tabular} \\ \hline FBS & 74237 \(\pm\) 585 a & 572 \(\pm\) 40 a & 532.07 \(\pm\) 37.76 a & 746.43 \(\pm\) 61.45 a & 0.94 \(\pm\) 0.65 a & 0.153 \(\pm\) 0.122 a & 0.999 \\FBQ & 66418 \(\pm\) 2492 b & 918 \(\pm\) 219 a & 894.6 \(\pm\) 220.75 ab & 1121.15 \(\pm\) 179.79 b & 7.25 \(\pm\) 0.31 b & 0.983 \(\pm\) 0.004 b & 0.999 \\ ZC & 64536 \(\pm\) 4107 b & 973 \(\pm\) 239 a & 960.3 \(\pm\) 235.73 b & 1111.26 \(\pm\) 238.53 ab & 7.42 \(\pm\) 0.46 b & 0.985 \(\pm\) 0.006 b & 0.999 \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Bacterial alpha diversity index of normal and spoiled Mianning ham. The number of OUTs was lower in deeply spoiled ham than in surface spoiled ham and normal ham (\(p>0.05\)), and the highest number of OUTs was found in normal ham. There was a significant difference (\(p<0.05\)) in the bacterial abundance between deeply spoiled ham and surface spoiled ham; there were fewer bacterial species present in deeply spoiled ham than in surface spoiled ham. There was a significant difference (\(p<0.05\)) in the bacterial diversity among deeply spoiled ham and surface spoiled ham and normal ham, and the diversity of bacterial communities in deeply spoiled ham was lower than surface spoiled ham and normal ham. The coverage of all three ham samples was 0.999, indicating that the sequencing depth of the method was sufficient to reflect the bacterial community of the samples and the data could be used for subsequent analysis. To further understand the bacterial community structure of deeply spoiled ham, surface spoiled ham and normal ham, this experiment analyzed the colony composition of Mianning ham at both phylum and genus levels. The bacterial abundance was visualized in the form of a stack diagram. At the phylum level (Figure 2a), the top 30 microbial phyla in terms of abundance, such as Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. The dominant phylum in deeply spoiled ham was Firmicutes, which accounted for 95.4% of the total number of bacteria that dominated the spoilage of ham. In Jinhua ham, Proteobacteria, Bacteroidetes and Firmicutes dominated the bacterial populations, which were closer to the results of this test [36]. Meanwhile, Bacteroidota and Proteobacteria were the dominant phylum in surface spoiled ham and normal ham. At the genus level (Figure 2b), the top 30 microbial genera in terms of abundance, such as _Clostridium_sensu_stricto_2, Leptotrichia_, _Prevotella_ and _Murbaculaceae_, were identified. _Clostridium_sensu_stricto_2_ was the dominant genus, with 92.01% in deeply spoiled ham and 5.38% and 0.03% in surface spoiled and normal ham, respectively. _Clostridium_sensu_stricto_2_ may have caused or promoted the spoilage of the ham to some extent. Meanwhile, the dominant genus of surface spoiled ham and normal ham was _Leptotrichia_.