Fig. 6: Correlation network analysis and gene expression profiles of stress-related functions in Leuconostoc starter strains during kimchi fermentation.
From: Unravelling the key factors for the dominance of Leuconostoc starters during kimchi fermentation
The average transcripts per million (TPM) values of 1238 genes in 33 categories based on KEGG BRITE hierarchical classifications were calculated, and 83 genes that exhibited transcript levels above 2000 TPM were selected. Spearman correlation coefficients were calculated between the relative abundance of Leuconostoc ASV001 and the TPM values mapped to Leuconostoc mesenteroides ATCC 8293T, Leuconostoc mesenteroides WiKim32, Leuconostoc mesenteroides WiKim33, and Leuconostoc mesenteroides WiKim0121 in the kimchi samples CTR, W32, W33, and W0121 samples, respectively, and between the relative abundance of Leuconostoc ASV002 and the TPM values mapped to Leuconostoc sp. CBA3628 in the C3628 sample. Then, a a network analysis was performed. The colours of nodes represent the following: red, bacterial relative abundances; yellow-green, KO number within oxidative phosphorylation category; grey, KO number within ribosome category; white-yellow, KO number within translation factors category; pink, KO number within chaperones and folding catalysts category; green, KO number within membrane trafficking category; blue, KO number within mitochondrial biogenesis category; apricot, KO number within exosome category; and sky-blue, KO number within the categories more than two. The edges represent Spearman correlations, with thicker edges indicating a stronger positive correlation and thinner edges displaying a weaker correlation or a negative correlation, as per the correlation scale ranging from −1.0 to 1.0. The highly ‘strong’ positive correlation of over 0.6 is visualised with red edges. b The TPM values of genes encoding F-type ATPase and chaperone proteins from five strains in each kimchi sample during fermentation were visualised using the heatmap. Gene expression levels are indicated by colour intensity, with red representing higher TPM values (0 to 50,000 or greater). The pH values at each time point are provided above the heatmap, with the intensity of colour (yellow–black) indicating the pH, as shown on the scale bar (4.06‒5.14). The boxes of gene names are filled with colours corresponding to each category described in the network analysis. The kimchi samples inoculated with strains WiKim32, WiKim33, WiKim0121, and CBA3628, and saline solution were labelled as 'W32', 'W33', 'W0121', 'C3628', and 'CTR', respectively.
