Fig. 6: Proteomics analysis of bacterial cells and conditioned media of B. theta grown on carbon sources with significant alterations in their immune-modulatory effects.

a Heatmap of significantly altered proteins found in the conditioned media (p-value < 0.01, ANOVA test with permutated-based FDR and 250 randomizations), samples were clustered by hierarchical clustering using the average linkage method based on Pearson correlations. Different carbon sources are marked by their color, n = 3. b STRING analysis and interactions map of all 136 significantly altered proteins. Blue - Starch binding (GO:2001070), Green - Outer membrane (GOCC:0019867), Yellow - SusD family (PF07980), Red - TonB-dependent outer membrane protein, SusC/RagA (IPR023996). c Annotation enrichment analysis of the significantly altered proteins in the conditioned media. Enriched domains and proteins families’ categories according to GOBP. Number of observed gene counts are marked by each category. d Heatmap of significantly altered proteins found in the bacterial cells (p-value < 0.01, ANOVA test with permutated-based FDR and 250 randomizations). Hierarchical clustering of both rows and columns was performed using the average linkage method based on Pearson correlations. Rows were split into clusters based on this hierarchical clustering. Carbon sources are marked by different colors, n = 3. e–k Annotation enrichment analysis of the significantly altered proteins in the bacterial cells by clusters. (Clusters 1–5 KEGG pathways enrichment, clusters 6–7 Domains or GOBP enrichment). a, d ANOVA test with permutation-based FDR and 250 randomizations. All exact p-values are listed in Supplementary Data 5. Source data are provided as a Source Data file.