Fig. 2

Analysis of differentially expressed genes and gene sets of the shared genome. a Principal component analysis plot of normalized expression values for the shared genome of the three different E. coli strains. The PCA-plot was calculated with the DESeq2 package, using TPM normalized gene counts (with the respective strain-specific gene lengths) for the shared genome [25]. Differences between the growth conditions in lamb’s lettuce medium are depicted as dots, and in M9 minimal medium as triangles. E. coli O157:H7 strain Sakai is shown in blue, E. coli O157:H⁻ strain 3072/96 in green, and E. coli O104:H4 strain C227–11φcu in red. b Venn diagram of differentially regulated shared genes shown for all three strains. Up- and downregulated genes resulted from transcriptional patterns of cells grown in lamb’s lettuce medium compared to cells grown in M9 minimal medium. Differentially regulated genes are shown in circles, intersections show overlapping genes of two or three strains. E. coli O157:H7 strain Sakai is marked in blue, E. coli O157:H⁻ strain 3072/96 in green and E. coli O104:H4 strain C227–11φcu in red. c Gene set enrichment analysis showing selected up- and downregulated gene sets derived from transcriptomic analyses of E. coli O157:H⁻ strain 3072/96 (black), E. coli O104:H4 strain C227–11φcu (shaded), and E. coli O157:H7 strain Sakai (grey) after growth in lamb’s lettuce medium and M9 minimal medium