Fig. 1: Differential metabolomic flux and profiling between tigecycline-resistant and -susceptible bacteria.

a Venn diagrams of annotated genes, 1146 represents the shared genes between two bacteria (Tig-R and -S). b Differentially expressed genes (DEGs) in Tig-R vs Tig-S. Tig-S, E. coli DH5α (pUC19); Tig-R, E. coli DH5α (pUC19-tet(X4)). One subset of significant DEGs was annotated. Yellow dots, up-regulated; gray dots, not-significant; blue dots, down-regulated. Log₂FC were calculated to take the direction of the expression difference into account. −Log₁₀FDR value ≥ 1 and log₂FC ≥ 1 or log₂FC ≤ −1 were identified as significant different DEGs. c PCA analysis of metabolomics, an unsupervised PCA plot was applied to examine the clustering characteristics of different metabolites. Colored dots representing individual samples, n = 6 per group. d KEGG pathway classification based on the significantly altered genes, including the first and secondary pathways. The pathways involved in genetic information processing (pink), metabolism (blue), cellular processes (yellow), organismal systems (purple) and environmental information processing (dark blue). e Clustering heatmap showing an abundance of top 30 differential metabolites in Tig-R compared with Tig-S. The light blue region on the left (S_1 ~ S_6) contains metabolites that were downregulated in Tig-R, while the corresponding dark blue region contains upregulated metabolites. L-Met was highlighted with red. f A network graph visualizing the relationships between various pathways based on KEGG enrichment analysis. The node size represents the number of genes enriched in KEGG pathway, while the gradient color of the node represents the P-value in KEGG enrichment analysis. The connections between certain amino acid pathways were specifically highlighted with orange lines. g A functional multi-omics integration and covariate adjustment of genomics and metabolomics, 61 associations at −log₁₀ (P-value) > 0 identified mainly discrepant pathways between Tig-R and -S. Pathway impact displays an integration of the centrality and pathway enrichment pathway. Cys & Met metabolism (Pathway Impact 0.2) was labeled red. Adjusted P values were determined using two-way ANOVA with Sidak’s multiple comparison test, the Fisher’s method (−2*∑Log(P)) was used for information integration. h The global metabolic difference network when compared Tig-R with Tig-S, of focus on amino acids metabolism, energy metabolism, nucleotide metabolism and carbohydrate metabolism. Red represents up-regulated genes or metabolites, and green represents down-regulated genes or metabolites in Tig-R. GUA Guanidoacetic acid, CYSTAT Cystathionine, Xob 2-Oxobutanoate, Asp-4-semi L-Aspartate-4-semialdehyde, Homoser L-homoserine, 4-P-Asp L-4-Aspartyl-phosphate, SRH S-D-Ribosyl-L-homocysteine, SAH S-Adenosyl-L-methionine, KGDH α-Ketoglutaric acid, 4-MOA 4-Methylthio-2-oxobutanoic acid, CP Carbamoyl phosphate, PRA 5-Phosphoribosylamine, Xyp Xypoxanthine, Hyp Hypoxanthine, NAC N-Acetylserotonin. SRH S-D-Ribosyl-L-homocysteine.