To identify metabolites that were differentially altered by conjugation, the detected features were filtered using the following criteria: P < 0.05, coefficient of variation (CV) < 20%, variable importance in projection (VIP) > 1, and a fold change ≥ 1.5. Metabolite analysis and visualization were performed using MetaboAnalyst 6.0 (https://www.metaboanalyst.ca/) (49), using the “Statistical Analysis [one factor]” module and the E. coli KEGG pathway library options. Among the statistically significant metabolites, those relevant to the subject were identified for the pathway analysis based on the EcoCyc database (50).
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - positive"],"chromatography_protocol":["The chromatographic separation was performed on an ACQUITY UPLC HSS T3 column (100 mm × 2.1 mm I.D., 1.8 μm, 100 Å; Waters Corporation) using a binary mobile phase system consisting of solvent A (10 mM ammonium formate and 0.1% formic acid in water) and solvent B (0.1% formic acid in 80% acetonitrile). The gradient was programmed as follows: 1% B at 0 min, held at 1% B until 1.5 min, increased linearly to 60% B at 14.5 min, ramped to 96% B at 16.5 min, maintained at 96% B until 16.5 min, and then returned to 1% B at 20 min for column re-equilibration. The flow rate was set to 0.25 mL/min, and mass spectrometric detection was carried out in positive ionization mode over a mass range of 100-1,000 m/z.
"],"publication":["Metabolomic Reprogramming Induced by Conjugative Acquisition of Carbapenemase-producing IncX3 Plasmid Revealed by Untargeted LC-MS/MS Profiling."],"submitter_name":["Su Min Kyung"],"submitter_affiliation":["Seoul National University"],"organism_part":["Whole Organism"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Cells were resuspended in 50 mM ammonium bicarbonate and then lysed by adjustment of QSonica Sonicator Q125. The protein concentration of each sample was estimated to adjust the volume of metabolites to extract, using a bicinchoninic acid (BCA) protein assay kit (Pierce Biotechnology, Rockford, IL). Metabolites were then extracted by vortexing samples after adding ice-cold 100% methanol, followed by incubation in -20℃ for an hour. The metabolites were then centrifuged in 14,000 × g for 15 minutes, then dried out using speed-vac. The dried extracts were reconstituted in 0.1% formic acid in water, and sample filtration was subsequently performed using a spin filter. Water was first added to the spin filter and centrifuged at 1,000 × g for 5 min to collect the flow-through. The eluted water was discarded, and the filter was placed back into the centrifuge tube. The sample was then loaded onto the filter and centrifuged at 1,000 × g for 3 min to obtain the filtrate. The filtered samples were transferred to MS vials, and 5 μL of each sample was injected for LC-MS/MS analysis.
"],"organism":["Escherichia coli"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS13918"],"author":["Su Min Kyung. Seoul National University. stevekyung25@snu.ac.kr."],"data_transformation_protocol":["Raw data files for each sample were processed using Compound Discoverer 3.3™ for data analysis, employing the “Untargeted Metabolomics with Statistics Detect Unknowns with ID using Online Database and mzLogic” workflow. Putative metabolite identification was performed using mzCloud (ddMS2) and ChemSpider (formula or exact mass), and all compounds were subjected to ddMS2 data similarity searches against the mzCloud spectral library. To increase annotation confidence, features were filtered according to the Metabolomics Standards Initiative (MSI) criteria, retaining only Level 2 (mass accuracy < 10 ppm, mzCloud score > 80) and Level 3 (ChemSpider match error < 5 ppm) compounds, while duplicate metabolites were removed based on peak area.
"],"study_factor":["Transconjugant"],"submitter_email":["stevekyung25@snu.ac.kr"],"sample_collection_protocol":["Three biological replicates of unconjugated J53 and four of the transconjugants were prepared by inoculating overnight cultures into fresh LB broth and harvesting at mid-log phase. Bacterial pellets were stored at -80℃ until all of the samples were processed to next stage.
"],"omics_type":["Metabolomics"],"study_design":["AMR","Conjugation","untargeted metabolite profiling"],"curator_keywords":["AMR","Conjugation","untargeted metabolite profiling"],"mass_spectrometry_protocol":["The chromatographic separation was performed on an ACQUITY UPLC HSS T3 column (100 mm × 2.1 mm I.D., 1.8 μm, 100 Å; Waters Corporation) using a binary mobile phase system consisting of solvent A (10 mM ammonium formate and 0.1% formic acid in water) and solvent B (0.1% formic acid in 80% acetonitrile). The gradient was programmed as follows: 1% B at 0 min, held at 1% B until 1.5 min, increased linearly to 60% B at 14.5 min, ramped to 96% B at 16.5 min, maintained at 96% B until 16.5 min, and then returned to 1% B at 20 min for column re-equilibration. The flow rate was set to 0.25 mL/min, and mass spectrometric detection was carried out in positive ionization mode over a mass range of 100-1,000 m/z.
"],"metabolite_name":["90","80","70","60","50","40","30"],"additional_accession":[]},"is_claimable":false,"name":"Metabolomic Reprogramming Induced by Conjugative Acquisition of Carbapenemase-producing IncX3 Plasmid Revealed by Untargeted LC-MS/MS Profiling","description":"This study aimed to elucidate the metabolic process of IncX3 plasmid within conjugated strains, by utilizing untargeted LC-MS/MS profiling. In this study, the blaNDM-5-carrying IncX3 plasmid was successfully conjugated into Escherichia coli J53, which was confirmed to enhance both carbapenem resistance and host fitness. Untargeted LC-MS/MS profiling revealed strategic remodeling response induced by the acquisition of the IncX3 plasmid.
","dates":{"publication":"2026-09-27","submission":"2026-02-17"},"accession":"MTBLS13918","cross_references":{}}