MetaboLights

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ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/m_MTBLS14677_LC-MS_positive_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/m_MTBLS14677_LC-MS_negative_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/a_MTBLS14677_LC-MS_negative_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/a_MTBLS14677_LC-MS_positive_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/s_MTBLS14677.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Neg-BP20250090-SDX-2.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Pos-BP20250090-KDX-1.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Neg-BP20250090-KDX-1.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Pos-BP20250090-KDX-2.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Pos-BP20250090-QC1.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Pos-BP20250090-SDX-2.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Neg-BP20250090-QC1.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Neg-BP20250090-SDX-1.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Neg-BP20250090-KDX-2.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Pos-BP20250090-SDX-1.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Neg-BP20250090-KDX-3.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Pos-BP20250090-SDX-3.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Pos-BP20250090-QC2.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Neg-BP20250090-QC2.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Pos-BP20250090-KDX-3.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677/FILES/RAW_FILES/Neg-BP20250090-SDX-3.rawprimary200OKftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14677Metabolite identification was performed by accurate mass matching (mass tolerance <10 ppm) and MS/MS spectral matching (mass tolerance <0.01 Da). Databases searched included public databases (HMDB, MassBank, GNPS) and the in-house BP-DB (Biotree metabolome database).MetaboLightsPublicLiquid Chromatography MS - negative - reverse-phaseLiquid Chromatography MS - positive - reverse-phaseInstrument: SHIMADZU LC-30 UHPLC system.Column: ACQUITY UPLC HSS T3 (2.1 x 100 mm, 1.8 microm, Waters).Injection volume: 4 microL.Column temperature: 40°C.Flow rate: 0.3 mL/min.Mobile phase A: 0.1% formic acid in water; Mobile phase B: 0.1% formic acid in acetonitrile.Gradient elution program:0-2 min, 0% B;2-6 min, B linearly increased to 48%;6-10 min, B linearly increased to 100%;10-12 min, B held at 100%;12-12.1 min, B linearly decreased to 0%;12.1-15 min, B held at 0%.Multi-Omics Elucidation of Cyclic Lipopeptide Pseudodesmin A-Mediated Biofilm eradication in Vancomycin-Resistant Enterococcus faecalis.Peking UniversityDuo Keaibacterial cellsmass spectrometry assaySamples were thawed at 4°C, then 200 microL pre-chilled water and 800 microL pre-chilled methanol were added. After vortex mixing, samples were ultrasonicated in an ice bath for 20 min, incubated at -20°C for 1 h to precipitate proteins, and centrifuged at 16,000 g for 20 min at 4°C. The supernatant was collected. The precipitated protein was air-dried, then 200 microL SDT was added for BCA quantification. The supernatant was dried in a vacuum centrifugal concentrator. For MS analysis, the residue was reconstituted in 60 microL pre-chilled methanol-water (1:1, v/v), centrifuged at 20,000 g for 20 min at 4°C, and the appropriate amount of supernatant was injected. QC samples (pooled from equal volumes of all samples) were prepared for system conditioning and stability assessment.Vancomycin-Resistant Enterococcus faecalishttps://www.ebi.ac.uk/metabolights/MTBLS14677XingMei Gao. Dali University. 15758099263@163.com.Kai-Ling Wang. Dali University. kailingw@dali.edu.cn.Raw data were processed using MSDIAL ver.4.9 software for peak alignment, retention time correction, and peak area extraction. Ion peaks with >50% missing values within a group were removed. Data from positive and negative modes were normalized separately by total peak area, then combined. Python software was used for pattern recognition. Data were UV-scaled (Unit variance scaling) before subsequent analysis.Groupkeaiduoduo998@126.comMature VREF biofilms formed at 37°C for 24 h were treated with the purified compound at 75 microg/mL or an equivalent volume of DMSO as the vehicle control for 10 h. After treatment, the biofilms were washed with sterile 1x PBS, gently detached, collected, and centrifuged at 8000 rpm for 5 min at 4°C. The resulting pellets were washed three times with sterile 1x PBS and snap-frozen in liquid nitrogen. Three biological replicates were prepared for each group, and all samples were shipped on dry ice for subsequent sequencing and mass spectrometry analyses.MetabolomicsMulti-OmicsBacterial cell pelletsMetabolomicsVancomycin-Resistant Enterococcus faecalisPseudodesmin AShimadzu Nexera X2 LC-30ADuntargeted analysisBiofilmbacterial cellsThermo Scientific Q Exactive PlusMulti-OmicsBacterial cell pelletsMetabolomicsVancomycin-Resistant Enterococcus faecalisShimadzu Nexera X2 LC-30ADPseudodesmin Auntargeted analysisBiofilmbacterial cellsThermo Scientific Q Exactive PlusInstrument: Thermo Scientific Q Exactive Plus mass spectrometer.Ion source: HESI.Ionization modes: positive (+) and negative (-) separately.Positive mode spray voltage: 3.8 kV; negative mode: 3.2 kV.Capillary temperature: 320°C.Sheath gas: 30 arb; Aux gas: 5 arb.Probe heater temperature: 350°C.S-Lens RF level: 50.Full MS: scan range 75-1050 m/z, resolution 70,000 @ m/z 200, AGC target 3e6, maximum IT 100 ms.MS2: data-dependent acquisition of top 10 precursor ions per full scan, resolution 17,500 @ m/z 200, AGC target 1e5, maximum IT 50 ms, HCD (stepped NCE: 20, 30, 40), isolation window 2 m/z.Acquisition time: 15 min.(10betaH,11xi)-11-Hydroxy-13-nor-6-eremophilen-8-onebeta-D-FucoseThymidineLPE(16:0)UTPEcgonineCellobioseLeu-Pro-IleL-Agaridoxin1-Aminocyclopropane-1-carboxylic acid2-AminopurineFloionolic acidPantetheine 4'-phosphateHydroxyprolyl-LeucineN-Benzoylaspartic acid4-Deoxyerythronic acidXyloseLysinegamma-GlutamylalanineN2,N5-DiacetylornithineCalystegine A74,5,6-trihydroxy-2-oxohexanoic acid4-PyridoxateN-Palmitoyl IsoleucineSuccinic anhydrideImidazole lactateGlutathione (oxidized)MyoinositolAsp-GluCoenzyme AIndole-3-Lactic AcidAlanineAllopregnanolone sulfateIsovalerylglutamic acid6-Acetamidohexanoic acidFADN-Palmitoyl tyrosine2-[4-(sulfooxy)phenyl]acetic acid2-Hydroxy-2-ethylsuccinic acid1-acetylpyrrolidine-2-carboxylic acidN-Arachidonoyl AlanineArabinonic acidTyrosyl-Threonineprolyl-hydroxyprolineCitraconic acidNorvalineN-AcetylalanineATPKainic acidLumichromefalseMulti-Omics Elucidation of Cyclic Lipopeptide Pseudodesmin A-Mediated Biofilm eradication in Vancomycin-Resistant Enterococcus faecalisIn this study, we isolated and purified cyclic lipopeptide PDMA from our in-house strain Pseudomonas tolaasii ZTB4. We evaluated its antibacterial and antibiofilm activities against VREF, demonstrating that PDMA effectively eradicates mature biofilms. To decipher the mechanisms underlying this eradication, we employed an integrated multi-omics approach combining transcriptomics, proteomics, and metabolomics to identify key intracellular targets. This represents the first study to investigate the antibiofilm mechanism of PDMA using multi-omics analysis, along with hemolytic assay to evaluate biosafety for future structure-activity relationship analysis. Our findings highlight PDMA as a promising scaffold, underscoring its potential for structural optimization and application in combating biofilm-related drug tolerance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