The raw data were analyzed by MS-Dial version 5.3 against three databases, including MS-Dial ESI (+/-) MS/MS from authentic standards, Fiehn/Vaniya natural product, and BMDMS-NP.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["10 µl of sample was injected into a Poroshell 120 EC-C18 2.1 × 100 mm; 2.7 µm column (Agilent) kept at 50 °C, and separation was performed at 0.4 mL/min flow with 0.1% formic acid in water (A) and 0.1% formic acid in acetonitrile (B).
"],"publication":["Metabolomic and Proteomic Profiling of the Antimicrobial Potentials from Lactobacillus johnsonii KD1 Cell-Free Supernatant against Foodborne Pathogenic Bacteria."],"submitter_affiliation":["Mahidol University"],"submitter_name":["Kanokwan Dekham"],"organism_part":["culture fluid","Growth Medium","Quality Control"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Three biological replicates of KD1 CFS (KD1-KD3) and the control MRS (MRS1-MRS3) were extracted with 100% methanol, containing 50 ng/ml sulfadimethoxine. Then, the samples were centrifuged at 14,000 rpm for 10 min, and the supernatant was collected. 20 µl of each sample was taken for the pool QC sample. Six dilutions of the undiluted pool QC sample (100%) were subsequently prepared at 80%, 50%, 20%, 10%, 1% and 0% in concentration. The supernatant was subjected to an LC-MS (Agilent LC-QTOF 6545XT).
"],"organism":["blank","Lactobacillus johnsonii","Quality Control"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS14550"],"author":["Kanokwan Dekham. Mahidol University. kanokwan.dek@gmail.com.","Soraya Chaturongakul. Mahidol University. soraya.cha@mahidol.ac.th."],"data_transformation_protocol":["Peak intensity was normalized with the LOWESS method with sulfadimethoxine (IS). Data quality criteria included retention time limits at 0.2-18 min, coefficient of variation (%CV) among QC < 30%, and identification score ≥ 0.70. Features that did not meet these criteria were excluded from further analysis.
"],"study_factor":["Group"],"submitter_email":["kanokwan.dek@gmail.com"],"sample_collection_protocol":["The probiotic Lactobacillus johnsonii KD1 was cultured in de Man Rogosa Sharpe (MRS) agar at 37 °C for 48 h. A single colony of the probiotic was inoculated in 50 ml of MRS broth and incubated at 37 °C for 24 h without shaking. Then the bacterial culture was centrifuged at 5,000 rpm, at 4 °C for 10 min, and the supernatant was collected. Supernatants were filtered through 0.22 membranes to remove bacterial cells, and the probiotic CFS was stored at 4 °C until use.
Mass spectrometry analysis was operated in high-resolution mode with electrospray ionization in both positive (pos) and negative (neg) polarities. The MS operating parameters were set as follows: drying gas temperature, 325 °C; drying gas flow, 13 L/h; sheath gas temperature, 275 °C; sheath gas flow, 12 L/h; nebulizer pressure, 45 psi; capillary voltage, 4000 V (pos) and 3000 V (neg); isotope width, 1.3 m/z; and scan mass ranges of 40-1700 m/z for MS1 and 25-1000 m/z for MS2. The collision energies were 20 eV for positive and 10 eV for negative modes. Data were acquired at a rate of 3.35 spectra/s, with a maximum of 10 precursors selected per cycle and a precursor threshold of 5000 counts. Continuous mass calibration was performed using reference masses at m/z 121.0509 and 922.0098 (positive mode), and m/z 112.9856 and 1033.9881 (negative mode) to ensure retention time threshold accuracy of 0.001%.
"],"additional_accession":[]},"is_claimable":false,"name":"Metabolomic and Proteomic Profiling of the Antimicrobial Potentials from Lactobacillus johnsonii KD1 Cell-Free Supernatant against Foodborne Pathogenic Bacteria","description":"This study characterized functions and metabolic profiles of cell-free supernatants (CFS) from Lactobacillus johnsonii KD1 against three foodborne pathogens: the Gram-negative bacteria Vibrio parahaemolyticus 3HP and Salmonella enterica serovar Typhimurium LT2, and the Gram-positive bacterium Listeria monocytogenes 10403S. The minimum inhibitory concentration (MIC) at 25% CFS inhibited the growth of all tested pathogens. At this concentration, the CFS exhibited bactericidal activity against both Gram-negative bacteria, while only bacteriostatic activity was observed against the Gram-positive bacterium. Neutralized CFS demonstrated that antimicrobial activity was pH-dependent, as the MIC increased to 50% CFS for V. parahaemolyticus and no inhibition was observed against S. Typhimurium. The stability of CFS at low temperature for 90 days has maintained antimicrobial activity with MIC from 12% to 25% against V. parahaemolyticus with bactericidal effects. Untargeted metabolomic profiling revealed numerous significant features, including 433 in positive ionization mode and 102 in negative mode. Highly abundant metabolites in the positive mode were primarily classified as aminoglycosides, while the random forest analysis identified key discriminative metabolites from aminoglycosides, cardenolides and derivatives, and steroid esters. In the negative mode, metabolites were mainly associated with probiotic metabolism, with 4-hydroxyphenyllactic acid identified as a potential biomarker contributing to inhibition of L. monocytogenes. Strong correlations were observed among key metabolites. Proteomic analysis identified 24 proteins significantly secreted in the CFS from MRS media and the probiotic with glyceraldehyde-3-phosphate dehydrogenase, which served as a marker for L. johnsonii KD1 CFS. These findings suggest that the probiotic CFS can be used to combat foodborne bacteria and its application as a biopreservative in the food industry.
","dates":{"publication":"2026-09-24","submission":"2026-05-21"},"accession":"MTBLS14550","cross_references":{}}