{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002770","ANALYSIS_ID":"AN004507","VERSION":"1","CREATED_ON":"July 5, 2023, 10:17 pm"}, "PROJECT":{"PROJECT_TITLE":"Bacillus-Derived Compounds Against a Vibrio","PROJECT_SUMMARY":"Metabolomics was employed in conjunction with bioactivity screening to identify the antibacterial compounds from Bacillus strains against the highly lethal Vibrio strain vp-HL.","INSTITUTE":"Third Institute of Oceanography, Ministry of Natural Resources","LAST_NAME":"Xia","FIRST_NAME":"Jinmei","ADDRESS":"Daxue Rd, Xiamen, China.","EMAIL":"xiajinmei@tio.org.cn","PHONE":"13003995626"}, "STUDY":{"STUDY_TITLE":"Metabolomics and Molecular Networking-Guided Screening of Bacillus-Derived Bioactive Compounds Against a Highly Lethal Vibrio Species","STUDY_SUMMARY":"During our search for active substances capable of inhibiting a newly discovered highly lethal Vibrio strain vp-HL, we found that the fermentation broth of multiple Bacillus strains exhibited antibacterial activity. However, the substances responsible for the activity remained unclear. Metabolomics was employed in conjunction with bioactivity screening to identify the antibacterial compounds from Bacillus strains. The Ethyl Acetate extracts of the broth of 20 Bacillus strains were analyzed using UPLC-MS/MS. Principal Component Analysis (PCA) and Orthogonal Partial Least Square - Discriminant Analysis (OPLS-DA) was used for pattern recognition. The strains fall into two groups in the scores plot from PCA. The S-plot from OPLS-DA offered information on biomarkers.","INSTITUTE":"Third Institute of Oceanography, Ministry of Natural Resources","LAST_NAME":"Xia","FIRST_NAME":"Jinmei","ADDRESS":"Daxue Rd, Xiamen, China.","EMAIL":"xiajinmei@tio.org.cn","PHONE":"13003995626"}, "SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Bacillus pumilus"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"2", "Factors":{"Group":"B1"}, "Additional sample data":{"RAW_FILE_NAME":"2.mzml"} }, { "Subject ID":"-", "Sample ID":"4", "Factors":{"Group":"B1"}, "Additional sample data":{"RAW_FILE_NAME":"4.mzml"} }, { "Subject ID":"-", "Sample ID":"7", "Factors":{"Group":"B1"}, "Additional sample data":{"RAW_FILE_NAME":"7.mzml"} }, { "Subject ID":"-", "Sample ID":"14", "Factors":{"Group":"B1"}, "Additional sample data":{"RAW_FILE_NAME":"14.mzml"} }, { "Subject ID":"-", "Sample ID":"15", "Factors":{"Group":"B1"}, "Additional sample data":{"RAW_FILE_NAME":"15.mzml"} }, { "Subject ID":"-", "Sample ID":"20", "Factors":{"Group":"B1"}, "Additional sample data":{"RAW_FILE_NAME":"20.mzml"} }, { "Subject ID":"-", "Sample ID":"22", "Factors":{"Group":"B1"}, "Additional sample data":{"RAW_FILE_NAME":"22.mzml"} }, { "Subject ID":"-", "Sample ID":"23", "Factors":{"Group":"B1"}, "Additional sample data":{"RAW_FILE_NAME":"23.mzml"} }, { "Subject ID":"-", "Sample ID":"24", "Factors":{"Group":"B1"}, "Additional sample data":{"RAW_FILE_NAME":"24.mzml"} }, { "Subject ID":"-", "Sample ID":"27", "Factors":{"Group":"B1"}, "Additional sample data":{"RAW_FILE_NAME":"27.mzml"} }, { "Subject ID":"-", "Sample ID":"34", "Factors":{"Group":"B2"}, "Additional sample data":{"RAW_FILE_NAME":"34.mzml"} }, { "Subject ID":"-", "Sample ID":"35", "Factors":{"Group":"B2"}, "Additional sample data":{"RAW_FILE_NAME":"35.mzml"} }, { "Subject ID":"-", "Sample ID":"38", "Factors":{"Group":"B2"}, "Additional sample data":{"RAW_FILE_NAME":"38.mzml"} }, { "Subject ID":"-", "Sample ID":"39", "Factors":{"Group":"B2"}, "Additional sample data":{"RAW_FILE_NAME":"39.mzml"} }, { "Subject ID":"-", "Sample ID":"43", "Factors":{"Group":"B2"}, "Additional sample data":{"RAW_FILE_NAME":"43.mzml"} }, { "Subject ID":"-", "Sample ID":"44", "Factors":{"Group":"B2"}, "Additional sample data":{"RAW_FILE_NAME":"44.mzml"} }, { "Subject ID":"-", "Sample ID":"46", "Factors":{"Group":"B2"}, "Additional sample data":{"RAW_FILE_NAME":"46.mzml"} }, { "Subject ID":"-", "Sample ID":"47", "Factors":{"Group":"B2"}, "Additional sample data":{"RAW_FILE_NAME":"47.mzml"} }, { "Subject ID":"-", "Sample ID":"50", "Factors":{"Group":"B2"}, "Additional sample data":{"RAW_FILE_NAME":"50.mzml"} }, { "Subject ID":"-", "Sample ID":"56", "Factors":{"Group":"B2"}, "Additional sample data":{"RAW_FILE_NAME":"56.mzml"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"The broth cultures were centrifuged at 7000 rpm for 10 min under 4 °C and the supernatants were collected.","SAMPLE_TYPE":"Bacterial cells"}, "TREATMENT":{"TREATMENT_SUMMARY":"The full-length 16S rRNA gene sequence was obtained for the studied Bacillus strains. The phylogenetic tree of the 16S rRNA gene showed that the strains formed two groups, which were defined as Group B1 and B2. The antagonistic activities of the Bacillus broth against the vp-HL strain were evaluated by the agar well diffusion method. The DI (diameters of the inhibition zones) values of the 20 Bacillus strains against the vp-HL strain were measured. All strains belonging to Group B2 showed DI values greater than those of strains from Group B1."}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"The broth cultures were centrifuged at 7000 rpm for 10 min under 4 °C and the supernatants were collected. Ethyl acetate (EtOAc) with 2 × volume was added and sonicated for 10 min. The samples were then centrifuged at 7000 rpm at 4 °C for 10 min and the organic phase was collected and dried using a rotary evaporator. The extracts were resuspended in 1:1 acetonitrile: H2O with 1% formic acid. These samples were diluted 20 times using methanol. All samples were filtrated through 0.22 µm syringe filters."}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Low pH polar","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um)","SOLVENT_A":"Water with 0.1% (vol/vol) formic acid","SOLVENT_B":"Acetonitrile with 0.1% (vol/vol) formic acid","FLOW_GRADIENT":"5%B was kept for 0.5 min, 0.5-2.5 min, 5% to 30% B; 2.5-3.5 min, 30% to 40% B; 3.5-9 min, 40% to 99% B; 9-10 min, 99% to 5% B; and 5%B was kept for 3 min.","FLOW_RATE":"0.35 mL/min","COLUMN_TEMPERATURE":"30"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"INSTRUMENT_NAME":"Waters Vion IMS QTof","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"UNIFI software (v. 1.8, Waters)","MS_RESULTS_FILE":"ST002770_AN004507_Results.txt UNITS:intensity Has m/z:Yes Has RT:Yes RT units:Minutes"} }