{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002804","ANALYSIS_ID":"AN004560","VERSION":"1","CREATED_ON":"July 28, 2023, 11:14 pm"}, "PROJECT":{"PROJECT_TITLE":"NMR spectra of cell extracts from Microbacterium sediminis YLB-01","PROJECT_TYPE":"NMR","PROJECT_SUMMARY":"The deep-sea microorganism Microbacterium sediminis YLB-01 was treated with high pressure (accompanied with low temperature)","INSTITUTE":"Xiamen University","LAST_NAME":"Qiu","FIRST_NAME":"Xu","ADDRESS":"No. 422, Siming South Road, Xiamen, Fujian, China.","EMAIL":"qiuxu@stu.xmu.edu.cn","PHONE":"13161342734"}, "STUDY":{"STUDY_TITLE":"Metabolic Adaptations of Microbacterium sediminis YLB-01 for Survival in the Challenging High-Pressure of the Deep Sea","STUDY_SUMMARY":"In this study, we investigated the metabolic adaptations of Microbacterium sediminis YLB-01, a cold and stress-tolerant microorganism isolated from deep-sea sediments, in response to high-pressure conditions. By using NMR-based metabolomic analysis and proteomic analysis, we conducted a comprehensive examination of the significantly altered metabolic pathways involved in the adaptation of YLB-01 cells to high-pressure conditions.","INSTITUTE":"Xiamen University","LAST_NAME":"Qiu","FIRST_NAME":"Xu","ADDRESS":"No. 422, Siming South Road, Xiamen, Fujian, China.","EMAIL":"qiuxu@stu.xmu.edu.cn","PHONE":"13161342734"}, "SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Microbacterium sediminis YLB-01"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"HP", "Sample ID":"NPLT_S1", "Factors":{"Treatment":"NPLT"}, "Additional sample data":{"RAW_FILE_NAME":"41"} }, { "Subject ID":"HP", "Sample ID":"NPLT_S3", "Factors":{"Treatment":"NPLT"}, "Additional sample data":{"RAW_FILE_NAME":"43"} }, { "Subject ID":"HP", "Sample ID":"NPLT_S4", "Factors":{"Treatment":"NPLT"}, "Additional sample data":{"RAW_FILE_NAME":"44"} }, { "Subject ID":"HP", "Sample ID":"NPLT_S5", "Factors":{"Treatment":"NPLT"}, "Additional sample data":{"RAW_FILE_NAME":"45"} }, { "Subject ID":"HP", "Sample ID":"NPLT_S6", "Factors":{"Treatment":"NPLT"}, "Additional sample data":{"RAW_FILE_NAME":"65"} }, { "Subject ID":"HP", "Sample ID":"NPLT_S7", "Factors":{"Treatment":"NPLT"}, "Additional sample data":{"RAW_FILE_NAME":"47"} }, { "Subject ID":"HP", "Sample ID":"NPLT_S8", "Factors":{"Treatment":"NPLT"}, "Additional sample data":{"RAW_FILE_NAME":"48"} }, { "Subject ID":"HP", "Sample ID":"HPLT_S1", "Factors":{"Treatment":"HPLT"}, "Additional sample data":{"RAW_FILE_NAME":"57"} }, { "Subject ID":"HP", "Sample ID":"HPLT_S2", "Factors":{"Treatment":"HPLT"}, "Additional sample data":{"RAW_FILE_NAME":"58"} }, { "Subject ID":"HP", "Sample ID":"HPLT_S3", "Factors":{"Treatment":"HPLT"}, "Additional sample data":{"RAW_FILE_NAME":"59"} }, { "Subject ID":"HP", "Sample ID":"HPLT_S4", "Factors":{"Treatment":"HPLT"}, "Additional sample data":{"RAW_FILE_NAME":"67"} }, { "Subject ID":"HP", "Sample ID":"HPLT_S5", "Factors":{"Treatment":"HPLT"}, "Additional sample data":{"RAW_FILE_NAME":"61"} }, { "Subject ID":"HP", "Sample ID":"HPLT_S6", "Factors":{"Treatment":"HPLT"}, "Additional sample data":{"RAW_FILE_NAME":"62"} }, { "Subject ID":"HP", "Sample ID":"HPLT_S7", "Factors":{"Treatment":"HPLT"}, "Additional sample data":{"RAW_FILE_NAME":"63"} }, { "Subject ID":"HP", "Sample ID":"HPLT_S8", "Factors":{"Treatment":"HPLT"}, "Additional sample data":{"RAW_FILE_NAME":"68"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"In this study, a single colony of the YLB-01 strain was inoculated from an agar plate into individual test tubes containing 5 mL of TSB medium. The test tubes were then incubated in a shaker at 28°C for 12 h. Subsequently, the seed cultures were transferred to 150-mL Erlenmeyer flasks at a ratio of 1:20, with each flask containing 100 mL of TSB medium. To ensure an adequate cell count, YLB-01 cultures were initially cultivated under optimal conditions (28°C, 0.1 MPa) for 24 h. The optical density at 600 nm (OD600 nm) of the cell cultures was measured using an automatic growth curve analyzer (FP-1100-C, Growth Curves Ab Ltd., Finland). Once the cultures reached the stationary phase of growth, the cells were transferred into a 100-mL sterile saline bag and placed in a high-pressure culture kettle. This kettle, obtained from Nantong Feiyu Company, China, was specifically designed to simulate the high-pressure conditions of the deep sea (Zhang et al. 2015). The cells were then exposed to either 30 MPa (the HPLT group, N=8) or 0.1 MPa (the NPLT group, N=7) at 4°C for 7 days. Hydrostatic pressure was generated by injecting pure water into the vessel.","SAMPLE_TYPE":"Bacterial cells","STORAGE_CONDITIONS":"Described in summary"}, "TREATMENT":{"TREATMENT_SUMMARY":"To ensure an adequate cell count, YLB-01 cultures were initially cultivated under optimal conditions (28°C, 0.1 MPa) for 24 h. The optical density at 600 nm (OD600 nm) of the cell cultures was measured using an automatic growth curve analyzer (FP-1100-C, Growth Curves Ab Ltd., Finland). Once the cultures reached the stationary phase of growth, the cells were transferred into a 100-mL sterile saline bag and placed in a high-pressure culture kettle. The cells were then exposed to either 30 MPa (the HPLT group, N=8) or 0.1 MPa (the NPLT group, N=7) at 4°C for 7 days."}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"After culturing the YLB-01 cells, each 100 mL of the culture was transferred into a 250-mL centrifuge bottle and centrifuged at 4°C (6000 g, 5 min). The supernatant was carefully decanted, and the cell pellets were rapidly cooled to -40°C using 100 mL of a buffer composed of a 3:2 methanol/water mixture containing 0.85% (wt/vol) NaCl. The mixture was centrifuged again at 4°C (6000 g, 5 min). The cell pellets were washed three times with 5 mL of cold phosphate-buffered saline (PBS) and centrifuged at 4°C (6000 g, 5 min) after each wash. Finally, the cell pellets were stored at -80°C until further use. Initially, 600 μL of a cold extraction buffer consisting of a 1:1 mixture of distilled water and acetonitrile was added to homogenize the samples. The mixtures were then sonicated on wet ice for 180 cycles, with each cycle consisting of 2 seconds of ultrasound followed by a 3-second pause. After centrifugation at 4°C (12000 g, 10 min), the supernatants were collected and lyophilized, resulting in an extract powder that was stored at -80°C for further analysis.","PROCESSING_STORAGE_CONDITIONS":"Described in summary","EXTRACT_STORAGE":"Described in summary"}, "ANALYSIS":{"ANALYSIS_TYPE":"NMR"}, "NM":{"INSTRUMENT_NAME":"Bruker Avance III 600 MHz","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","SPECTROMETER_FREQUENCY":"600 MHz","NMR_RESULTS_FILE":"ST002804_AN004560_Results.txt UNITS:ppm"} }