#METABOLOMICS WORKBENCH qiuxu_20230618_080144 DATATRACK_ID:4096 STUDY_ID:ST002804 ANALYSIS_ID:AN004560 PROJECT_ID:PR001751
VERSION             	1
CREATED_ON             	July 28, 2023, 11:14 pm
#PROJECT
PR:PROJECT_TITLE                 	NMR spectra of cell extracts from Microbacterium sediminis YLB-01
PR:PROJECT_TYPE                  	NMR
PR:PROJECT_SUMMARY               	The deep-sea microorganism Microbacterium sediminis YLB-01 was treated with high
PR:PROJECT_SUMMARY               	pressure (accompanied with low temperature)
PR:INSTITUTE                     	Xiamen University
PR:LAST_NAME                     	Qiu
PR:FIRST_NAME                    	Xu
PR:ADDRESS                       	No. 422, Siming South Road, Xiamen, Fujian, China.
PR:EMAIL                         	qiuxu@stu.xmu.edu.cn
PR:PHONE                         	13161342734
#STUDY
ST:STUDY_TITLE                   	Metabolic Adaptations of Microbacterium sediminis YLB-01 for Survival in the
ST:STUDY_TITLE                   	Challenging High-Pressure of the Deep Sea
ST:STUDY_SUMMARY                 	In this study, we investigated the metabolic adaptations of Microbacterium
ST:STUDY_SUMMARY                 	sediminis YLB-01, a cold and stress-tolerant microorganism isolated from
ST:STUDY_SUMMARY                 	deep-sea sediments, in response to high-pressure conditions. By using NMR-based
ST:STUDY_SUMMARY                 	metabolomic analysis and proteomic analysis, we conducted a comprehensive
ST:STUDY_SUMMARY                 	examination of the significantly altered metabolic pathways involved in the
ST:STUDY_SUMMARY                 	adaptation of YLB-01 cells to high-pressure conditions.
ST:INSTITUTE                     	Xiamen University
ST:LAST_NAME                     	Qiu
ST:FIRST_NAME                    	Xu
ST:ADDRESS                       	No. 422, Siming South Road, Xiamen, Fujian, China.
ST:EMAIL                         	qiuxu@stu.xmu.edu.cn
ST:PHONE                         	13161342734
#SUBJECT
SU:SUBJECT_TYPE                  	Bacteria
SU:SUBJECT_SPECIES               	Microbacterium sediminis YLB-01
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	HP	NPLT_S1	Treatment:NPLT	RAW_FILE_NAME=41
SUBJECT_SAMPLE_FACTORS           	HP	NPLT_S3	Treatment:NPLT	RAW_FILE_NAME=43
SUBJECT_SAMPLE_FACTORS           	HP	NPLT_S4	Treatment:NPLT	RAW_FILE_NAME=44
SUBJECT_SAMPLE_FACTORS           	HP	NPLT_S5	Treatment:NPLT	RAW_FILE_NAME=45
SUBJECT_SAMPLE_FACTORS           	HP	NPLT_S6	Treatment:NPLT	RAW_FILE_NAME=65
SUBJECT_SAMPLE_FACTORS           	HP	NPLT_S7	Treatment:NPLT	RAW_FILE_NAME=47
SUBJECT_SAMPLE_FACTORS           	HP	NPLT_S8	Treatment:NPLT	RAW_FILE_NAME=48
SUBJECT_SAMPLE_FACTORS           	HP	HPLT_S1	Treatment:HPLT	RAW_FILE_NAME=57
SUBJECT_SAMPLE_FACTORS           	HP	HPLT_S2	Treatment:HPLT	RAW_FILE_NAME=58
SUBJECT_SAMPLE_FACTORS           	HP	HPLT_S3	Treatment:HPLT	RAW_FILE_NAME=59
SUBJECT_SAMPLE_FACTORS           	HP	HPLT_S4	Treatment:HPLT	RAW_FILE_NAME=67
SUBJECT_SAMPLE_FACTORS           	HP	HPLT_S5	Treatment:HPLT	RAW_FILE_NAME=61
SUBJECT_SAMPLE_FACTORS           	HP	HPLT_S6	Treatment:HPLT	RAW_FILE_NAME=62
SUBJECT_SAMPLE_FACTORS           	HP	HPLT_S7	Treatment:HPLT	RAW_FILE_NAME=63
SUBJECT_SAMPLE_FACTORS           	HP	HPLT_S8	Treatment:HPLT	RAW_FILE_NAME=68
#COLLECTION
CO:COLLECTION_SUMMARY            	In this study, a single colony of the YLB-01 strain was inoculated from an agar
CO:COLLECTION_SUMMARY            	plate into individual test tubes containing 5 mL of TSB medium. The test tubes
CO:COLLECTION_SUMMARY            	were then incubated in a shaker at 28°C for 12 h. Subsequently, the seed
CO:COLLECTION_SUMMARY            	cultures were transferred to 150-mL Erlenmeyer flasks at a ratio of 1:20, with
CO:COLLECTION_SUMMARY            	each flask containing 100 mL of TSB medium. To ensure an adequate cell count,
CO:COLLECTION_SUMMARY            	YLB-01 cultures were initially cultivated under optimal conditions (28°C, 0.1
CO:COLLECTION_SUMMARY            	MPa) for 24 h. The optical density at 600 nm (OD600 nm) of the cell cultures was
CO:COLLECTION_SUMMARY            	measured using an automatic growth curve analyzer (FP-1100-C, Growth Curves Ab
CO:COLLECTION_SUMMARY            	Ltd., Finland). Once the cultures reached the stationary phase of growth, the
CO:COLLECTION_SUMMARY            	cells were transferred into a 100-mL sterile saline bag and placed in a
CO:COLLECTION_SUMMARY            	high-pressure culture kettle. This kettle, obtained from Nantong Feiyu Company,
CO:COLLECTION_SUMMARY            	China, was specifically designed to simulate the high-pressure conditions of the
CO:COLLECTION_SUMMARY            	deep sea (Zhang et al. 2015). The cells were then exposed to either 30 MPa (the
CO:COLLECTION_SUMMARY            	HPLT group, N=8) or 0.1 MPa (the NPLT group, N=7) at 4°C for 7 days.
CO:COLLECTION_SUMMARY            	Hydrostatic pressure was generated by injecting pure water into the vessel.
CO:SAMPLE_TYPE                   	Bacterial cells
CO:STORAGE_CONDITIONS            	Described in summary
#TREATMENT
TR:TREATMENT_SUMMARY             	To ensure an adequate cell count, YLB-01 cultures were initially cultivated
TR:TREATMENT_SUMMARY             	under optimal conditions (28°C, 0.1 MPa) for 24 h. The optical density at 600
TR:TREATMENT_SUMMARY             	nm (OD600 nm) of the cell cultures was measured using an automatic growth curve
TR:TREATMENT_SUMMARY             	analyzer (FP-1100-C, Growth Curves Ab Ltd., Finland). Once the cultures reached
TR:TREATMENT_SUMMARY             	the stationary phase of growth, the cells were transferred into a 100-mL sterile
TR:TREATMENT_SUMMARY             	saline bag and placed in a high-pressure culture kettle. The cells were then
TR:TREATMENT_SUMMARY             	exposed to either 30 MPa (the HPLT group, N=8) or 0.1 MPa (the NPLT group, N=7)
TR:TREATMENT_SUMMARY             	at 4°C for 7 days.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	After culturing the YLB-01 cells, each 100 mL of the culture was transferred
SP:SAMPLEPREP_SUMMARY            	into a 250-mL centrifuge bottle and centrifuged at 4°C (6000 g, 5 min). The
SP:SAMPLEPREP_SUMMARY            	supernatant was carefully decanted, and the cell pellets were rapidly cooled to
SP:SAMPLEPREP_SUMMARY            	-40°C using 100 mL of a buffer composed of a 3:2 methanol/water mixture
SP:SAMPLEPREP_SUMMARY            	containing 0.85% (wt/vol) NaCl. The mixture was centrifuged again at 4°C (6000
SP:SAMPLEPREP_SUMMARY            	g, 5 min). The cell pellets were washed three times with 5 mL of cold
SP:SAMPLEPREP_SUMMARY            	phosphate-buffered saline (PBS) and centrifuged at 4°C (6000 g, 5 min) after
SP:SAMPLEPREP_SUMMARY            	each wash. Finally, the cell pellets were stored at -80°C until further use.
SP:SAMPLEPREP_SUMMARY            	Initially, 600 μL of a cold extraction buffer consisting of a 1:1 mixture of
SP:SAMPLEPREP_SUMMARY            	distilled water and acetonitrile was added to homogenize the samples. The
SP:SAMPLEPREP_SUMMARY            	mixtures were then sonicated on wet ice for 180 cycles, with each cycle
SP:SAMPLEPREP_SUMMARY            	consisting of 2 seconds of ultrasound followed by a 3-second pause. After
SP:SAMPLEPREP_SUMMARY            	centrifugation at 4°C (12000 g, 10 min), the supernatants were collected and
SP:SAMPLEPREP_SUMMARY            	lyophilized, resulting in an extract powder that was stored at -80°C for
SP:SAMPLEPREP_SUMMARY            	further analysis.
SP:PROCESSING_STORAGE_CONDITIONS 	Described in summary
SP:EXTRACT_STORAGE               	Described in summary
#ANALYSIS
AN:ANALYSIS_TYPE                 	NMR
#NMR
NM:INSTRUMENT_NAME               	Bruker Avance III 600 MHz
NM:INSTRUMENT_TYPE               	FT-NMR
NM:NMR_EXPERIMENT_TYPE           	1D-1H
NM:SPECTROMETER_FREQUENCY        	600 MHz
#FACTORS
NM:NMR_RESULTS_FILE               	ST002804_AN004560_Results.txt	UNITS:ppm
#END