Summary of Study ST002804
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001751. The data can be accessed directly via it's Project DOI: 10.21228/M8CH9W This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST002804 |
| Study Title | Metabolic Adaptations of Microbacterium sediminis YLB-01 for Survival in the Challenging High-Pressure of the Deep Sea |
| Study Summary | By using NMR-based metabolomic analysis, we investigated the metabolic adaptations of Microbacterium sediminis YLB-01 in response to high-pressure conditions. We recorded the 600 MHz 1D 1H-NMR spectra on aqueous extracts from YLB-01 cells, and then assigned resonances of 31 metabolites. The distinct metabolic separation between the HPLT and NPLT groups highlighted the significant effect of high-pressure treatment on the metabolism of YLB-01 cells. |
| Institute | Xiamen University |
| Last Name | Qiu |
| First Name | Xu |
| Address | No. 422, Siming South Road, Xiamen, Fujian, China. |
| qiuxu@stu.xmu.edu.cn | |
| Phone | 13161342734 |
| Submit Date | 2023-06-18 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2023-08-22 |
| Release Version | 1 |
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Project:
| Project ID: | PR001751 |
| Project DOI: | doi: 10.21228/M8CH9W |
| 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 |
Subject:
| Subject ID: | SU002911 |
| Subject Type: | Bacteria |
| Subject Species: | Microbacterium sediminis YLB-01 |
| Species Group: | Bacteria |
Factors:
Subject type: Bacteria; Subject species: Microbacterium sediminis YLB-01 (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA300832 | HPLT_S4 | HPLT |
| SA300833 | HPLT_S3 | HPLT |
| SA300834 | HPLT_S5 | HPLT |
| SA300835 | HPLT_S7 | HPLT |
| SA300836 | HPLT_S8 | HPLT |
| SA300837 | HPLT_S2 | HPLT |
| SA300838 | HPLT_S6 | HPLT |
| SA300839 | HPLT_S1 | HPLT |
| SA300840 | NPLT_S4 | NPLT |
| SA300841 | NPLT_S3 | NPLT |
| SA300842 | NPLT_S5 | NPLT |
| SA300843 | NPLT_S6 | NPLT |
| SA300844 | NPLT_S8 | NPLT |
| SA300845 | NPLT_S7 | NPLT |
| SA300846 | NPLT_S1 | NPLT |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO002904 |
| 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 ID: | TR002920 |
| 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. |
Sample Preparation:
| Sampleprep ID: | SP002917 |
| 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 ID: | AN004560 |
| Analysis Type: | NMR |
| Results File: | ST002804_AN004560_Results.txt |
| Units: | ppm |
NMR:
| NMR ID: | NM000266 |
| Analysis ID: | AN004560 |
| Instrument Name: | Bruker Avance III 600 MHz |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Standard Concentration: | 1 mM TSP |
| Spectrometer Frequency: | 600 MHz |
| NMR Solvent: | H2O+D2O |
| NMR Tube Size: | 5 mm |
| Pulse Sequence: | noesygppr1d [(RD)-90°-t1-90°-τm-90°-ACQ] |
| Receiver Gain: | 71.8 |
| Offset Frequency: | 15.1 ppm |
| Temperature: | 25 |
| Number Of Scans: | 32 |
| Dummy Scans: | 4 |
| Acquisition Time: | 2 s |
| Spectral Width: | 20 ppm |
| Num Data Points Acquired: | 64 K |
| Line Broadening: | 0.3 Hz |
| Baseline Correction Method: | Auto-baseline correction of integral by abs |
| Chemical Shift Ref Std: | TSP (0.000 ppm) |
| Binned Data Excluded Range: | δ 4.700-5.100 ppm |
| NMR Results File: | microHP.txt UNITS:ppm |
