Summary of Study ST003078
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 PR001917. The data can be accessed directly via it's Project DOI: 10.21228/M8XH8G This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003078 |
| Study Title | Dynamic exometabolomics reveals metabolic adaptations of Staphylococcus epidermidis to pH-mimicking skin and bloodstream |
| Study Summary | A common human skin coloniser, Staphylococcus epidermidis (SE), is often the cause of infections associated with medical devices. Strains that retain this pathogenic and commensal potential coexist in human skin, belonging to clonal lineages A/C and B, respectively. The pH is an abiotic factor that changes during infection when SE is transferred from host skin to blood. However, pathogenicity mechanisms are poorly understood in this organism and recognizing how it deals with increments of pH, is relevant to design effective prevention and treatment strategies against SE infections. To investigate the metabolic adaptations of A/C and B representative strains to an increase in pH, we mimicked the pH conditions of skin and blood (5.5 and 7.4). Biomass formation, growth media pH and 1H-NMR exometabolomic data were measured until the stationary phase was reached, at the two selected pH values. Higher biomass was reached for both strains when grown at pH 7.4. For all experimental conditions, media pH significantly changed during growth, revealing several pH adaptation mechanisms. SE metabolism relies on saccharides and amino acids uptake, citric acid cycle, mixed acid and alcoholic fermentations at a higher extent in blood than at skin pH. This study highlighted accumulation of extracellular formate by the pathogenic strain at blood pH, consistent with the absence of a formate dehydrogenase gene in this strain. This, most likely constitutes a virulence factor that, together with higher media acidification, impacts on host invasion. This work depicts the relevance of specific metabolic processes in determining SE commensalism and pathogenicity, thus providing helpful information towards new design strategies against SE infections. |
| Institute | ITQB NOVA |
| Last Name | Morais |
| First Name | Elisabete |
| Address | Campus de Campolide |
| elisabete.morais@itqb.unl.pt | |
| Phone | (+351) 21 446 91 00 |
| Submit Date | 2024-02-15 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2024-05-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001917 |
| Project DOI: | doi: 10.21228/M8XH8G |
| Project Title: | Dynamic exometabolomics reveals metabolic adaptations of Staphylococcus epidermidis to pH-mimicking skin and bloodstream |
| Project Summary: | A common human skin coloniser, Staphylococcus epidermidis (SE), is often the cause of infections associated with medical devices. Strains that retain this pathogenic and commensal potential coexist in human skin, belonging to clonal lineages A/C and B, respectively. The pH is an abiotic factor that changes during infection when SE is transferred from host skin to blood. However, pathogenicity mechanisms are poorly understood in this organism and recognizing how it deals with increments of pH, is relevant to design effective prevention and treatment strategies against SE infections. To investigate the metabolic adaptations of A/C and B representative strains to an increase in pH, we mimicked the pH conditions of skin and blood (5.5 and 7.4). Biomass formation, growth media pH and 1H-NMR exometabolomic data were measured until the stationary phase was reached, at the two selected pH values. Higher biomass was reached for both strains when grown at pH 7.4. For all experimental conditions, media pH significantly changed during growth, revealing several pH adaptation mechanisms. SE metabolism relies on saccharides and amino acids uptake, citric acid cycle, mixed acid and alcoholic fermentations at a higher extent in blood than at skin pH. This study highlighted accumulation of extracellular formate by the pathogenic strain at blood pH, consistent with the absence of a formate dehydrogenase gene in this strain. This, most likely constitutes a virulence factor that, together with higher media acidification, impacts on host invasion. This work depicts the relevance of specific metabolic processes in determining SE commensalism and pathogenicity, thus providing helpful information towards new design strategies against SE infections. |
| Institute: | ITQB NOVA |
| Last Name: | Morais |
| First Name: | Elisabete |
| Address: | Campus de Campolide, ITQB NOVA, Av. da República, 2780-157 Oeiras |
| Email: | elisabete.morais@itqb.unl.pt |
| Phone: | (+351) 21 446 91 00 |
Subject:
| Subject ID: | SU003193 |
| Subject Type: | Bacteria |
| Subject Species: | Staphylococcus epidermidis |
| Taxonomy ID: | 1282 |
| Genotype Strain: | 19N/ICE25 |
Factors:
Subject type: Bacteria; Subject species: Staphylococcus epidermidis (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Strain | initial pH | Time (h) | Replica |
|---|---|---|---|---|---|---|
| SA332599 | EM_N5_2_220720 | 19N | 19N | 5.5 | 0 | 1 |
| SA332600 | EM_N5_0a_220811 | 19N | 19N | 5.5 | 0 | 2 |
| SA332601 | EM_N5_0b_220812 | 19N | 19N | 5.5 | 0 | 3 |
| SA332602 | EM_N5_10a_220811 | 19N | 19N | 5.5 | 10 | 2 |
| SA332603 | EM_N5_10b_220811 | 19N | 19N | 5.5 | 10 | 3 |
| SA332604 | EM_N5_4_20720 | 19N | 19N | 5.5 | 2 | 1 |
| SA332605 | EM_N5_2a_220811 | 19N | 19N | 5.5 | 2 | 2 |
| SA332606 | EM_N5_2b_220812 | 19N | 19N | 5.5 | 2 | 3 |
| SA332607 | EM_N5_5_221012 | 19N | 19N | 5.5 | 3 | 1 |
| SA332608 | EM_N5_6_220720 | 19N | 19N | 5.5 | 4 | 1 |
| SA332609 | EM_N5_4a_220811 | 19N | 19N | 5.5 | 4 | 2 |
| SA332610 | EM_N5_4b_220812 | 19N | 19N | 5.5 | 4 | 3 |
| SA332611 | EM_N5_7_221012 | 19N | 19N | 5.5 | 5 | 1 |
| SA332612 | EM_N5_5a_221012 | 19N | 19N | 5.5 | 5 | 2 |
| SA332613 | EM_N5_5b_221012_ | 19N | 19N | 5.5 | 5 | 3 |
| SA332614 | EM_N5_8_220720 | 19N | 19N | 5.5 | 6 | 1 |
| SA332615 | EM_N5_6a_220811 | 19N | 19N | 5.5 | 6 | 2 |
| SA332616 | EM_N5_6b_220812 | 19N | 19N | 5.5 | 6 | 3 |
| SA332617 | EM_N5_7a_221012 | 19N | 19N | 5.5 | 7 | 2 |
| SA332618 | EM_N5_7b_221012 | 19N | 19N | 5.5 | 7 | 3 |
| SA332619 | EM_N5_10_220720 | 19N | 19N | 5.5 | 8 | 1 |
| SA332620 | EM_N5_8a_220811 | 19N | 19N | 5.5 | 8 | 2 |
| SA332621 | EM_N5_8b_220812 | 19N | 19N | 5.5 | 8 | 3 |
| SA332622 | EM_N7_2_220720 | 19N | 19N | 7.4 | 0 | 1 |
| SA332623 | EM_N7_0a_220811 | 19N | 19N | 7.4 | 0 | 2 |
| SA332624 | EM_N7_0b_220812 | 19N | 19N | 7.4 | 0 | 3 |
| SA332625 | EM_N7_12_221109 | 19N | 19N | 7.4 | 10 | 1 |
| SA332626 | EM_N7_10a_220812 | 19N | 19N | 7.4 | 10 | 2 |
| SA332627 | EM_N7_12b_221109 | 19N | 19N | 7.4 | 11 | 3 |
| SA332628 | EM_N7_2b_220812 | 19N | 19N | 7.4 | 1 | 3 |
| SA332629 | EM_N7_4_220720 | 19N | 19N | 7.4 | 2 | 1 |
| SA332630 | EM_N7_2a_220811 | 19N | 19N | 7.4 | 2 | 2 |
| SA332631 | EM_N7_5_221012 | 19N | 19N | 7.4 | 3 | 1 |
| SA332632 | EM_N7_4b_220812 | 19N | 19N | 7.4 | 3 | 3 |
| SA332633 | EM_N7_6_220720 | 19N | 19N | 7.4 | 4 | 1 |
| SA332634 | EM_N7_4a_220811 | 19N | 19N | 7.4 | 4 | 2 |
| SA332635 | EM_N7_5b_221012 | 19N | 19N | 7.4 | 4 | 3 |
| SA332636 | EM_N7_7_221012 | 19N | 19N | 7.4 | 5 | 1 |
| SA332637 | EM_N7_5a_221012 | 19N | 19N | 7.4 | 5 | 2 |
| SA332638 | EM_N7_6b_220812 | 19N | 19N | 7.4 | 5 | 3 |
| SA332639 | EM_N7_8_220720 | 19N | 19N | 7.4 | 6 | 1 |
| SA332640 | EM_N7_6a_220811 | 19N | 19N | 7.4 | 6 | 2 |
| SA332641 | EM_N7_7b_221012 | 19N | 19N | 7.4 | 6 | 3 |
| SA332642 | EM_N7_7a_221012 | 19N | 19N | 7.4 | 7 | 2 |
| SA332643 | EM_N7_8b_220812 | 19N | 19N | 7.4 | 7 | 3 |
| SA332644 | EM_N7_10_220720 | 19N | 19N | 7.4 | 8 | 1 |
| SA332645 | EM_N7_8a_220811 | 19N | 19N | 7.4 | 8 | 2 |
| SA332646 | EM_N7_10b_220812 | 19N | 19N | 7.4 | 9 | 3 |
| SA332647 | EM_I5_2_220720 | ICE25 | ICE25 | 5.5 | 0 | 1 |
| SA332648 | EM_I5_0a_220811 | ICE25 | ICE25 | 5.5 | 0 | 2 |
| SA332649 | EM_I5_0b_220812 | ICE25 | ICE25 | 5.5 | 0 | 3 |
| SA332650 | EM_I5_10a_220811 | ICE25 | ICE25 | 5.5 | 10 | 2 |
| SA332651 | EM_I5_10b_220812 | ICE25 | ICE25 | 5.5 | 10 | 3 |
| SA332652 | EM_I5_5_221012_ | ICE25 | ICE25 | 5.5 | 2 | 1 |
| SA332653 | EM_I5_2a_220811 | ICE25 | ICE25 | 5.5 | 2 | 2 |
| SA332654 | EM_I5_2b_220812 | ICE25 | ICE25 | 5.5 | 2 | 3 |
| SA332655 | EM_I5_6_220720 | ICE25 | ICE25 | 5.5 | 3 | 1 |
| SA332656 | EM_I5_3a_220812 | ICE25 | ICE25 | 5.5 | 3 | 2 |
| SA332657 | EM_I5_3b_220812 | ICE25 | ICE25 | 5.5 | 3 | 3 |
| SA332658 | EM_I5_7_221012 | ICE25 | ICE25 | 5.5 | 4 | 1 |
| SA332659 | EM_I5_4a_220811 | ICE25 | ICE25 | 5.5 | 4 | 2 |
| SA332660 | EM_I5_4b_220812 | ICE25 | ICE25 | 5.5 | 4 | 3 |
| SA332661 | EM_I5_8_220720 | ICE25 | ICE25 | 5.5 | 5 | 1 |
| SA332662 | EM_I5_5a_220812 | ICE25 | ICE25 | 5.5 | 5 | 2 |
| SA332663 | EM_I5_5b_220812 | ICE25 | ICE25 | 5.5 | 5 | 3 |
| SA332664 | EM_I5_6a_220811 | ICE25 | ICE25 | 5.5 | 6 | 2 |
| SA332665 | EM_I5_6b_220812 | ICE25 | ICE25 | 5.5 | 6 | 3 |
| SA332666 | EM_I5_10_220720 | ICE25 | ICE25 | 5.5 | 7 | 1 |
| SA332667 | EM_I5_7a_220812 | ICE25 | ICE25 | 5.5 | 7 | 2 |
| SA332668 | EM_I5_7b_220812 | ICE25 | ICE25 | 5.5 | 7 | 3 |
| SA332669 | EM_I5_8a_220811 | ICE25 | ICE25 | 5.5 | 8 | 2 |
| SA332670 | EM_I5_8b_220812 | ICE25 | ICE25 | 5.5 | 8 | 3 |
| SA332671 | EM_I5_12_221109 | ICE25 | ICE25 | 5.5 | 9 | 1 |
| SA332672 | EM_7_0_221012 | ICE25 | ICE25 | 7.4 | 0 | 1 |
| SA332673 | EM_I7_0a_220811 | ICE25 | ICE25 | 7.4 | 0 | 2 |
| SA332674 | EM_7_0b_221012 | ICE25 | ICE25 | 7.4 | 0 | 3 |
| SA332675 | EM_I7_10_220720 | ICE25 | ICE25 | 7.4 | 10 | 1 |
| SA332676 | EM_I7_10a_220812 | ICE25 | ICE25 | 7.4 | 10 | 2 |
| SA332677 | EM_I7_10b_220812 | ICE25 | ICE25 | 7.4 | 10 | 3 |
| SA332678 | EM_I7_2_220720 | ICE25 | ICE25 | 7.4 | 2 | 1 |
| SA332679 | EM_I7_2a_220811 | ICE25 | ICE25 | 7.4 | 2 | 2 |
| SA332680 | EM_I7_2b_220812 | ICE25 | ICE25 | 7.4 | 2 | 3 |
| SA332681 | EM_I7_4_220720 | ICE25 | ICE25 | 7.4 | 4 | 1 |
| SA332682 | EM_I7_4a_220811 | ICE25 | ICE25 | 7.4 | 4 | 2 |
| SA332683 | EM_I7_4b_220812 | ICE25 | ICE25 | 7.4 | 4 | 3 |
| SA332684 | EM_I7_5_221012 | ICE25 | ICE25 | 7.4 | 5 | 1 |
| SA332685 | EM_I7_5a_221012 | ICE25 | ICE25 | 7.4 | 5 | 2 |
| SA332686 | EM_I7_5b_221012 | ICE25 | ICE25 | 7.4 | 5 | 3 |
| SA332687 | EM_I7_6_220720 | ICE25 | ICE25 | 7.4 | 6 | 1 |
| SA332688 | EM_I7_6a_220811 | ICE25 | ICE25 | 7.4 | 6 | 2 |
| SA332689 | EM_I7_6b_220812 | ICE25 | ICE25 | 7.4 | 6 | 3 |
| SA332690 | EM_I7_7_221012 | ICE25 | ICE25 | 7.4 | 7 | 1 |
| SA332691 | EM_I7_7a_221012 | ICE25 | ICE25 | 7.4 | 7 | 2 |
| SA332692 | EM_I7_7b_221012 | ICE25 | ICE25 | 7.4 | 7 | 3 |
| SA332693 | EM_I7_8_220720 | ICE25 | ICE25 | 7.4 | 8 | 1 |
| SA332694 | EM_I7_8a_220812 | ICE25 | ICE25 | 7.4 | 8 | 2 |
| SA332695 | EM_I7_8b_220812 | ICE25 | ICE25 | 7.4 | 8 | 3 |
| Showing results 1 to 97 of 97 |
Collection:
| Collection ID: | CO003186 |
| Collection Summary: | Hourly, an 800 µL aliquot was collected to measure OD600nm and the medium was separated from the cells by centrifugation at 5000 g, 5 min and 4°C. The supernatants were kept at -20°C until NMR analysis (for a maximum duration of 3 months). |
| Sample Type: | Bacterial cells |
| Storage Conditions: | -20℃ |
Treatment:
| Treatment ID: | TR003202 |
| Treatment Summary: | SE growth assays were performed for 19N and ICE25 strains at pH mimicking SE skin colonisation and blood infection (pH 5.5 and 7.4, respectively) in three independent replicates. A total of eight time-points were analysed: t0h collected immediately after inoculation, t2h-6h hourly during the exponential phase, t8h and t10h during the late exponential and beginning of the stationary phase. |
Sample Preparation:
| Sampleprep ID: | SP003199 |
| Sampleprep Summary: | After thawing, 540 µL of the media samples were transferred to 5 mm NMR tubes and 60 µL of the NMR buffer (1 M phosphate potassium buffer, 2 mM sodium azide, 3.22 mM 3-(Trimethylsilyl)propionic-2,2,3,3-d4 acid sodium salt (TSP), pH 7.0) was added. |
Analysis:
| Analysis ID: | AN005036 |
| Analysis Type: | NMR |
| Num Factors: | 97 |
| Num Metabolites: | 47 |
| Units: | mM |
NMR:
| NMR ID: | NM000275 |
| Analysis ID: | AN005036 |
| Instrument Name: | Bruker Avance II+ 800 MHz |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Spectrometer Frequency: | 800 |
| NMR Probe: | 5 mm TXI-Z H/C/N/-D |
| NMR Solvent: | 90% H20 + 10% D2O |
| NMR Tube Size: | 5 mm |
| Shimming Method: | Topshim |
| Pulse Sequence: | noesygppr1d |
| Receiver Gain: | 57 |
| Chemical Shift Ref Cpd: | TSP |
| Temperature: | 25 |
| Number Of Scans: | 64 |
| Dummy Scans: | 4 |
