Summary of Study ST002868

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 PR001791. The data can be accessed directly via it's Project DOI: 10.21228/M86M7M 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	ST002868
Study Title	Pathogenic Staphylococcus epidermidis ICE25 response to skin and blood pH
Study Summary	Staphylococcus epidermidis (SE) is one of the most common bacteria of the human skin microbiota. Despite its role as a commensal, SE has emerged as an opportunistic pathogen, associated with 80% of medical devices related infections. Moreover, these bacteria are extremely difficult to treat due to their ability to form biofilms and accumulate resistance to almost all classes of antimicrobials developed so far. Thus new preventive and therapeutic strategies are urgently needed. In spite of its clinical importance, the molecular mechanisms associated with SE colonisation and disease are still poorly understood. A deeper understanding of the metabolic and cellular processes associated with response to environmental factors characteristic of SE ecological niches in health and disease might provide new clues on colonisation and disease processes. Here we studied the impact of pH conditions, mimicking the skin pH (5.5) and blood pH (7.4), in a S. epidermidis pathogenic strain, belonging to the A/C clonal lineage, by means of next-generation proteomics and 1H NMR-based metabolomics. Moreover, we evaluated the metabolic changes occurring when a sudden pH change arise, simulating the skin barrier break produced by a catheter.
Institute	ITQB NOVA
Last Name	Gonçalves
First Name	Luís G.
Address	Avenida Republica
Email	lgafeira@itqb.unl.pt
Phone	214469464
Submit Date	2023-09-13
Raw Data Available	Yes
Raw Data File Type(s)	fid
Analysis Type Detail	NMR
Release Date	2024-01-02
Release Version	1

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Project:

Project ID:	PR001791
Project DOI:	doi: 10.21228/M86M7M
Project Title:	Pathogenic Staphylococcus epidermidis ICE25 response to skin and blood pH
Project Type:	Proteomic and metabolomic study
Project Summary:	Staphylococcus epidermidis (SE) is one of the most common bacteria of the human skin microbiota. Despite its role as a commensal, SE has emerged as an opportunistic pathogen, associated with 80% of medical devices related infections. Moreover, these bacteria are extremely difficult to treat due to their ability to form biofilms and accumulate resistance to almost all classes of antimicrobials developed so far. Thus new preventive and therapeutic strategies are urgently needed. In spite of its clinical importance, the molecular mechanisms associated with SE colonisation and disease are still poorly understood. A deeper understanding of the metabolic and cellular processes associated with response to environmental factors characteristic of SE ecological niches in health and disease might provide new clues on colonisation and disease processes. Here we studied the impact of pH conditions, mimicking the skin pH (5.5) and blood pH (7.4), in a S. epidermidis pathogenic strain, belonging to the A/C clonal lineage, by means of next-generation proteomics and 1H NMR-based metabolomics. Moreover, we evaluated the metabolic changes occurring when a sudden pH change arise, simulating the skin barrier break produced by a catheter.
Institute:	ITQB NOVA
Last Name:	Gonçalves
First Name:	Luís
Address:	Avenida Republica, Oeiras, Not USCanada, 2780-157 Oeiras, Portugal
Email:	lgafeira@itqb.unl.pt
Phone:	214469464

Subject:

Subject ID:	SU002980
Subject Type:	Bacteria
Subject Species:	Staphylococcus epidermidis
Taxonomy ID:	1282
Genotype Strain:	Staphylococcus epidermidis ICE25

Factors:

Subject type: Bacteria; Subject species: Staphylococcus epidermidis (Factor headings shown in green)

mb_sample_id	local_sample_id	Class
SA313040	SE_a11_190712	I55
SA313041	SE_a07_190712	I55
SA313042	SE_a04_190712	I55
SA313043	SE_24_190530	I55
SA313044	SE_18_190530	I55
SA313045	SE_23_190530	I55
SA313046	SE_a18_190712	I55
SA313047	SE_a09_190712	I57
SA313048	SE_a13_190712_rep	I57
SA313049	SE_a17_190712	I57
SA313050	SE_a03_190712	I57
SA313051	SE_7_190530	I57
SA313052	SE_4_190530	I57
SA313053	SE_10_190530	I57
SA313054	SE_11_190530	I57
SA313055	SE_a20_190712	I77
SA313056	SE_a16_190712	I77
SA313057	SE_a12_190712	I77
SA313058	SE_a06_190712	I77
SA313059	SE_9_190530	I77
SA313060	SE_6_190530	I77
SA313061	SE_1_190530	I77
SA313062	SE_5_190530	I77

Showing results 1 to 23 of 23

Showing results 1 to 23 of 23

Collection:

Collection ID:	CO002973
Collection Summary:	The Staphylococcus epidermidis 19N strain was collected from the anterior nares of a healthy person in Portugal in 2001. This strain was previously characterised by whole genome sequencing and belongs to clonal lineage B. A single colony from a S. epidermidis 19N strain culture grown O/N at 37ºC (TSA, BactoTM), was used to pre-inoculate Tryptic Soy Broth (TSB) medium with two different pH (5.5 and 7.4) that was incubated overnight at 37ºC under agitation. Pre-inoculums were adjusted either to pH 5.5 or pH 7.4, with hydrochloric acid. In this work, three pH transitions from pre-inoculum to inoculum were assayed. S. epidermidis pre-inoculums and the growth were performed at medium with pH 7.4, to mimic the blood pH; and pH 5.5, to mimic the skin pH. The pre-inoculum cellular density was adjusted to 0.06 (OD600) (aprox.1.5x108 CFU/mL) and used to inoculate fresh medium in the three conditions depicted in Figure 1, simulating S. epidermidis at skin and blood and a pH shock endured by S. epidermidis during the infection process from skin to blood transition. The cell cultures incubated at 37ºC with 225 rpm were followed by OD600 and recovered at mid-exponential phase for further analysis.
Sample Type:	Staphylococcus epidermidis intracellular
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR002989
Treatment Summary:	In this work, three pH transitions from pre-inoculum to inoculum were assayed. S. epidermidis pre-inoculums and the growth were performed at medium with pH 7.4, to mimic the blood pH; and pH 5.5, to mimic the skin pH. The pre-inoculum cellular density was adjusted to 0.06 (OD600) (aprox.1.5x108 CFU/mL) and used to inoculate fresh medium in the three conditions depicted in Figure 1, simulating S. epidermidis at skin and blood and a pH shock endured by S. epidermidis during the infection process from skin to blood transition. The cell cultures incubated at 37ºC with 225 rpm were followed by OD600 and recovered at mid-exponential phase for further analysis. Pre-inocula were prepared in TSB medium at pH 5.5 or 7.4. Inocula at pH 5.5 was used for the cultures grown at 5.5 (N55) and 7.4 (N57), and the inoculum at pH 7.4 for the culture at the same pH (N77). The cells were harvested at mid-exponential phase.

Treatment ID:

TR002989

Treatment Summary:

In this work, three pH transitions from pre-inoculum to inoculum were assayed. S. epidermidis pre-inoculums and the growth were performed at medium with pH 7.4, to mimic the blood pH; and pH 5.5, to mimic the skin pH. The pre-inoculum cellular density was adjusted to 0.06 (OD600) (aprox.1.5x108 CFU/mL) and used to inoculate fresh medium in the three conditions depicted in Figure 1, simulating S. epidermidis at skin and blood and a pH shock endured by S. epidermidis during the infection process from skin to blood transition. The cell cultures incubated at 37ºC with 225 rpm were followed by OD600 and recovered at mid-exponential phase for further analysis. Pre-inocula were prepared in TSB medium at pH 5.5 or 7.4. Inocula at pH 5.5 was used for the cultures grown at 5.5 (N55) and 7.4 (N57), and the inoculum at pH 7.4 for the culture at the same pH (N77). The cells were harvested at mid-exponential phase.

Sample Preparation:

Sampleprep ID:	SP002986
Sampleprep Summary:	Cells were recovered at mid-exponential phase from 100 mL cultures following a protocol adapted from Somerville & Powers (Somerville and Powers 2014). Eight biological replicates of each independent growth condition were obtained. Cells were harvested by centrifugation at 5000 x g for 5 min at 4ºC. Cells were washed with 20 mM phosphate buffer pH 7.2-7.4 and centrifuged for 1 min at 13,000 rpm. Cell pellet was suspended in the same buffer with a final OD600 of 20 and stored at -80ºC for further metabolite extraction. Cells were thawed in a water bath at room temperature and 750 µL of 60% methanol were added and subjected to three freeze-thaw cycles using liquid nitrogen. Extracted samples were centrifuged at 21,000 g for 5 min at 4ºC. The extraction process on the pellets was repeated twice. The supernatants were kept and stored together at -20ºC overnight and dried in a SpeedVac. Dried samples were dissolved in: 750 µL phosphate buffer (33 mM, pH 7.0 in D2O with 2 mM of sodium azide) with 0.21 mM of 3-(trimethylsilyl)propionic-2,2,3,3-d4 (TSP). The suspensions were centrifuged at 21,000 g for 5 min at 4ºC and the resulting supernatants were then transferred to 5 mm NMR tubes.

Sampleprep ID:

SP002986

Sampleprep Summary:

Cells were recovered at mid-exponential phase from 100 mL cultures following a protocol adapted from Somerville & Powers (Somerville and Powers 2014). Eight biological replicates of each independent growth condition were obtained. Cells were harvested by centrifugation at 5000 x g for 5 min at 4ºC. Cells were washed with 20 mM phosphate buffer pH 7.2-7.4 and centrifuged for 1 min at 13,000 rpm. Cell pellet was suspended in the same buffer with a final OD600 of 20 and stored at -80ºC for further metabolite extraction. Cells were thawed in a water bath at room temperature and 750 µL of 60% methanol were added and subjected to three freeze-thaw cycles using liquid nitrogen. Extracted samples were centrifuged at 21,000 g for 5 min at 4ºC. The extraction process on the pellets was repeated twice. The supernatants were kept and stored together at -20ºC overnight and dried in a SpeedVac. Dried samples were dissolved in: 750 µL phosphate buffer (33 mM, pH 7.0 in D2O with 2 mM of sodium azide) with 0.21 mM of 3-(trimethylsilyl)propionic-2,2,3,3-d4 (TSP). The suspensions were centrifuged at 21,000 g for 5 min at 4ºC and the resulting supernatants were then transferred to 5 mm NMR tubes.

Analysis:

Analysis ID:	AN004701
Analysis Type:	NMR
Num Factors:	3
Num Metabolites:	43
Units:	nanomoles

NMR:

NMR ID:	NM000267
Analysis ID:	AN004701
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:	D2O
NMR Tube Size:	5 mm
Shimming Method:	Topshim
Chemical Shift Ref Cpd:	TSP
Temperature:	25