Summary of Study ST003777

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 PR002355. The data can be accessed directly via it's Project DOI: 10.21228/M8753X 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.

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Study ID	ST003777
Study Title	Separation and Characterization of a Clinically-Derived Staphylococcus epidermidis Strain HE23: Revealing Its Antibiotic Resistome and Metabolic Potential
Study Summary	Neonatal incubators, while essential for infant care, are high-risk environments for nosocomial infections due to microbial colonization. Staphylococcus epidermidis, a biofilm-forming opportunistic pathogen, frequently contaminates medical devices, yet its metabolic adaptation mechanisms and virulence potential in incubator settings remain poorly understood. This study integrates genomics and metabolomics to comprehensively profile a multidrug-resistant S. epidermidis HE23 strain isolated from neonatal incubators, aiming to reveal its antibiotic resistance determinants and toxic metabolite production linked to clinical pathogenicity. A bacterial strain (HE23) was isolated from a neonatal incubator and identified as Staphylococcus epidermidis by 16S rRNA sequencing. Whole genome sequencing was performed using Illumina and Oxford Nanopore platforms, and a high-quality genome was obtained by hybrid assembly (Unicycler). And metabolomic analysis was performed by liquid mass spectrometry detection. Metabolomic profiling of Staphylococcus epidermidis HE23 revealed 47 differentially expressed metabolites (15 upregulated, 32 downregulated; VIP > 1.0, p < 0.05). Among upregulated metabolites, two clinically significant toxins were identified:Harmaline (m/z 446.2529 ), Cinobufagin (m/z 460.2686). Pathway enrichment highlighted glutathione metabolism (VIP = 2.1, p = 0.008) and branched-chain amino acid degradation (VIP = 1.8, p = 0.015), suggesting redox stress adaptation and nutrient scavenging strategies.
Institute	Anhui Medical University
Department	College of Life Sciences
Laboratory	College of Life Sciences, Anhui Medical University
Last Name	Chen
First Name	Qingru
Address	81 Meishan Road, Hefei, Anhui 230032, China
Email	chenqr95@foxmail.com
Phone	18156455228
Submit Date	2025-03-02
Raw Data Available	Yes
Raw Data File Type(s)	mzML, raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2025-03-07
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002355
Project DOI:	doi: 10.21228/M8753X
Project Title:	Metabolomics of Staphylococcus epidermidis HE23 isolated from the hospital environment
Project Summary:	Metabolomic analysis of Staphylococcus epidermidis HE23 isolated from the hospital environment to investigate its metabolic profile and potential hazards
Institute:	Anhui Medical University
Last Name:	Chen
First Name:	Qingru
Address:	81 Meishan Road, Hefei, Anhui 230032, China
Email:	chenqr95@foxmail.com
Phone:	18156455228

Subject:

Subject ID:	SU003911
Subject Type:	Bacteria
Subject Species:	Staphylococcus epidermidis
Taxonomy ID:	1282
Genotype Strain:	Staphylococcus epidermidis HE23

Factors:

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

mb_sample_id	local_sample_id	Sample source	Sample_type
SA409971	H1	Bacteria	Bacterial cells
SA409972	H2	Bacteria	Bacterial cells
SA409973	H3	Bacteria	Bacterial cells
SA409974	C1	Blank	control
SA409975	C2	Blank	control
SA409976	C3	Blank	control
SA409977	QC01	QC	QC(Internal Standard)
SA409978	QC02	QC	QC(Internal Standard)
SA409979	QC03	QC	QC(Internal Standard)

Showing results 1 to 9 of 9

Showing results 1 to 9 of 9

Collection:

Collection ID:	CO003904
Collection Summary:	The Staphylococcus epidermidis HE23 strain was isolated from the inner surface of a neonatal incubator in the Neonatal Intensive Care Unit (NICU) at the First Affiliated Hospital of Anhui Medical University (Hefei, China). Post-sampling, the isolate was purified via streak-plating on LB agar. Taxonomic classification was confirmed through 16S ribosomal RNA gene sequencing (primers 27F/1492R). For experimental analyses, HE23 was cultured in standard LB broth (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl; pH 7.2) under aerobic conditions. Pre-inoculum was prepared by incubating at 37°C with 200 rpm orbital shaking for 16–18 hours to reach mid-log phase (OD₆₀₀ ≈ 0.8). Cells were harvested by centrifugation (4,000 ×g, 10 min, 4°C) and washed twice with sterile phosphate-buffered saline (PBS) prior to downstream assays.
Sample Type:	Bacterial cells

Treatment:

Treatment ID:	TR003920
Treatment Summary:	NA

Sample Preparation:

Sampleprep ID:	SP003917
Sampleprep Summary:	Accurately pipette 200 μL of sample into a 1.5 mL centrifuge tube; Add 400 μL of extraction solution (methanol:acetonitrile=1:1 (v:v)) containing four internal standards (e.g., L-2-chlorophenylalanine (0.02 mg/mL), etc.); vortex and mix for 30 s, and then ultrasonic extraction was carried out for 30 min at low temperature (5°C, 40 KHz); the sample was left at -20°C for 30 min; centrifuged for 15 min (13,000g, 4°C), and the supernatant was removed and The samples were allowed to stand at -20℃ for 30 minutes, centrifuged for 15 minutes (13000g, 4℃), the supernatant was pipetted and blown dry with nitrogen; 120 μL of reconstituted solution (acetonitrile:water=1:1) was added to reconstitute the sample; the samples were vortexed again for 30 seconds, and then sonicated at low temperature for 5 minutes (5℃, 40KHz); the samples were then centrifuged for 10 minutes (13000g, 4℃), and the supernatant was pipetted to the feeder vials with the cannulae for analysis. In addition, 20 μL of supernatant was pipetted separately for each sample and mixed as a quality control sample.

Sampleprep ID:

SP003917

Sampleprep Summary:

Accurately pipette 200 μL of sample into a 1.5 mL centrifuge tube; Add 400 μL of extraction solution (methanol:acetonitrile=1:1 (v:v)) containing four internal standards (e.g., L-2-chlorophenylalanine (0.02 mg/mL), etc.); vortex and mix for 30 s, and then ultrasonic extraction was carried out for 30 min at low temperature (5°C, 40 KHz); the sample was left at -20°C for 30 min; centrifuged for 15 min (13,000g, 4°C), and the supernatant was removed and The samples were allowed to stand at -20℃ for 30 minutes, centrifuged for 15 minutes (13000g, 4℃), the supernatant was pipetted and blown dry with nitrogen; 120 μL of reconstituted solution (acetonitrile:water=1:1) was added to reconstitute the sample; the samples were vortexed again for 30 seconds, and then sonicated at low temperature for 5 minutes (5℃, 40KHz); the samples were then centrifuged for 10 minutes (13000g, 4℃), and the supernatant was pipetted to the feeder vials with the cannulae for analysis. In addition, 20 μL of supernatant was pipetted separately for each sample and mixed as a quality control sample.

Combined analysis:

Analysis ID	AN006203	AN006204
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Dionex Ultimate 3000	Thermo Dionex Ultimate 3000
Column	Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)	Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive HF-X Orbitrap	Thermo Q Exactive HF-X Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	Peak area	Peak area

Chromatography:

Chromatography ID:	CH004706
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:	40℃
Flow Gradient:	0–0.5 min: 40% B (isocratic) 0.5–3.5 min: 40% B → 55% B (linear) 3.5–6.0 min: 55% B → 70% B (linear) 6.0–7.0 min: 70% B → 100% B (linear) 7.0–8.0 min: 100% B (isocratic) Mobile Phase B gradient changes throughout the process.
Flow Rate:	0.4 mL/min
Solvent A:	95% water/5% acetonitrile; 0.1% formic acid
Solvent B:	47.5% acetonitrile/47.5% isopropanol/5% water; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS005907
Analysis ID:	AN006203
Instrument Name:	Thermo Q Exactive HF-X Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The samples were ionized by electrospray ionization, and the data were collected in positive ion scanning mode; the scanning range was 70-1050 m/z; the sheath gas flow rate was set to 50 arb, and the auxiliary gas flow rate was 13 arb; the heating temperature was set to 425 °C, and the capillary tube temperature was 325 °C; the spray voltage (positive mode) was 3500 V; the S-Lens RF Level was set to 50; the normalized The collision energy was set to 20%, 40%, and 60%, respectively; and the full-scan resolution was set to 60,000.
Ion Mode:	POSITIVE

MS ID:	MS005908
Analysis ID:	AN006204
Instrument Name:	Thermo Q Exactive HF-X Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The samples were ionized by electrospray ionization, and the data were collected in negative ion scanning mode; the scanning range was 70-1050 m/z; the sheath gas flow rate was set at 50 arb, and the auxiliary gas flow rate was 13 arb; the heating temperature was set at 425 °C, and the capillary tube temperature was 325 °C; the spray voltage (in negative mode) was -3500 V; and the S-Lens RF Level was set at 50; The normalized collision energies were 20%, 40%, and 60%, respectively; and the full-scan resolution was set to 60,000.
Ion Mode:	NEGATIVE