Summary of Study ST004204
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 PR002650. The data can be accessed directly via it's Project DOI: 10.21228/M83V73 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004204 |
| Study Title | The growth and virulence of S. aureus is inhibited by C. striatum by inhibiting its arginine biosynthesis pathway |
| Study Summary | Background: Patients with chronic rhinosinusitis (CRS) exhibit signs of nasal microbiota dysbiosis, specifically manifested by an increase in the relative abundance of Staphylococcus species and a decrease in the relative abundance of Corynebacterium species. This alteration may be closely associated with the pathogenesis of CRS. Understanding how commensal bacteria interact with pathogenic bacteria can help us reconstruct the homeostasis of nasal microbiota and promote nasal health. Method and Results: We conducted an in vitro co-culture model of Staphylococcus aureus and Corynebacterium striatum. Through metabolomic analysis, we discovered that the metabolic pathways of S. aureus were downregulated considerably during co-culture, especially for the arginine biosynthesis pathway. We later conducted validation experiments involving arginine supplementation and air-liquid interface culture of human nasal epithelial cells. Conclusion: The growth and virulence of S. aureus is inhibited by C. striatum by inhibiting its arginine biosynthesis pathway. |
| Institute | Sun Yat-sen University |
| Department | Otorhinolaryngology, First Affiliated Hospital of Sun Yat-sen University |
| Laboratory | Otorhinolaryngology Institute of Sun Yat-sen University |
| Last Name | Xinyu |
| First Name | Zhang |
| Address | No.74 Zhongshan Er Road |
| zhangxy2236@mail.sysu.edu.cn | |
| Phone | +86 15920583447 |
| Submit Date | 2025-09-04 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-10-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002650 |
| Project DOI: | doi: 10.21228/M83V73 |
| Project Title: | Metabolic profiles of Staphylococcus aureus and Corynebacterium striatum under monoculture and co-culture conditions |
| Project Summary: | This study conducted an in vitro co-culture model of Staphylococcus aureus and Corynebacterium striatum. Then untargeted metabolome was used to discover underlying metabolic changes during the co-culture condition. |
| Institute: | Sun Yat-sen University |
| Department: | Otorhinolaryngology, First Affiliated Hospital of Sun Yat-sen University |
| Laboratory: | Otorhinolaryngology Institute of Sun Yat-sen University |
| Last Name: | Xinyu |
| First Name: | Zhang |
| Address: | No.74 Zhongshan Er Road |
| Email: | zhangxy2236@mail.sysu.edu.cn |
| Phone: | +86 15920583447 |
Subject:
| Subject ID: | SU004356 |
| Subject Type: | Bacteria |
| Subject Species: | Staphylococcus aureus |
| Taxonomy ID: | 1280 |
Factors:
Subject type: Bacteria; Subject species: Staphylococcus aureus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment | Sample source |
|---|---|---|---|
| SA484451 | Co_2 | co-culture | bacteria cell |
| SA484452 | Co_4 | co-culture | bacteria cell |
| SA484453 | Co_3 | co-culture | bacteria cell |
| SA484454 | Co_1 | co-culture | bacteria cell |
| SA484455 | SA_2 | monoculture | bacteria cell |
| SA484456 | CS_4 | monoculture | bacteria cell |
| SA484457 | CS_3 | monoculture | bacteria cell |
| SA484458 | CS_2 | monoculture | bacteria cell |
| SA484459 | CS_1 | monoculture | bacteria cell |
| SA484460 | SA_4 | monoculture | bacteria cell |
| SA484461 | SA_3 | monoculture | bacteria cell |
| SA484462 | SA_1 | monoculture | bacteria cell |
| SA484447 | blank | NA | blank |
| SA484448 | QC_3 | NA | quality control |
| SA484449 | QC_2 | NA | quality control |
| SA484450 | QC_1 | NA | quality control |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO004349 |
| Collection Summary: | Bacterial cells collection: The culture broths of monoculture groups and co-cultrue groups were centrifuged at 5,000 rpm for 5 min at 4° C, and cells were washed three times with pre-cooled PBS. Then the cells were frozen in liquid nitrogen for 15 min, and then stored at -80° C for subsequent experiments. |
| Sample Type: | Bacterial cells |
| Storage Conditions: | -80℃ |
| Collection Tube Temp: | 4℃ |
Treatment:
| Treatment ID: | TR004365 |
| Treatment Summary: | Bacterial culture and co-culture model establishment: Single colonies of S. aureus and C. striatum were selected and grown in LB broth with shaking at 220 rpm at 37° C overnight to OD600nm=1.0 and then were diluted 1:100 into fresh LB for further culture for 9 h (C. striatum) and 3 h (S. aureus) respectively, according to the results of our preliminary experiments. Then the culture broths of S. aureus and C. striatum were mixed 1:1 as the co-culture group, and the fresh LB medium was mixed 1:1 as the monoculture group. All groups were cultured for 12 h before samples were collected. |
| Treatment Protocol Filename: | Treatment_protocol.pdf |
| Treatment Compound: | bacterial cells of Corynebacterium striatum |
| Treatment Route: | direct adding |
| Treatment Dose: | 1mL culture broth of Corynebacterium striatum into 1mL culture broth of Staphylococcus aureus |
| Treatment Dosevolume: | 1mL |
| Treatment Doseduration: | 12 hours |
Sample Preparation:
| Sampleprep ID: | SP004362 |
| Sampleprep Summary: | For one bacterial sample, add 300μl of 80% methanol aqueous solution, place it in liquid nitrogen for rapid freezing for 5 minutes; after thawing on ice, vortex for 30 seconds, and sonicate for 6 minutes. Centrifuge at 5000 rpm at 4°C for 1 minute, transfer the supernatant to a new centrifuge tube, and lyophilize into dry powder. Then, dissolve with the corresponding 10% methanol solution according to the volume of the sample taken and proceed with liquid chromatography–mass spectrometry (LC-MS) analysis. Take 1mL of supernatant and lyophilize it in a freeze dryer, then add 100 μL of an 80% methanol aqueous solution. Vortex the mixture, let it stand in an ice bath for 5 minutes, and then centrifuge at 15000 g at 4°C for 15 minutes. Take a certain volume of the supernatant and dilute it with mass spectrometry-grade water to a methanol concentration of 53%. Centrifuge again at 15000 g at 4°C for 15 minutes, collect the supernatant, and proceed with LC-MS analysis. Equal volume samples were taken from each experimental sample and mixed as Quality control (QC) samples. A 53% methanol solution was used as a blank sample. |
Combined analysis:
| Analysis ID | AN006990 | AN006991 |
|---|---|---|
| Chromatography ID | CH005307 | CH005307 |
| MS ID | MS006687 | MS006688 |
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Hypersil Gold aQ C18 (100x2.1mm, 1.9um) | Thermo Hypersil Gold aQ C18 (100x2.1mm, 1.9um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | relative abundance | relative abundance |
Chromatography:
| Chromatography ID: | CH005307 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Hypersil Gold aQ C18 (100x2.1mm, 1.9um) |
| Column Temperature: | 40℃ |
| Flow Gradient: | 0 to 1.5 min: remain 98% A(A: 0.1% formic acid) and 2% B (B: methyl alcohol) solution; 1.5 to 3 min: 98%A to 15%A, 2%B to 85%B ; 3 to 10 min: 15%A to 0%A, 85%B to 100% B; 10.1 to 12 min: remain 98%A and 2% B |
| Flow Rate: | 0.2mL/min |
| Solvent A: | 100% water; 0.1% Formic acid |
| Solvent B: | 100% Methyl alcohol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS006687 |
| Analysis ID: | AN006990 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS analysis was carried out on Thermo scientific Q Exactive™ HF. MS in both positive and negative ion models: The scanning range was set to m/z 100–1500. The ESI source parameters were configured as follows: Spray Voltage, 3.5 kV; Sheath Gas Flow Rate, 35 psi; Aux Gas Flow Rate, 10 L/min; Capillary Temperature, 320°C; S-Lens RF Level, 60; Aux Gas Heater Temperature, 350°C; Polarity, positive and negative. The MS/MS secondary scan was set to data-dependent acquisition mode. The raw data (.raw) files were imported into CD 3.3 search library software for processing. Preliminary screening of each metabolite was conducted based on parameters such as retention time and mass-to-charge ratio. Subsequently, the first quality control (QC) sample was utilized for peak area correction to improve the accuracy of metabolite identification. Peak extraction was then performed by setting a mass deviation threshold of 5 ppm, a signal intensity deviation threshold of 30%, minimum signal intensity criteria, and adduct ion parameters, while also quantifying the peak area. Following this, target ions were integrated. Molecular formula prediction was conducted based on molecular ion peaks and fragment ions, and the results were cross-referenced with the mzCloud (https://www.mzcloud.org/), mzVault, and Masslist databases. Background ions were removed using blank sample data. The original quantitative results were normalized using the following formula: sample original quantitative value / (total sum of sample metabolite quantitative values / total sum of QC1 sample metabolite quantitative values), yielding the relative peak area. Metabolites with a coefficient of variation (CV) of the relative peak area in QC samples exceeding 30% were excluded from further analysis. Finally, the identification and relative quantification results of metabolites were obtained. The data processing was conducted on the Linux operating system (CentOS version 6.6), utilizing R and Python software tools. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 320℃ |
| Dry Gas Flow: | 35psi |
| Spray Voltage: | 3.5kV |
| MS ID: | MS006688 |
| Analysis ID: | AN006991 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS analysis was carried out on Thermo scientific Q Exactive™ HF. MS in both positive and negative ion models: The scanning range was set to m/z 100–1500. The ESI source parameters were configured as follows: Spray Voltage, 3.5 kV; Sheath Gas Flow Rate, 35 psi; Aux Gas Flow Rate, 10 L/min; Capillary Temperature, 320°C; S-Lens RF Level, 60; Aux Gas Heater Temperature, 350°C; Polarity, positive and negative. The MS/MS secondary scan was set to data-dependent acquisition mode. The raw data (.raw) files were imported into CD 3.3 search library software for processing. Preliminary screening of each metabolite was conducted based on parameters such as retention time and mass-to-charge ratio. Subsequently, the first quality control (QC) sample was utilized for peak area correction to improve the accuracy of metabolite identification. Peak extraction was then performed by setting a mass deviation threshold of 5 ppm, a signal intensity deviation threshold of 30%, minimum signal intensity criteria, and adduct ion parameters, while also quantifying the peak area. Following this, target ions were integrated. Molecular formula prediction was conducted based on molecular ion peaks and fragment ions, and the results were cross-referenced with the mzCloud (https://www.mzcloud.org/), mzVault, and Masslist databases. Background ions were removed using blank sample data. The original quantitative results were normalized using the following formula: sample original quantitative value / (total sum of sample metabolite quantitative values / total sum of QC1 sample metabolite quantitative values), yielding the relative peak area. Metabolites with a coefficient of variation (CV) of the relative peak area in QC samples exceeding 30% were excluded from further analysis. Finally, the identification and relative quantification results of metabolites were obtained. The data processing was conducted on the Linux operating system (CentOS version 6.6), utilizing R and Python software tools. |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 320℃ |
| Dry Gas Flow: | 35psi |
| Spray Voltage: | 3.5kV |
