Summary of Study ST000083
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 PR000075. The data can be accessed directly via it's Project DOI: 10.21228/M86K5H This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000083 |
| Study Title | A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection |
| Study Type | Timecourse of Infection |
| Study Summary | The potential for commensal microorganisms indigenous to a host (the microbiome or microbiota) to alter infection outcome by influencing host-pathogen interplay is largely unknown. We used a multi-omics systems approach, incorporating proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular interplay between the murine host, the pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium), and commensal gut microorganisms during intestinal infection with S. Typhimurium. We find proteomic evidence that S. Typhimurium thrives within the infected 129/SvJ mouse gut without antibiotic pre-treatment, inducing inflammation and disrupting the intestinal microbiome (e.g., suppressing Bacteroidetes and Firmicutes while promoting growth of Salmonella and Enterococcus). Alteration of the host microbiome population structure was highly correlated with gut environmental changes, including the accumulation of metabolites normally consumed by commensal microbiota. Finally, the less characterized phase of S. Typhimuriums lifecycle was investigated, and both proteomic and glycomic evidence suggests S. Typhimurium may take advantage of increased fucose moieties to metabolize fucose while growing in the gut. The application of multiple omics measurements to Salmonella-induced intestinal inflammation provides insights into complex molecular strategies employed during pathogenesis between host, pathogen, and the microbiome. |
| Institute | Pacific Northwest National Laboratory |
| Department | Biological Separation and Mass Spectrometry |
| Last Name | Metz |
| First Name | Thomas |
| thomas.metz@pnnl.gov | |
| Submit Date | 2014-06-25 |
| Num Groups | 4 |
| Total Subjects | 30 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf, d |
| Uploaded File Size | 268 M |
| Analysis Type Detail | GC-MS |
| Release Date | 2014-07-30 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000075 |
| Project DOI: | doi: 10.21228/M86K5H |
| Project Title: | Systems Biology for EnteroPathogens |
| Project Type: | MS analysis |
| Project Summary: | sysbep.org |
| Institute: | Pacific Northwest National Laboratory |
| Department: | Biological Separation and Mass Spectrometry |
| Last Name: | Joshua |
| First Name: | Adkins |
| Email: | Joshua.Adkins@pnnl.gov |
Subject:
| Subject ID: | SU000102 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | 129/SvJ |
| Age Or Age Range: | 6- to 8-week-old |
| Gender: | Female |
| Animal Animal Supplier: | Jackson Laboratories,Bar Harbor, ME |
| Animal Housing: | specific pathogen-free conditions in filter-top cages |
| Animal Feed: | food provided ad libitum |
| Animal Water: | sterile water |
| Species Group: | Mammals |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Infection | Experimental Group | Harvest Day |
|---|---|---|---|---|
| SA004253 | SBEP_Microbiome.001 | Control | Control Group 1 | -1 |
| SA004254 | SBEP_Microbiome.002 | Control | Control Group 1 | 1 |
| SA004255 | SBEP_Microbiome.005 | Control | Control Group 1 | 10 |
| SA004256 | SBEP_Microbiome.006 | Control | Control Group 1 | 14 |
| SA004257 | SBEP_Microbiome.007 | Control | Control Group 1 | 21 |
| SA004258 | SBEP_Microbiome.008 | Control | Control Group 1 | 28 |
| SA004259 | SBEP_Microbiome.003 | Control | Control Group 1 | 3 |
| SA004260 | SBEP_Microbiome.004 | Control | Control Group 1 | 6 |
| SA004261 | SBEP_Microbiome.009 | Control | Control Group 2 | -1 |
| SA004262 | SBEP_Microbiome.010 | Control | Control Group 2 | 1 |
| SA004263 | SBEP_Microbiome.013 | Control | Control Group 2 | 10 |
| SA004264 | SBEP_Microbiome.014 | Control | Control Group 2 | 14 |
| SA004265 | SBEP_Microbiome.015 | Control | Control Group 2 | 21 |
| SA004266 | SBEP_Microbiome.016 | Control | Control Group 2 | 28 |
| SA004267 | SBEP_Microbiome.011 | Control | Control Group 2 | 3 |
| SA004268 | SBEP_Microbiome.012 | Control | Control Group 2 | 6 |
| SA004269 | SBEP_Microbiome.017 | Infected | Experimental 1 | -1 |
| SA004270 | SBEP_Microbiome.018 | Infected | Experimental 1 | 1 |
| SA004271 | SBEP_Microbiome.021 | Infected | Experimental 1 | 10 |
| SA004272 | SBEP_Microbiome.022 | Infected | Experimental 1 | 14 |
| SA004273 | SBEP_Microbiome.023 | Infected | Experimental 1 | 21 |
| SA004274 | SBEP_Microbiome.024 | Infected | Experimental 1 | 28 |
| SA004275 | SBEP_Microbiome.019 | Infected | Experimental 1 | 3 |
| SA004276 | SBEP_Microbiome.020 | Infected | Experimental 1 | 6 |
| SA004277 | SBEP_Microbiome.025 | Infected | Experimental 2 | -1 |
| SA004278 | SBEP_Microbiome.026 | Infected | Experimental 2 | 1 |
| SA004279 | SBEP_Microbiome.029 | Infected | Experimental 2 | 10 |
| SA004280 | SBEP_Microbiome.030 | Infected | Experimental 2 | 14 |
| SA004281 | SBEP_Microbiome.027 | Infected | Experimental 2 | 3 |
| SA004282 | SBEP_Microbiome.028 | Infected | Experimental 2 | 6 |
| Showing results 1 to 30 of 30 |
Collection:
| Collection ID: | CO000085 |
| Collection Summary: | Feces collected and frozen at seven time points post infection and one time point pre-infection |
| Collection Protocol Comments: | On the day prior to infection (day -1), and at seven time points post-infection, mice from one cage were transferred to a clean cage and fecal samples produced at that time were collected, pooled, and immediately frozen at -80° C. Samples were collected on days -1, 1, 3, 6, 10, 14, 21, and 28. |
| Sample Type: | Feces |
| Collection Method: | Fecal matter collection |
| Collection Location: | mice from one cage were transferred to a clean cage and fecal samples produced |
| Collection Frequency: | days -1, 1, 3, 6, 10, 14, 21, and 28 relative to day of infection (day 0) |
| Collection Time: | days -1, 1, 3, 6, 10, 14, 21, and 28 relative to day of infection (day 0) |
| Volumeoramount Collected: | four to 25 fecal pellets per pooled sample |
| Storage Conditions: | frozen at -80° C |
Treatment:
| Treatment ID: | TR000103 |
| Treatment Summary: | Experimental: Infected with 1.6 x 10^8 CFU S. Typhimurium | mouse | Control: treated with equal volume saline solution |
| Treatment Protocol Comments: | A final inoculum of 1.6 x 10^8 CFU S. Typhimurium/mouse was delivered by oral gavage to 10 mice (two cages of five mice each = Salmonella-infected). An equal number of mock-infected animals (two cages of five mice each = control) were administered an equal volume of sterile saline. Our infecting dose (10^8 CFU/mouse) aimed to establish a persistent infection that would ensure observation of S. Typhimurium proteins in downstream analyses. |
| Treatment: | Biotic / Abiotic |
| Treatment Compound: | S. Typhimurium / Saline |
| Treatment Dose: | 1.6 x 10^8 CFU S. Typhimurium/mouse / equal volume saline solution |
| Treatment Vehicle: | Saline |
| Animal Fasting: | 14 h before orogastric inoculation |
| Animal Endp Euthanasia: | Carbon Dioxide Asphixiation followed by Cervical Dislocaton |
| Animal Endp Tissue Coll List: | Feces |
| Animal Endp Tissue Proc Method: | Homogenization |
Sample Preparation:
| Sampleprep ID: | SP000098 |
| Sampleprep Summary: | Feces thawed, buffer added, vortexed, filtered and centrifuged after which supernatant subjected to further centrifugation and chemical derivatization |
| Sampleprep Protocol Comments: | After thawing, 150 mM ammonium bicarbonate buffer was added to the sample (between 1-2.5 ml based upon starting weight; volumes were recorded and used for downstream normalization), which was subsequently vortexed to disrupt fecal pellets. The resulting slurry was filtered through a 70 mm sieve to separate and remove large debris (mostly undigested food particles). Filtrate was centrifuged (900 x g for 10 min), and the protein-rich pellet thought to contain cellular material was retained as P1. The supernatant was centrifuged to further clarify the sample (15,000 x g for 10 min). The pellet was retained as P2 and the supernatant retained as SN2. All chemicals and reagents used in metabolomics analyses were purchased from Sigma-Aldrich (St. Louis, MO), except for ammonium bicarbonate (Merck, Darmstadt, Germany), mixture of fatty acid methyl esters (FAMEs) and deuterated myristic acid (Agilent Technologies, Santa Clara, CA). Deionized and purified water was used to prepare buffer and standard solutions (Nanopure Infinity ultrapure water system, Barnstead, Newton, WA). SN2 samples (see Fecal sample preparation) were transferred to 0.6 ml microcentrifuge tubes, and water soluble metabolites were extracted with four volumes of chilled (-20° C) chloroform: methanol mixture (2:1). After separating the two phases via centrifugation (12,000 x g, 5 min), the upper aqueous layers were transferred to glass vials and dried under a vacuum concentrator (SpeedVac; Thermo Scientific, Waltham, MA). All extracted metabolites were subjected to chemical derivatization to enhance their stability and volatility during GC-MS analysis. Methoxyamine in pyridine (30 mg/ml) was added to each dried sample, and incubated at 37° C with shaking for 90 min to protect carbonyl groups and reduce the number of tautomeric peaks. N-methyl-N- (trimethylsilyl) trifluoroacetamide (MSTFA) with 1% trimethylchlorosilane (TMCS) was then added, followed by incubation at 37° C with shaking for 30 min to transform hydroxyl and amine groups to trimethylsilyated (TMS) forms. The samples were then allowed to cool to room temperature and were analyzed using gas chromatography (GC)-MS. |
| Processing Method: | Homogenization, Filtration, Centrifugation |
| Extraction Method: | SN2 samples (see Fecal sample preparation) were transferred to 0.6 ml microcentrifuge tubes, and water soluble metabolites were extracted with four volumes of chilled (-20° C) chloroform: methanol mixture (2:1). After separating the two phases via centrifugation (12,000 x g, 5 min), the upper aqueous layers were transferred to glass vials and dried under a vacuum concentrator (SpeedVac; Thermo Scientific, Waltham, MA). |
| Extract Concentration Dilution: | chloroform: methanol mixture (2:1) |
| Extract Enrichment: | dried under a vacuum concentrator |
| Extract Storage: | dried under a vacuum concentrator |
| Sample Resuspension: | Methoxyamine in pyridine (30 mg/ml) |
| Sample Derivatization: | Methoxyamine in pyridine (30 mg/ml), N-methyl-N- (trimethylsilyl) trifluoroacetamide (MSTFA) with 1% trimethylchlorosilane (TMCS) |
Chromatography:
| Chromatography ID: | CH000095 |
| Chromatography Summary: | Agilent 7890A gas chromatograph with a HP-5MS gas chromatography column using Chemstation |
| Chromatography Comments: | Chromatography was carried out on an Agilent 7890A gas chromatograph using the manufacturer's software (Chemstation) and a HP-5MS gas chromatography column (Agilent Technologies, Santa Clara, CA; 30 m x 0.25 mm x 0.25 m film thickness). The sample injection mode was splitless, and 1 L of each sample was injected. The injection port temperature was held at 250 C throughout the analysis. The GC oven was held at 60 C for 1 min after injection, and the temperature was then increased to 325 C by 10 C/min, followed by a 5 min hold at 325 C. The helium gas flow rates for each Experiment were determined by the Agilent Retention Time Locking function based on analysis of deuterated myristic acid and were in the range of 0.450.5 mL/min. |
| Instrument Name: | Agilent 7890A |
| Column Name: | Agilent HP5-MS (30m × 0.25mm, 0.25 um) |
| Flow Rate: | 0.450.5 mL/min |
| Injection Temperature: | 250 C |
| Sample Injection: | 1 L, splitless |
| Analytical Time: | 37.5 min |
| Oven Temperature: | 60 C for 1 min, then increased to 325 C by 10 C/min, followed by a 5 min hold at 325 C |
| Sample Syringe Size: | 10 L |
| Chromatography Type: | GC |
Analysis:
| Analysis ID: | AN000135 |
| Laboratory Name: | Biological Separations & Mass Spectrometry group, Pacific Northwest National Laboratory (www.omics.pnl.gov) |
| Analysis Type: | MS |
| Analysis Comments: | GC-MS raw data files from each Experiment were processed using the Metabolite Detector software, version 2.0.6 beta. Briefly, Agilent.D files were converted to netCDF format using Agilent Chemstation, followed by conversion to binary files using Metabolite Detector. Retention indices of detected metabolites were calculated based on the analysis of the FAMEs mixture, followed by their chromatographic alignment across all analyses after deconvolution. Metabolites were initially identified by matching experimental spectra to an augmented version of FiehnLib (i.e., the Agilent Fiehn Metabolomics Retention Time Locked (RTL) Library, containing spectra and validated retention indices for over 700 metabolites), using a Metabolite Detector match probability threshold of 0.6 (combined retention index and spectral probability). All metabolite identifications were manually validated to reduce deconvolution errors during automated data-processing and to eliminate false identifications. The NIST 08 GC-MS library was also used to cross validate the spectral matching scores obtained using the Agilent library and to provide identifications of unmatched metabolites. The three most abundant fragment ions in the spectra of each identified metabolite were automatically determined by Metabolite Detector, and their summed abundances were integrated across the GC elution profile; fragment ions due to trimethylsilylation (i.e. m/z 73 and 147) were excluded from the determination of metabolite abundance. Features resulting from GC column bleeding were removed from the data matrices prior to further data processing and analysis. |
| Acquisition Date: | 6/24/11 to 6/25/11 |
| Instrument Name: | Agilent 7890A GC / 5975C MS |
| Software Version: | Metabolite Detector vs. 2.0.6 beta |
| Data Format: | Raw .D.Zip; Processed .CDF |
| Chromatography ID: | CH000095 |
| Num Factors: | 30 |
| Num Metabolites: | 14 |
| Units: | Peak area |
