{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000083","ANALYSIS_ID":"AN000135","VERSION":"1","CREATED_ON":"2016-09-17"},
"PROJECT":{"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","ADDRESS":"-","EMAIL":"Joshua.Adkins@pnnl.gov","PHONE":"-"},
"STUDY":{"STUDY_TITLE":"A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Infection","STUDY_TYPE":"Timecourse of Infection","STUDY_SUMMARY":"The potential for commensal microorganisms indigenous to a host (the or microbiota) to alter infection outcome by influencing host-pathogen is largely unknown. We used a multi-omics systems approach, proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular between the murine host, the pathogen Salmonella enterica serovar Typhimurium Typhimurium), and commensal gut microorganisms during intestinal infection with Typhimurium. We find proteomic evidence that S. Typhimurium thrives within the 129/SvJ mouse gut without antibiotic pre-treatment, inducing inflammation and the intestinal microbiome (e.g., suppressing Bacteroidetes and Firmicutes while growth of Salmonella and Enterococcus). Alteration of the host microbiome structure was highly correlated with gut environmental changes, including the of metabolites normally consumed by commensal microbiota. Finally, the less phase of S. Typhimuriums lifecycle was investigated, and both proteomic and evidence suggests S. Typhimurium may take advantage of increased fucose to metabolize fucose while growing in the gut. The application of multiple measurements to Salmonella-induced intestinal inflammation provides insights complex molecular strategies employed during pathogenesis between host, and the microbiome.","INSTITUTE":"Pacific Northwest National Laboratory","DEPARTMENT":"Biological Separation and Mass Spectrometry","LAST_NAME":"Metz","FIRST_NAME":"Thomas","ADDRESS":"-","EMAIL":"thomas.metz@pnnl.gov","PHONE":"-","NUM_GROUPS":"4","TOTAL_SUBJECTS":"30"},
"SUBJECT":{"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":"Mammal"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.002",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 1","Harvest Day":"1"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.001",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 1","Harvest Day":"-1"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.005",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 1","Harvest Day":"10"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.006",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 1","Harvest Day":"14"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.007",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 1","Harvest Day":"21"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.008",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 1","Harvest Day":"28"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.003",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 1","Harvest Day":"3"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.004",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 1","Harvest Day":"6"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.010",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 2","Harvest Day":"1"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.009",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 2","Harvest Day":"-1"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.013",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 2","Harvest Day":"10"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.014",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 2","Harvest Day":"14"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.015",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 2","Harvest Day":"21"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.016",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 2","Harvest Day":"28"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.011",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 2","Harvest Day":"3"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.012",
"Factors":{"Infection":"Control","Experimental Group":"Control Group 2","Harvest Day":"6"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.018",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 1","Harvest Day":"1"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.017",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 1","Harvest Day":"-1"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.021",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 1","Harvest Day":"10"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.022",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 1","Harvest Day":"14"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.023",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 1","Harvest Day":"21"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.024",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 1","Harvest Day":"28"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.019",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 1","Harvest Day":"3"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.020",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 1","Harvest Day":"6"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.026",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 2","Harvest Day":"1"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.025",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 2","Harvest Day":"-1"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.029",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 2","Harvest Day":"10"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.030",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 2","Harvest Day":"14"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.027",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 2","Harvest Day":"3"}
},
{
"Subject ID":"-",
"Sample ID":"SBEP_Microbiome.028",
"Factors":{"Infection":"Infected","Experimental Group":"Experimental 2","Harvest Day":"6"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Feces collected and frozen at seven time points post infection and one time pre-infection","COLLECTION_PROTOCOL_COMMENTS":"On the day prior to infection (day -1), and at seven time points mice from one cage were transferred to a clean cage and fecal samples produced that time were collected, pooled, and immediately frozen at -80° C. Samples 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_SUMMARY":"Experimental: Infected with 1.6 x 10^8 CFU S. Typhimurium | mouse | Control: 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 to 10 mice (two cages of five mice each = Salmonella-infected). An equal number mock-infected animals (two cages of five mice each = control) were administered equal volume of sterile saline. Our infecting dose (10^8 CFU/mouse) aimed to a persistent infection that would ensure observation of S. Typhimurium proteins 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"},
"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Feces thawed, buffer added, vortexed, filtered and centrifuged after which subjected to further centrifugation and chemical derivatization","SAMPLEPREP_PROTOCOL_COMMENTS":"After thawing, 150 mM ammonium bicarbonate buffer was added to the sample 1-2.5 ml based upon starting weight; volumes were recorded and used for normalization), which was subsequently vortexed to disrupt fecal pellets. The slurry was filtered through a 70 mm sieve to separate and remove large debris undigested food particles). Filtrate was centrifuged (900 x g for 10 min), and protein-rich pellet thought to contain cellular material was retained as P1. supernatant was centrifuged to further clarify the sample (15,000 x g for 10 The pellet was retained as P2 and the supernatant retained as SN2. All and reagents used in metabolomics analyses were purchased from Sigma-Aldrich Louis, MO), except for ammonium bicarbonate (Merck, Darmstadt, Germany), of fatty acid methyl esters (FAMEs) and deuterated myristic acid (Agilent Santa Clara, CA). Deionized and purified water was used to prepare buffer and solutions (Nanopure Infinity ultrapure water system, Barnstead, Newton, WA). samples (see Fecal sample preparation) were transferred to 0.6 ml tubes, and water soluble metabolites were extracted with four volumes of (-20° C) chloroform: methanol mixture (2:1). After separating the two phases centrifugation (12,000 x g, 5 min), the upper aqueous layers were transferred glass vials and dried under a vacuum concentrator (SpeedVac; Thermo Scientific, MA). All extracted metabolites were subjected to chemical derivatization to their stability and volatility during GC-MS analysis. Methoxyamine in pyridine mg/ml) was added to each dried sample, and incubated at 37° C with shaking for min to protect carbonyl groups and reduce the number of tautomeric peaks. (trimethylsilyl) trifluoroacetamide (MSTFA) with 1% trimethylchlorosilane was then added, followed by incubation at 37° C with shaking for 30 min to hydroxyl and amine groups to trimethylsilyated (TMS) forms. The samples were allowed to cool to room temperature and were analyzed using gas chromatography","PROCESSING_METHOD":"Homogenization, Filtration, Centrifugation","EXTRACTION_METHOD":"SN2 samples (see Fecal sample preparation) were transferred to 0.6 ml tubes, and water soluble metabolites were extracted with four volumes of (-20° C) chloroform: methanol mixture (2:1). After separating the two phases centrifugation (12,000 x g, 5 min), the upper aqueous layers were transferred glass vials and dried under a vacuum concentrator (SpeedVac; Thermo Scientific, MA).","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) (MSTFA) with 1% trimethylchlorosilane (TMCS)"},
"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Agilent 7890A gas chromatograph with a HP-5MS gas chromatography column using","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 7890A","COLUMN_NAME":"Agilent HP5-MS (30m × 0.25mm, 0.25 um)","CHROMATOGRAPHY_COMMENTS":"Chromatography was carried out on an Agilent 7890A gas chromatograph using the software (Chemstation) and a HP-5MS gas chromatography column (Agilent Santa Clara, CA; 30 m x 0.25 mm x 0.25 m film thickness). The sample injection was splitless, and 1 L of each sample was injected. The injection port was held at 250 C throughout the analysis. The GC oven was held at 60 C for 1 after injection, and the temperature was then increased to 325 C by 10 C/min, by a 5 min hold at 325 C. The helium gas flow rates for each Experiment were by the Agilent Retention Time Locking function based on analysis of deuterated acid and were in the range of 0.450.5 mL/min.","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 325 C","SAMPLE_SYRINGE_SIZE":"10 L"},
"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Biological Separations & Mass Spectrometry group, Pacific Northwest National (www.omics.pnl.gov)","ACQUISITION_DATE":"6/24/11 to 6/25/11","SOFTWARE_VERSION":"Metabolite Detector vs. 2.0.6 beta","DATA_FORMAT":"Raw .D.Zip; Processed .CDF"},
"MS":{"INSTRUMENT_NAME":"Agilent 5975C","INSTRUMENT_TYPE":"Single quadrupole","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"GC-MS raw data files from each Experiment were processed using the Metabolite software, version 2.0.6 beta. Briefly, Agilent.D files were converted to netCDF using Agilent Chemstation, followed by conversion to binary files using Detector. Retention indices of detected metabolites were calculated based on analysis of the FAMEs mixture, followed by their chromatographic alignment all analyses after deconvolution. Metabolites were initially identified by experimental spectra to an augmented version of FiehnLib (i.e., the Agilent Metabolomics Retention Time Locked (RTL) Library, containing spectra and retention indices for over 700 metabolites), using a Metabolite Detector match threshold of 0.6 (combined retention index and spectral probability). All identifications were manually validated to reduce deconvolution errors during data-processing and to eliminate false identifications. The NIST 08 GC-MS was also used to cross validate the spectral matching scores obtained using the library and to provide identifications of unmatched metabolites. The three most fragment ions in the spectra of each identified metabolite were automatically by Metabolite Detector, and their summed abundances were integrated across the elution profile; fragment ions due to trimethylsilylation (i.e. m/z 73 and 147) excluded from the determination of metabolite abundance. Features resulting GC column bleeding were removed from the data matrices prior to further data and analysis.","SCAN_RANGE_MOVERZ":"50-550 m/z"},
"MS_METABOLITE_DATA":{
"Units":"Peak area",
"Data":[{"Metabolite":"2-ketohexanoic 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