{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002311","ANALYSIS_ID":"AN003776","VERSION":"1","CREATED_ON":"September 13, 2022, 6:58 am"},

"PROJECT":{"PROJECT_TITLE":"Cecal Microbiota in Phage-treated Salmonella-infected broilers","PROJECT_SUMMARY":"Analysis of the gastrointestinal metabolome of Salmonella-infected broilers has been carried out after the application of encapsulated bacteriophages in the feed, during the production cycle under farm conditions","INSTITUTE":"Universidad Cardenal Herrera CEU","LAST_NAME":"Lorenzo-Rebenaque","FIRST_NAME":"Laura","ADDRESS":"Ed. Seminario. S/n, Moncada, Valencia, 46113, Spain","EMAIL":"laura.lorenzorebenaque@uchceu.es","PHONE":"615056012"},

"STUDY":{"STUDY_TITLE":"Cecal Microbiota in Phage-treated Salmonella-infected broilers","STUDY_SUMMARY":"Analysis of the gastrointestinal microbiota of Salmonella-infected broilers has been carried out after the application of encapsulated bacteriophages in the feed, during the production cycle under farm conditions","INSTITUTE":"Universidad Cardenal Herrera CEU","LAST_NAME":"Lorenzo-Rebenaque","FIRST_NAME":"Laura","ADDRESS":"Ed. Seminario. S/n, Moncada, Valencia, 46113, Spain","EMAIL":"laura.lorenzorebenaque@uchceu.es","PHONE":"615056012"},

"SUBJECT":{"SUBJECT_TYPE":"Bird","SUBJECT_SPECIES":"Gallus gallus","TAXONOMY_ID":"9031"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"29",
"Factors":{"Group":"Salmonella","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"H1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"30",
"Factors":{"Group":"Salmonella","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"H2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"31",
"Factors":{"Group":"Salmonella","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"H3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"32",
"Factors":{"Group":"Salmonella","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"H4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"33",
"Factors":{"Group":"Phage","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"I1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"34",
"Factors":{"Group":"Phage","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"I.raw"}
},
{
"Subject ID":"-",
"Sample ID":"35",
"Factors":{"Group":"Phage","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"I3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"36",
"Factors":{"Group":"Phage","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"I4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"37",
"Factors":{"Group":"Salmonella","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"J1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"38",
"Factors":{"Group":"Salmonella","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"J2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"39",
"Factors":{"Group":"Salmonella","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"J3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"40",
"Factors":{"Group":"Salmonella","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"J4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"41",
"Factors":{"Group":"Phage","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"K1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"42",
"Factors":{"Group":"Phage","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"K2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"43",
"Factors":{"Group":"Phage","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"K3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"44",
"Factors":{"Group":"Phage","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"K4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"45",
"Factors":{"Group":"Salmonella","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"L1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"46",
"Factors":{"Group":"Salmonella","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"L2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"47",
"Factors":{"Group":"Salmonella","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"L3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"48",
"Factors":{"Group":"Salmonella","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"L4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"49",
"Factors":{"Group":"Phage","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"M1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"50",
"Factors":{"Group":"Phage","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"M2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"51",
"Factors":{"Group":"Phage","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"M3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"52",
"Factors":{"Group":"Phage","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"M4.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cecal sample were collected and immediately snap frozen for metabolomics analysis at the end of experiment","SAMPLE_TYPE":"Cecum"},

"TREATMENT":{"TREATMENT_SUMMARY":"Half of the animals in each experimental group were challenged with Salmonella Enteritidis (105 CFU/bird) at 24 h after placing. During the first 21 days of the chicken rearing period, Φ-treated group received 0.1% microencapsulated Salmonella-phage (108 PFU/g) encapsulated in Eudragit®L100 (a pH-responsive formulation) with the starter diet feed, and the control group did not receive any phage"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Cecal contents were lyophilized and homogenated. Then, 10 mg of the sample were mixed with 0.75mL of cold 75% (v/v) methanol, 0.1% (v/v) formic acid, spiked with 10μg/ml formononetin as internal standard. Then, the mix were shaked for 40’ at 20Hz using a Mixer Mill 300 (Qiagen) and centrifuged at 20,000 xg for 15 min at 4°C. The suspension (600μL) was transferred to a new 2-mL conical tube."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Phenomenex Luna (100x2.1, 2.5um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"For the untargeted metabolomic analysis, Compound Discoverer software (Thermofisher Scientific) was used to identify the peaks, peak filtration, and peak alignment, and performed chromatogram alignment, peak picking, and public database (e.g., ChemSpider, KEGG, Metabolika) querying based on accurate masses (m/z).","MS_RESULTS_FILE":"ST002311_AN003776_Results.txt UNITS:m/z ratio Has m/z:Yes Has RT:Yes RT units:Minutes"}

}