#METABOLOMICS WORKBENCH laura_lorenzorebenaque_20220913_074525 DATATRACK_ID:3457 STUDY_ID:ST002312 ANALYSIS_ID:AN003777 PROJECT_ID:PR001482 VERSION 1 CREATED_ON September 13, 2022, 7:59 am #PROJECT PR:PROJECT_TITLE Serum metabolome in Phage-treated Salmonella-infected broilers PR:PROJECT_SUMMARY Analysis of the serum metabolome of Salmonella-infected broilers has been PR:PROJECT_SUMMARY carried out after the application of encapsulated bacteriophages in the feed, PR:PROJECT_SUMMARY during the production cycle under farm conditions PR:INSTITUTE Universidad Cardenal Herrera CEU PR:LAST_NAME Lorenzo-Rebenaque PR:FIRST_NAME Laura PR:ADDRESS Ed. Seminario. S/n, Moncada, Valencia, 46113, Spain PR:EMAIL laura.lorenzorebenaque@uchceu.es PR:PHONE 615056012 #STUDY ST:STUDY_TITLE Serum metabolome in Phage-treated Salmonella-infected broilers ST:STUDY_SUMMARY Analysis of the serum metabolome of Salmonella-infected broilers has been ST:STUDY_SUMMARY carried out after the application of encapsulated bacteriophages in the feed, ST:STUDY_SUMMARY during the production cycle under farm conditions ST:INSTITUTE Universidad Cardenal Herrera CEU ST:LAST_NAME Lorenzo-Rebenaque ST:FIRST_NAME Laura ST:ADDRESS Ed. Seminario. S/n, Moncada, Valencia, 46113, Spain ST:EMAIL laura.lorenzorebenaque@uchceu.es ST:PHONE 615056012 #SUBJECT SU:SUBJECT_TYPE Bird SU:SUBJECT_SPECIES Gallus gallus SU:TAXONOMY_ID 9031 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - 29 Group:Salmonella | Moment:Week 4 RAW_FILE_NAME=H1.raw SUBJECT_SAMPLE_FACTORS - 30 Group:Salmonella | Moment:Week 4 RAW_FILE_NAME=H2.raw SUBJECT_SAMPLE_FACTORS - 31 Group:Salmonella | Moment:Week 4 RAW_FILE_NAME=H3.raw SUBJECT_SAMPLE_FACTORS - 32 Group:Salmonella | Moment:Week 4 RAW_FILE_NAME=H4.raw SUBJECT_SAMPLE_FACTORS - 33 Group:Phage | Moment:Week 4 RAW_FILE_NAME=I1.raw SUBJECT_SAMPLE_FACTORS - 34 Group:Phage | Moment:Week 4 RAW_FILE_NAME=I.raw SUBJECT_SAMPLE_FACTORS - 35 Group:Phage | Moment:Week 4 RAW_FILE_NAME=I3.raw SUBJECT_SAMPLE_FACTORS - 36 Group:Phage | Moment:Week 4 RAW_FILE_NAME=I4.raw SUBJECT_SAMPLE_FACTORS - 37 Group:Salmonella | Moment:Week 5 RAW_FILE_NAME=J1.raw SUBJECT_SAMPLE_FACTORS - 38 Group:Salmonella | Moment:Week 5 RAW_FILE_NAME=J2.raw SUBJECT_SAMPLE_FACTORS - 39 Group:Salmonella | Moment:Week 5 RAW_FILE_NAME=J3.raw SUBJECT_SAMPLE_FACTORS - 40 Group:Salmonella | Moment:Week 5 RAW_FILE_NAME=J4.raw SUBJECT_SAMPLE_FACTORS - 41 Group:Phage | Moment:Week 5 RAW_FILE_NAME=K1.raw SUBJECT_SAMPLE_FACTORS - 42 Group:Phage | Moment:Week 5 RAW_FILE_NAME=K2.raw SUBJECT_SAMPLE_FACTORS - 43 Group:Phage | Moment:Week 5 RAW_FILE_NAME=K3.raw SUBJECT_SAMPLE_FACTORS - 44 Group:Phage | Moment:Week 5 RAW_FILE_NAME=K4.raw SUBJECT_SAMPLE_FACTORS - 45 Group:Salmonella | Moment:Week 6 RAW_FILE_NAME=L1.raw SUBJECT_SAMPLE_FACTORS - 46 Group:Salmonella | Moment:Week 6 RAW_FILE_NAME=L2.raw SUBJECT_SAMPLE_FACTORS - 47 Group:Salmonella | Moment:Week 6 RAW_FILE_NAME=L3.raw SUBJECT_SAMPLE_FACTORS - 48 Group:Salmonella | Moment:Week 6 RAW_FILE_NAME=L4.raw SUBJECT_SAMPLE_FACTORS - 49 Group:Phage | Moment:Week 6 RAW_FILE_NAME=M1.raw SUBJECT_SAMPLE_FACTORS - 50 Group:Phage | Moment:Week 6 RAW_FILE_NAME=M2.raw SUBJECT_SAMPLE_FACTORS - 51 Group:Phage | Moment:Week 6 RAW_FILE_NAME=M3.raw SUBJECT_SAMPLE_FACTORS - 52 Group:Phage | Moment:Week 6 RAW_FILE_NAME=M4.raw #COLLECTION CO:COLLECTION_SUMMARY serum samples were collected and immediately snap frozen for metabolomic CO:COLLECTION_SUMMARY analysis at the end of the experiment CO:SAMPLE_TYPE Blood (serum) #TREATMENT TR:TREATMENT_SUMMARY Half of the animals (25/50) in each experimental group (control and Φ-treated TR:TREATMENT_SUMMARY groups) were challenged with Salmonella Enteritidis (105 CFU/bird) at 24 h after TR:TREATMENT_SUMMARY placing. During the first 21 days of the chicken rearing period, Φ-treated TR:TREATMENT_SUMMARY group received 0.1% encapsulated Salmonella-phage (108 PFU/g) with the starter TR:TREATMENT_SUMMARY diet feed, and the control group did not receive any phage. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY serum samples were lyophilized and homogenated. Then, 10 mg of the sample were SP:SAMPLEPREP_SUMMARY mixed with 0.75mL of cold 75% (v/v) methanol, 0.1% (v/v) formic acid, spiked SP:SAMPLEPREP_SUMMARY with 10μg/ml formononetin as internal standard. Then, the mix were shaked for SP:SAMPLEPREP_SUMMARY 40’ at 20Hz using a Mixer Mill 300 (Qiagen) and centrifuged at 20,000 xg for SP:SAMPLEPREP_SUMMARY 15 min at 4°C. The suspension (600μL) was transferred to a new 2-mL conical SP:SAMPLEPREP_SUMMARY tube. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Dionex Ultimate 3000 CH:COLUMN_NAME Phenomenex Luna (100x2.1, 2.5um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS For the untargeted metabolomic analysis, Compound Discoverer MS:MS_COMMENTS software(Thermofisher Scientific) was used to identify the peaks, peak MS:MS_COMMENTS filtration, and peak alignment, and performed chromatogram alignment, peak MS:MS_COMMENTS picking, and public database (e.g., ChemSpider, KEGG, Metabolika) querying based MS:MS_COMMENTS on accurate masses(m/z). MS:MS_RESULTS_FILE ST002312_AN003777_Results.txt UNITS:m/z ratio Has m/z:Yes Has RT:Yes RT units:Minutes #END