#METABOLOMICS WORKBENCH laura_lorenzorebenaque_20220912_003732 DATATRACK_ID:3454 STUDY_ID:ST002310 ANALYSIS_ID:AN003773 PROJECT_ID:PR001481 VERSION 1 CREATED_ON September 12, 2022, 2:09 am #PROJECT PR:PROJECT_TITLE Cecal Microbiome in Phage treated broilers PR:PROJECT_SUMMARY The objective of this study was to assess the impact of Salmonella bacteriophage PR:PROJECT_SUMMARY treatment on microbiome in the ceca and serum of the broilers during the rearing PR:PROJECT_SUMMARY period 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 Cecal Microbiome in Phage treated broilers ST:STUDY_SUMMARY The objective of this study was to assess the impact of Salmonella bacteriophage ST:STUDY_SUMMARY treatment on microbiome in the ceca and serum of the broilers during the rearing ST:STUDY_SUMMARY period ST:INSTITUTE La Agenzia nazionale per le nuove tecnologie, l'energia e lo sviluppo económico ST:INSTITUTE sostenibile ST:LAST_NAME Lorenzo Rebenaque ST:FIRST_NAME Laura ST:ADDRESS Ed. Seminario. S/n ST:EMAIL laura.lorenzorebenaque@uchceu.com 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 - J1 Group:Control | Moment:Week 4 RAW_FILE_NAME=J1.raw SUBJECT_SAMPLE_FACTORS - J2 Group:Control | Moment:Week 4 RAW_FILE_NAME=J2.raw SUBJECT_SAMPLE_FACTORS - J3 Group:Control | Moment:Week 4 RAW_FILE_NAME=J3.raw SUBJECT_SAMPLE_FACTORS - J4 Group:Control | Moment:Week 4 RAW_FILE_NAME=J4.raw SUBJECT_SAMPLE_FACTORS - K1 Group:Water | Moment:Week 4 RAW_FILE_NAME=K1.raw SUBJECT_SAMPLE_FACTORS - K2 Group:Water | Moment:Week 4 RAW_FILE_NAME=K2.raw SUBJECT_SAMPLE_FACTORS - K3 Group:Water | Moment:Week 4 RAW_FILE_NAME=K3.raw SUBJECT_SAMPLE_FACTORS - K4 Group:Water | Moment:Week 4 RAW_FILE_NAME=K4.raw SUBJECT_SAMPLE_FACTORS - L1 Group:Feed | Moment:Week 4 RAW_FILE_NAME=L1.raw SUBJECT_SAMPLE_FACTORS - L2 Group:Feed | Moment:Week 4 RAW_FILE_NAME=L2.raw SUBJECT_SAMPLE_FACTORS - L3 Group:Feed | Moment:Week 4 RAW_FILE_NAME=L3.raw SUBJECT_SAMPLE_FACTORS - L4 Group:Feed | Moment:Week 4 RAW_FILE_NAME=L4.raw SUBJECT_SAMPLE_FACTORS - M2 Group:Control | Moment:Week 5 RAW_FILE_NAME=M2.raw SUBJECT_SAMPLE_FACTORS - M3 Group:Control | Moment:Week 5 RAW_FILE_NAME=M3.raw SUBJECT_SAMPLE_FACTORS - M4 Group:Control | Moment:Week 5 RAW_FILE_NAME=M4.raw SUBJECT_SAMPLE_FACTORS - M5 Group:Control | Moment:Week 5 RAW_FILE_NAME=M5.raw SUBJECT_SAMPLE_FACTORS - N1 Group:Water | Moment:Week 5 RAW_FILE_NAME=N1.raw SUBJECT_SAMPLE_FACTORS - N2 Group:Water | Moment:Week 5 RAW_FILE_NAME=N2.raw SUBJECT_SAMPLE_FACTORS - N3 Group:Water | Moment:Week 5 RAW_FILE_NAME=N3.raw SUBJECT_SAMPLE_FACTORS - O1 Group:Feed | Moment:Week 5 RAW_FILE_NAME=O1.raw SUBJECT_SAMPLE_FACTORS - O2 Group:Feed | Moment:Week 5 RAW_FILE_NAME=O2.raw SUBJECT_SAMPLE_FACTORS - O3 Group:Feed | Moment:Week 5 RAW_FILE_NAME=O3.raw SUBJECT_SAMPLE_FACTORS - O4 Group:Feed | Moment:Week 5 RAW_FILE_NAME=O4.raw SUBJECT_SAMPLE_FACTORS - P1 Group:Control | Moment:Week 6 RAW_FILE_NAME=P1.raw SUBJECT_SAMPLE_FACTORS - P2 Group:Control | Moment:Week 6 RAW_FILE_NAME=P2.raw SUBJECT_SAMPLE_FACTORS - P3 Group:Control | Moment:Week 6 RAW_FILE_NAME=P3.raw SUBJECT_SAMPLE_FACTORS - P4 Group:Control | Moment:Week 6 RAW_FILE_NAME=P4.raw SUBJECT_SAMPLE_FACTORS - Q1 Group:Water | Moment:Week 6 RAW_FILE_NAME=Q1.raw SUBJECT_SAMPLE_FACTORS - Q2 Group:Water | Moment:Week 6 RAW_FILE_NAME=Q2.raw SUBJECT_SAMPLE_FACTORS - Q3 Group:Water | Moment:Week 6 RAW_FILE_NAME=Q3.raw SUBJECT_SAMPLE_FACTORS - Q4 Group:Water | Moment:Week 6 RAW_FILE_NAME=Q4.raw SUBJECT_SAMPLE_FACTORS - Q5 Group:Water | Moment:Week 6 RAW_FILE_NAME=Q5.raw SUBJECT_SAMPLE_FACTORS - R1 Group:Feed | Moment:Week 6 RAW_FILE_NAME=R1.raw SUBJECT_SAMPLE_FACTORS - R2 Group:Feed | Moment:Week 6 RAW_FILE_NAME=R2.raw SUBJECT_SAMPLE_FACTORS - R3 Group:Feed | Moment:Week 6 RAW_FILE_NAME=R3.raw SUBJECT_SAMPLE_FACTORS - R4 Group:Feed | Moment:Week 6 RAW_FILE_NAME=R4.raw SUBJECT_SAMPLE_FACTORS - R5 Group:Feed | Moment:Week 6 RAW_FILE_NAME=R5.raw #COLLECTION CO:COLLECTION_SUMMARY Cecal sample were collected and immediately snap frozen for metabolomics CO:COLLECTION_SUMMARY analysis at the end of experiment CO:SAMPLE_TYPE Cecum #TREATMENT TR:TREATMENT_SUMMARY The water group received a 108 PFU/mL phage concentration via drinking water, TR:TREATMENT_SUMMARY the feed group received a 108 PFU/g phage concentration via feed (encapsulated), TR:TREATMENT_SUMMARY and the control group did not receive a phage. Caecal samples were obtained 1 TR:TREATMENT_SUMMARY day after delivery of the phage. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Cecal contents 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 software MS:MS_COMMENTS (Thermofisher Scientific) was used to identify the peaks, peak filtration, and MS:MS_COMMENTS peak alignment, and performed chromatogram alignment, peak picking, and public MS:MS_COMMENTS database (e.g., ChemSpider, KEGG, Metabolika) querying based on accurate masses MS:MS_COMMENTS (m/z). MS:MS_RESULTS_FILE ST002310_AN003773_Results.txt UNITS:m/z ratio Has m/z:Yes Has RT:Yes RT units:Minutes #END