Summary of Study ST002310

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 PR001481. The data can be accessed directly via it's Project DOI: 10.21228/M8941F This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002310
Study TitleCecal Microbiome in Phage treated broilers
Study SummaryThe objective of this study was to assess the impact of Salmonella bacteriophage treatment on microbiome in the ceca and serum of the broilers during the rearing period
Institute
La Agenzia nazionale per le nuove tecnologie, l'energia e lo sviluppo económico sostenibile
Last NameLorenzo Rebenaque
First NameLaura
AddressEd. Seminario. S/n
Emaillaura.lorenzorebenaque@uchceu.com
Phone615056012
Submit Date2022-09-12
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-10-18
Release Version1
Laura Lorenzo Rebenaque Laura Lorenzo Rebenaque
https://dx.doi.org/10.21228/M8941F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001481
Project DOI:doi: 10.21228/M8941F
Project Title:Cecal Microbiome in Phage treated broilers
Project Summary:The objective of this study was to assess the impact of Salmonella bacteriophage treatment on microbiome in the ceca and serum of the broilers during the rearing period
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 ID:SU002396
Subject Type:Bird
Subject Species:Gallus gallus
Taxonomy ID:9031

Factors:

Subject type: Bird; Subject species: Gallus gallus (Factor headings shown in green)

mb_sample_id local_sample_id Group Moment
SA226980J1Control Week 4
SA226981J4Control Week 4
SA226982J3Control Week 4
SA226983J2Control Week 4
SA226984M3Control Week 5
SA226985M5Control Week 5
SA226986M2Control Week 5
SA226987M4Control Week 5
SA226988P2Control Week 6
SA226989P1Control Week 6
SA226990P4Control Week 6
SA226991P3Control Week 6
SA226992L2Feed Week 4
SA226993L1Feed Week 4
SA226994L3Feed Week 4
SA226995L4Feed Week 4
SA226996O2Feed Week 5
SA226997O4Feed Week 5
SA226998O3Feed Week 5
SA226999O1Feed Week 5
SA227000R3Feed Week 6
SA227001R2Feed Week 6
SA227002R4Feed Week 6
SA227003R1Feed Week 6
SA227004R5Feed Week 6
SA227005K2Water Week 4
SA227006K3Water Week 4
SA227007K4Water Week 4
SA227008K1Water Week 4
SA227009N3Water Week 5
SA227010N2Water Week 5
SA227011N1Water Week 5
SA227012Q1Water Week 6
SA227013Q2Water Week 6
SA227014Q4Water Week 6
SA227015Q3Water Week 6
SA227016Q5Water Week 6
Showing results 1 to 37 of 37

Collection:

Collection ID:CO002389
Collection Summary:Cecal sample were collected and immediately snap frozen for metabolomics analysis at the end of experiment
Sample Type:Cecum

Treatment:

Treatment ID:TR002408
Treatment Summary:The water group received a 108 PFU/mL phage concentration via drinking water, the feed group received a 108 PFU/g phage concentration via feed (encapsulated), and the control group did not receive a phage. Caecal samples were obtained 1 day after delivery of the phage.

Sample Preparation:

Sampleprep ID:SP002402
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.

Combined analysis:

Analysis ID AN003773 AN003774
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Phenomenex Luna (100 x 2.1mm,2.5um) Phenomenex Luna (100 x 2.1mm,2.5um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units m/z ratio m/z ratio

Chromatography:

Chromatography ID:CH002791
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Phenomenex Luna (100 x 2.1mm,2.5um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003516
Analysis ID:AN003773
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
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).
Ion Mode:POSITIVE
  
MS ID:MS003517
Analysis ID:AN003774
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
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).
Ion Mode:NEGATIVE
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