Summary of Study ST002311

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 PR001482. The data can be accessed directly via it's Project DOI: 10.21228/M8598K 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 IDST002311
Study TitleCecal Microbiota in Phage-treated Salmonella-infected broilers
Study SummaryAnalysis 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 NameLorenzo-Rebenaque
First NameLaura
AddressEd. Seminario. S/n, Moncada, Valencia, 46113, Spain
Emaillaura.lorenzorebenaque@uchceu.es
Phone615056012
Submit Date2022-09-13
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/M8598K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001482
Project DOI:doi: 10.21228/M8598K
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

Subject:

Subject ID:SU002397
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
SA22701733Phage Week 4
SA22701835Phage Week 4
SA22701936Phage Week 4
SA22702034Phage Week 4
SA22702143Phage Week 5
SA22702244Phage Week 5
SA22702342Phage Week 5
SA22702441Phage Week 5
SA22702550Phage Week 6
SA22702652Phage Week 6
SA22702751Phage Week 6
SA22702849Phage Week 6
SA22702930Salmonella Week 4
SA22703031Salmonella Week 4
SA22703132Salmonella Week 4
SA22703229Salmonella Week 4
SA22703339Salmonella Week 5
SA22703440Salmonella Week 5
SA22703538Salmonella Week 5
SA22703637Salmonella Week 5
SA22703745Salmonella Week 6
SA22703846Salmonella Week 6
SA22703947Salmonella Week 6
SA22704048Salmonella Week 6
Showing results 1 to 24 of 24

Collection:

Collection ID:CO002390
Collection Summary:Cecal sample were collected and immediately snap frozen for metabolomics analysis at the end of experiment
Sample Type:Cecum

Treatment:

Treatment ID:TR002409
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

Sample Preparation:

Sampleprep ID:SP002403
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 AN003775 AN003776
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:CH002792
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Phenomenex Luna (100 x 2.1mm,2.5um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003518
Analysis ID:AN003775
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:MS003519
Analysis ID:AN003776
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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