Summary of Study ST002985

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 PR001831. The data can be accessed directly via it's Project DOI: 10.21228/M81Q73 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 IDST002985
Study TitlePolar metabolomics of in vitro digestions of commercial cow's milk formula.
Study Type(un)targeted MS
Study SummaryThis study is part of a multi-part study, including a. longitudinal polar fecal metabolomics of mice undergoing sensitization to beta-lactoglobulin b. polar fecal metabolomics of a patient cohort c. fecal lipidomics of a patient cohort d. polar urinary metabolomics of a patient cohort e. polar metabolomics of in vitro digestions. This specific part is part e. polar metabolomics of in vitro digestions
Institute
Ghent University
DepartmentDepartment of Translational Physiology, Infectiology and Public Health
LaboratoryLaboratory for Integrative Metabolomics
Last NameDe Paepe
First NameEllen
AddressSalisburylaan 133, 9820 Merelbeke, Belgium
EmailEllen.DePaepe@UGent.be
Phone0032479081098
Submit Date2023-07-05
Num Groups4
Total Subjects81
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-11-29
Release Version1
Ellen De Paepe Ellen De Paepe
https://dx.doi.org/10.21228/M81Q73
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001831
Project DOI:doi: 10.21228/M81Q73
Project Title:Integrated gut metabolome and microbiome fingerprinting reveals that dysbiosis precedes allergic inflammation in IgE-mediated pediatric cow’s milk allergy
Project Type:(un)targeted MS
Project Summary:Background: IgE-mediated cow’s milk allergy (IgE-CMA) is one of the first allergies to arise in early childhood and may result from exposure to various milk allergens, of which β-lactoglobulin (BLG) and casein are the most important. Understanding the underlying mechanisms behind IgE-CMA is imperative for the discovery of novel biomarkers and the design of innovative treatment and prevention strategies. Methods: We report a longitudinal in vivo murine model, in which 2 mice strains (BALB/c and C57Bl/6) were sensitized to BLG using either cholera toxin or an oil emulsion (n=6 per group). After sensitization, mice were challenged orally, their clinical signs monitored, antibody (IgE and IgG1) and cytokine levels (IL-4 and IFN-γ) measured, and fecal samples subjected to metabolomics. The results of the murine models were further supported by fecal microbiome-metabolome data from our population of IgE-CMA (n=24) and healthy (n=23) children (Trial: NCT04249973), on which polar metabolomics, lipidomics and 16S rRNA metasequencing were performed. In vitro gastrointestinal digestions and multi-omics corroborated the microbial origin of proposed metabolic changes. Results: During sensitization, we observed multiple microbially derived metabolic alterations, most importantly bile acid, energy and tryptophan metabolites, that preceded allergic inflammation. The latter was reflected in a disturbed sphingolipid metabolism. We confirmed microbial dysbiosis, and its causal effect on metabolic alterations in our patient cohort, which was accompanied by metabolic signatures of low-grade inflammation. Conclusion: Our results indicate that gut dysbiosis precedes allergic inflammation and nurtures a chronic low-grade inflammation in children on elimination diets, opening important new opportunities for future prevention and treatment strategies.
Institute:Ghent University
Department:Translational Physiology, Infectiology and Public Health
Laboratory:Laboratory for Integrative Metabolomics
Last Name:De Paepe
First Name:Ellen
Address:Salisburylaan 133, Merelbeke, Oost-Vlaanderen, 9820, Belgium
Email:Ellen.DePaepe@UGent.be
Phone:0032479081098
Funding Source:Fonds Wetenschappelijk Onderzoek

Subject:

Subject ID:SU003098
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:< 5 years old
Gender:Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Group Milk powder Incubation
SA3238825AwHealthy Nutrilon T0
SA3238836AzHealthy Nutrilon T0
SA3238846AyHealthy Nutrilon T0
SA3238855AyHealthy Nutrilon T0
SA3238866AxHealthy Nutrilon T0
SA3238876AwHealthy Nutrilon T0
SA3238885AzHealthy Nutrilon T0
SA3238896Ax*Healthy Nutrilon T0
SA3238905AxHealthy Nutrilon T0
SA3238915Aw*Healthy Nutrilon T48
SA3238925Ay*Healthy Nutrilon T48
SA3238935Az*Healthy Nutrilon T48
SA3238946Ay*Healthy Nutrilon T48
SA3238955Ax*Healthy Nutrilon T48
SA3238966Aw*Healthy Nutrilon T48
SA3238976Az*Healthy Nutrilon T48
SA3238666CzHealthy Nutrilon Pepti T0
SA3238675CzHealthy Nutrilon Pepti T0
SA3238686CxHealthy Nutrilon Pepti T0
SA3238696CwHealthy Nutrilon Pepti T0
SA3238705CwHealthy Nutrilon Pepti T0
SA3238716CyHealthy Nutrilon Pepti T0
SA3238725CxHealthy Nutrilon Pepti T0
SA3238735CyHealthy Nutrilon Pepti T0
SA3238746Cw*Healthy Nutrilon Pepti T48
SA3238755Cx*Healthy Nutrilon Pepti T48
SA3238765Cy*Healthy Nutrilon Pepti T48
SA3238775Cw*Healthy Nutrilon Pepti T48
SA3238786Cx*Healthy Nutrilon Pepti T48
SA3238795Cz*Healthy Nutrilon Pepti T48
SA3238806Cz*Healthy Nutrilon Pepti T48
SA3238816Cy*Healthy Nutrilon Pepti T48
SA3239144AxIgE CMA Nutrilon T0
SA3239151AyIgE CMA Nutrilon T0
SA3239161AxIgE CMA Nutrilon T0
SA3239174AzIgE CMA Nutrilon T0
SA3239181AzIgE CMA Nutrilon T0
SA3239194Az*IgE CMA Nutrilon T0
SA3239204AwIgE CMA Nutrilon T0
SA3239211AwIgE CMA Nutrilon T0
SA3239224AyIgE CMA Nutrilon T0
SA3239234Ay*IgE CMA Nutrilon T48
SA3239241Aw*IgE CMA Nutrilon T48
SA3239251Ax*IgE CMA Nutrilon T48
SA3239264Ax*IgE CMA Nutrilon T48
SA3239271Ay*IgE CMA Nutrilon T48
SA3239281Az*IgE CMA Nutrilon T48
SA3239294Aw*IgE CMA Nutrilon T48
SA3238984CyIgE CMA Nutrilon Pepti T0
SA3238994CzIgE CMA Nutrilon Pepti T0
SA3239004CwIgE CMA Nutrilon Pepti T0
SA3239011CyIgE CMA Nutrilon Pepti T0
SA3239021CxIgE CMA Nutrilon Pepti T0
SA3239034CxIgE CMA Nutrilon Pepti T0
SA3239041CwIgE CMA Nutrilon Pepti T0
SA3239051CzIgE CMA Nutrilon Pepti T0
SA3239061Cx*IgE CMA Nutrilon Pepti T48
SA3239074Cz*IgE CMA Nutrilon Pepti T48
SA3239081Cz*IgE CMA Nutrilon Pepti T48
SA3239094Cx*IgE CMA Nutrilon Pepti T48
SA3239101Cy*IgE CMA Nutrilon Pepti T48
SA3239111Cw*IgE CMA Nutrilon Pepti T48
SA3239124Cy*IgE CMA Nutrilon Pepti T48
SA3239134Cw*IgE CMA Nutrilon Pepti T48
SA323930iQC24QC - -
SA323931iQC4QC - -
SA323932iQC6QC - -
SA323933iQC3QC - -
SA323934iQC2QC - -
SA323935iQC20QC - -
SA323936iQC9QC - -
SA323937iQC21QC - -
SA323938iQC22QC - -
SA323939iQC10QC - -
SA323940iQC1QC - -
SA323941iQC18QC - -
SA323942iQC14QC - -
SA323943iQC19QC - -
SA323944iQC8QC - -
SA323945iQC15QC - -
SA323946iQC16QC - -
SA323947iQC28QC - -
SA323948iQC25QC - -
SA323949iQC13QC - -
SA323950iQC27QC - -
SA323951iQC17QC - -
SA323952iQC7QC - -
SA323953iQC26QC - -
SA323954iQC23QC - -
SA323955iQC12QC - -
SA323956iQC11QC - -
SA323957iQC5QC - -
SA3239752AyResolution Nutrilon T0
SA3239762AzResolution Nutrilon T0
SA3239772AwResolution Nutrilon T0
SA3239782AxResolution Nutrilon T0
SA3239793AxResolution Nutrilon T0
SA3239803AzResolution Nutrilon T0
SA3239813AyResolution Nutrilon T0
SA3239823AwResolution Nutrilon T0
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Collection:

Collection ID:CO003091
Collection Summary:In vitro simulation of the gastrointestinal digestion consisted of enzymatic digestion (mouth, stomach, and duodenum) followed by colonic fermentation. ). Samples were taken immediately following the addition of SHIME (Simulator of the Human Intestinal Microbial Ecosystem) medium and fecal inoculum in Brain Heart Infusion (BHI) medium (duodenal samples, T0) and after colonic digestion (T48).
Sample Type:Digestive fluid
Collection Method:Spontaneous defecation
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003107
Treatment Summary:Two different CMP powder formulations were used, i.e., Nutrilon 1 and Nutrilon Pepti 1 (Nutricia, Amsterdam, The Netherlands). Feces were obtained from 6 children within the original cohort (<2 years old; 50% girls), without a history of antibiotic treatment 6 months prior to donation. Among the 6 participants, 2 children suffered from IgE-CMA, and 2 were designated as healthy controls. In vitro simulation of the gastrointestinal digestion consisted of enzymatic digestion (mouth, stomach, and duodenum) followed by colonic fermentation.
Treatment Compound:Nutrilon 1 and Nutrilon Pepti 1
Treatment Dose:920 mg
Treatment Doseduration:1

Sample Preparation:

Sampleprep ID:SP003104
Sampleprep Summary:Internal standard (75 uL of D-valine-d8 and L-alanine-d3 (100 ng/uL) was added to 1.5 mL of digestion fluid, which was then centrifuged (13,300 x g, 5 min). The supernatant was filtered through a polyvinylidene fluoride membrane (0.22 μ m, 33 mm ∅, Millex, USA). The filtrate was then diluted (1/5) with UP water and transferred to a LC-MS vial. An aliquot of 10 μL of sample was injected into the chromatographic system
Processing Storage Conditions:-80℃
Sample Spiking:Internal standard

Combined analysis:

Analysis ID AN004905
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000
Column Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units a.u.

Chromatography:

Chromatography ID:CH003700
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
Column Temperature:45
Flow Gradient:A gradient profile with following proportions (v/v) of solvent A was applied: 0-1.5 min at 98%, 1.5-7.0 min from 98% to 75%, 7.0-8.0 min from 75% to 40%, 8.0-12.0 min from 40% to 5%, 12.0-14.0 min at 5%, 14.0-14.1 min from 5 to 98%, followed by 4.0 min of re-equilibration.
Flow Rate:0.4 mL/min
Internal Standard:L-alanine-d3, D-valine-d8
Sample Injection:10 uL
Solvent A:0.1% formic acid in ultrapure water
Solvent B:0.1% formic acid in acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS004648
Analysis ID:AN004905
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS acquisition: Xcalibur Targeted data processing: Xcalibur Untargeted data acquisition: Compound Discoverer, R studio Ion mode is unspecified as analysis is performed in polarity switching mode, thereby generating data for both positive and negative ionization at the same time.
Ion Mode:UNSPECIFIED
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