Summary of Study ST002946
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.
| Study ID | ST002946 |
| Study Title | Fecal lipidomics of a patient cohort |
| Study Type | (un)targeted MS |
| Study Summary | This 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 c. Fecal lipidomics of a patient cohort |
| Institute | Ghent University |
| Department | Department of Translational Physiology, Infectiology and Public Health |
| Laboratory | Laboratory for Integrative Metabolomics |
| Last Name | De Paepe |
| First Name | Ellen |
| Address | Salisburylaan 133, 9820 Merelbeke, Belgium |
| Ellen.DePaepe@UGent.be | |
| Phone | 0032479081098 |
| Submit Date | 2023-07-06 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-11-01 |
| Release Version | 1 |
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: | SU003059 |
| 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 | IgE CMA |
|---|---|---|
| SA320801 | iQC14 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320802 | iQC15 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320803 | iQC16 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320804 | iQC13 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320805 | iQC12 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320806 | iQC1 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320807 | iQC11 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320808 | iQC2 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320809 | iQC10 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320810 | iQC8 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320811 | iQC3 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320812 | iQC7 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320813 | iQC9 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320814 | iQC6 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320815 | iQC4 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320816 | iQC5 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320817 | 56 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320818 | 68 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320819 | 65 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320820 | 51 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320821 | 45 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320822 | 81 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320823 | 49 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320824 | 54 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320825 | 112 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320826 | 130 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320827 | 43 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320828 | 116 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320829 | 113 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320830 | 108 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320831 | 109 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320832 | 104 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320833 | 60 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320834 | 38 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320835 | 4 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320836 | 3 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320837 | 22 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320838 | 27 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320839 | 40 | 0 | IgE other:0 | non-IgE CMA:0 | Healthy:1 |
| SA320840 | 80 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320841 | 78 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320842 | 25 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320843 | 20 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320844 | 31 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320845 | 127 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320846 | 123 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320847 | 42 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320848 | 92 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320849 | 91 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320850 | 79 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320851 | 14 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320852 | 10 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320853 | 41 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320854 | 7 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320855 | 37 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320856 | 64 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320857 | 35 | 0 | IgE other:0 | non-IgE CMA:1 | Healthy:0 |
| SA320858 | 52 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320859 | 99 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320860 | 1 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320861 | 5 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320862 | 70 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320863 | 44 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320864 | 115 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320865 | 96 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320866 | 97 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320867 | 8 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320868 | 12 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320869 | 32 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320870 | 73 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320871 | 58 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320872 | 82 | 0 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320873 | 18 | 0 | IgE other:1 | non-IgE CMA:1 | Healthy:0 |
| SA320874 | 34 | 0 | IgE other:1 | non-IgE CMA:1 | Healthy:0 |
| SA320875 | 6 | 0 | IgE other:1 | non-IgE CMA:1 | Healthy:0 |
| SA320876 | 136 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320877 | 24 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320878 | 9 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320879 | 86 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320880 | 36 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320881 | 53 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320882 | 2 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320883 | 39 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320884 | 57 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320885 | 84 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320886 | 26 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320887 | 29 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320888 | 30 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320889 | 85 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320890 | 128 | 1 | IgE other:0 | non-IgE CMA:0 | Healthy:0 |
| SA320891 | 95 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320892 | 59 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320893 | 50 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320894 | 72 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320895 | 28 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320896 | 21 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| SA320897 | 16 | 1 | IgE other:1 | non-IgE CMA:0 | Healthy:0 |
| Showing results 1 to 97 of 97 |
Collection:
| Collection ID: | CO003052 |
| Collection Summary: | Fecal samples were collected through spontaneous defecation in the diaper or using a Fecotainer® (AT Medical B.V., Enschede, The Netherlands). Samples were stored at -20 °C until pick-up (< 1 week). Following cooled transport (dry ice or icepacks), fecal samples were briefly stored at -80 °C, lyophilized, and homogenized in preparation for more long-term storage at -80 °C. |
| Sample Type: | Feces |
| Collection Method: | Spontaneous defecation |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003068 |
| Treatment Summary: | No treatment was applied, patients were divided into 4 different control groups: - IgE-mediated cow's milk allergy - other functional gastrointestinal disorder - IgE-mediated other food allergy - healthy brothers and sisters |
Sample Preparation:
| Sampleprep ID: | SP003065 |
| Sampleprep Summary: | The final protocol for generic extraction of lipids started with the addition of 1200 μL of methanol containing 0.01% BHT (w/v) to 200 ± 0.50 mg of lyophilized and homogenized fecal material. After this mixture was vortexed for 30 s, a total volume of 5.4 mL of methyl tertbutyl ether with 0.01% BHT (w/v) was added, after which a new vortex step of 30 s was applied. Subsequently, the sample was shaken for 20 min at 200 rpm at 20 °C in an incubator (New Brunswick Innova 42, Eppendorf). Thereafter, 3 mL of ultrapure water with 2.5% trichloroacetic acid (w/v) was added to induce phase separation, which was enforced by centrifugation for 5 min at 3000 rpm at 20 °C. Next, 1 mL of the upper layer, consisting of methyl tert-butyl ether, was collected and evaporated to dryness at 30 °C under a gentle stream of nitrogen. The residue was sequentially suspended in 250 μL of chloroform and 650 μL of methanol, after which a 50-μL subfraction was transferred to an amber glass vial and diluted 1/2 by the addition of 50 μL of methanol internal standard mixture (internal standard concentrations between 2 and 100 ng·μL−1). An aliquot (5 μL) of sample was injected into the chromatographic system. |
| Processing Storage Conditions: | -80℃ |
| Sample Spiking: | Internal standard |
Combined analysis:
| Analysis ID | AN004831 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | Waters ACQUITY UPLC BEH C18 (150 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | a.u. |
Chromatography:
| Chromatography ID: | CH003651 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC BEH C18 (150 x 2.1mm,1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | The following proportions (v/v) of solvent B were used: 0−1 min at 75%, 1−2 min from 75% to 90%, 2−6 min from 90% to 98%, 6−15 min from 98% to 100%, and 15−17 min at 100%, followed by 3 min of equilibration at initial conditions. |
| Flow Rate: | 0.3 mL/min |
| Internal Standard: | L-alanine-d3, D-valine-d8 |
| Sample Injection: | 10 uL |
| Solvent A: | 100% water; 3.5 mM ammonium acetate |
| Solvent B: | 100% methanol; 3.5 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004577 |
| Analysis ID: | AN004831 |
| 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: | UNSPECIFIED |
