{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002946","ANALYSIS_ID":"AN004831","VERSION":"1","CREATED_ON":"August 8, 2023, 7:03 am"},

"PROJECT":{"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"},

"STUDY":{"STUDY_TITLE":"Fecal lipidomics of a patient cohort","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","EMAIL":"Ellen.DePaepe@UGent.be","STUDY_TYPE":"(un)targeted MS","PHONE":"0032479081098"},

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},
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},
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},
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},
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},
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},
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"Sample ID":"130",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"1","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se113","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"136",
"Factors":{"IgE CMA":"1","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se081","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC1",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se022","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC10",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se077","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC11",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se089","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC12",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se090","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC13",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se102","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC14",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se103","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC15",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se116","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC16",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se117","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC2",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se023","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC3",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se035","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC4",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se036","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC5",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se046","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC6",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se047","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC7",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se062","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC8",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se063","Analysis type":"Lipidomics feces","":"-"}
},
{
"Subject ID":"-",
"Sample ID":"iQC9",
"Factors":{"IgE CMA":"0","IgE other":"0","non-IgE CMA":"0","Healthy":"0","Anaphylaxis":"0"},
"Additional sample data":{"RAW_FILE_NAME":"210525se076","Analysis type":"Lipidomics feces","":"-"}
}
],
"COLLECTION":{"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_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"},

"SAMPLEPREP":{"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"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Waters ACQUITY UPLC BEH C18 (150 x 2.1mm,1.7um)","SOLVENT_A":"100% water; 3.5 mM ammonium acetate","SOLVENT_B":"100% methanol; 3.5 mM ammonium acetate","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","COLUMN_TEMPERATURE":"40","INTERNAL_STANDARD":"L-alanine-d3, D-valine-d8","SAMPLE_INJECTION":"10 uL"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"MS acquisition: Xcalibur Targeted data processing: Xcalibur Untargeted data acquisition: Compound Discoverer, R studio","MS_RESULTS_FILE":"ST002946_AN004831_Results.txt UNITS:a.u. Has m/z:Neutral masses Has RT:Yes RT units:Minutes"}

}