Summary of Study ST003312

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 PR002060. The data can be accessed directly via it's Project DOI: 10.21228/M8BG0T 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 IDST003312
Study TitleIntegrative analysis of serum and fecal metabolome and the microbiome that herald Crohn Disease flare - serum
Study SummaryWe investigated the relationship between the host and gut microbiota in the context of Crohn Disease (CD), which is a relapsing-remitting condition. We analyzed paired omics of 80 CD patients and 43 controls, including 202 serum and 294 fecal metabolomics, and 258 microbiome samples. Our findings suggest that CD patients have an inverse shift in energy utilization from sugars and fat between serum and feces. In the serum, we noted a decrease in metabolites related to starch, sucrose, and tricarboxylic acid (TCA) cycle, as well as an increase in metabolites linked to fat in contrast to the feces, where we noted higher sugars and TCA cycle metabolites, and lower fat metabolites. Interestingly, fecal sugars were specifically linked with oral bacteria mislocated to the CD gut, while unsaturated fat derivatives of arachidonic acid were linked with R. gnavus and Fusobacteria. We identified consistent metabolite alterations in CD patients, which were also present in clinical/biomarkers active CD, and pre-flare samples of patients who experienced flare. Using pre-flare samples, we developed models that predicted a subsequent flare using metabolic serum and fecal signatures. We validated the fecal metabolomics predictions in another, similarly designed, independent CD cohort. Finally, we developed a clinical lab-based index [UA/Cr ratio+log2(CRP)] based on the serum metabolomics model, which was also predictive in the validation cohort. Here are the serum metabolomics samples.
Institute
Sheba hospital
Last NameBraun
First NameTzipi
AddressSheba hospital, Ramat Gan, Ramat Gan, 52621, Israel
Emailzipik0@gmail.com
Phone97235305000
Submit Date2024-06-16
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailOther
Release Date2024-08-01
Release Version1
Tzipi Braun Tzipi Braun
https://dx.doi.org/10.21228/M8BG0T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002060
Project DOI:doi: 10.21228/M8BG0T
Project Title:Integrative analysis of serum and fecal metabolome and the microbiome that herald Crohn Disease flare, serum samples
Project Summary:We investigated the relationship between the host and gut microbiota in the context of Crohn Disease (CD), which is a relapsing-remitting condition. We analyzed paired omics of 80 CD patients and 43 controls, including 202 serum and 294 fecal metabolomics, and 258 microbiome samples. Our findings suggest that CD patients have an inverse shift in energy utilization from sugars and fat between serum and feces. In the serum, we noted a decrease in metabolites related to starch, sucrose, and tricarboxylic acid (TCA) cycle, as well as an increase in metabolites linked to fat in contrast to the feces, where we noted higher sugars and TCA cycle metabolites, and lower fat metabolites. Interestingly, fecal sugars were specifically linked with oral bacteria mislocated to the CD gut, while unsaturated fat derivatives of arachidonic acid were linked with R. gnavus and Fusobacteria. We identified consistent metabolite alterations in CD patients, which were also present in clinical/biomarkers active CD, and pre-flare samples of patients who experienced flare. Using pre-flare samples, we developed models that predicted a subsequent flare using metabolic serum and fecal signatures. We validated the fecal metabolomics predictions in another, similarly designed, independent CD cohort. Finally, we developed a clinical lab-based index [UA/Cr ratio+log2(CRP)] based on the serum metabolomics model, which was also predictive in the validation cohort. Here are the serum metabolomics samples.
Institute:Sheba hospital
Last Name:Braun
First Name:Tzipi
Address:Sheba hospital, Ramat Gan, Ramat Gan, 52621, Israel
Email:zipik0@gmail.com
Phone:97235305000

Subject:

Subject ID:SU003433
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id Sex Smoking Sample source Fasting Dx
SA358910021_SMC_IIRN_p10s1Female current Serum N CD
SA358911051_SMC_IIRN_p15s4Female current Serum N CD
SA358912049_SMC_IIRN_p15s2Female current Serum N CD
SA358913106_SMC_IIRN_p42s1Female current Serum N CD
SA358914108_SMC_IIRN_p42s3Female current Serum N CD
SA358915109_SMC_IIRN_p42s4Female current Serum N CD
SA358916023_SMC_IIRN_p10s3Female current Serum N CD
SA358917024_SMC_IIRN_p10s4Female current Serum Y CD
SA358918022_SMC_IIRN_p10s2Female current Serum Y CD
SA358919050_SMC_IIRN_p15s3Female current Serum Y CD
SA358920107_SMC_IIRN_p42s2Female current Serum Y CD
SA358921048_SMC_IIRN_p15s1Female current Serum Y CD
SA358922154_SMC_SR_A017s1Female current Serum Y CD
SA358923160_SMC_SR_A023s1Female current Serum Y Control
SA358924158_SMC_SR_A021s1Female current Serum Y Control
SA358925045_SMC_IIRN_p14s2Female never_used Serum N CD
SA358926074_SMC_IIRN_p27s3Female never_used Serum N CD
SA358927075_SMC_IIRN_p27s4Female never_used Serum N CD
SA358928020_SMC_IIRN_p9s4Female never_used Serum N CD
SA358929194_SMC_CL_A087s4Female never_used Serum N CD
SA358930019_SMC_IIRN_p9s3Female never_used Serum N CD
SA358931193_SMC_CL_A087s3Female never_used Serum N CD
SA358932192_SMC_CL_A087s2Female never_used Serum N CD
SA358933018_SMC_IIRN_p9s2Female never_used Serum N CD
SA358934009_SMC_IIRN_p5s1Female never_used Serum N CD
SA358935047_SMC_IIRN_p14s4Female never_used Serum N CD
SA358936195_SMC_CL_A087s4Female never_used Serum N CD
SA358937113_SMC_IIRN_p43s4Female never_used Serum N CD
SA358938112_SMC_IIRN_p43s3Female never_used Serum N CD
SA358939012_SMC_IIRN_p5s4Female never_used Serum N CD
SA358940111_SMC_IIRN_p43s2Female never_used Serum N CD
SA358941011_SMC_IIRN_p5s3Female never_used Serum N CD
SA358942124_SMC_CL_A305s2Female never_used Serum N Control
SA358943123_SMC_CL_A305s1Female never_used Serum N Control
SA358944116_SMC_CL_A302s1Female never_used Serum N Control
SA358945117_SMC_CL_A302s2Female never_used Serum N Control
SA358946118_SMC_CL_A303s1Female never_used Serum N Control
SA358947119_SMC_CL_A303s2Female never_used Serum N Control
SA358948120_SMC_CL_A303s3Female never_used Serum N Control
SA358949115_SMC_CL_A301s2Female never_used Serum N Control
SA358950121_SMC_CL_A304s1Female never_used Serum N Control
SA358951122_SMC_CL_A304s2Female never_used Serum N Control
SA358952114_SMC_CL_A301s1Female never_used Serum N Control
SA358953139_SMC_CL_A313s2Female never_used Serum N Control
SA358954131_SMC_CL_A308s1Female never_used Serum N Control
SA358955132_SMC_CL_A308s2Female never_used Serum N Control
SA358956138_SMC_CL_A313s1Female never_used Serum N Control
SA358957169_SMC_EN_A200s1Female never_used Serum Y CD
SA358958168_SMC_EN_A193s1Female never_used Serum Y CD
SA358959180_SMC_EN_A221s1Female never_used Serum Y CD
SA358960181_SMC_EN_A087s1Female never_used Serum Y CD
SA358961110_SMC_IIRN_p43s1Female never_used Serum Y CD
SA358962046_SMC_IIRN_p14s3Female never_used Serum Y CD
SA358963044_SMC_IIRN_p14s1Female never_used Serum Y CD
SA358964172_SMC_EN_A230s1Female never_used Serum Y CD
SA358965017_SMC_IIRN_p9s1Female never_used Serum Y CD
SA358966153_SMC_SR_A016s1Female never_used Serum Y CD
SA358967010_SMC_IIRN_p5s2Female never_used Serum Y CD
SA358968148_SMC_SR_A011s1Female never_used Serum Y CD
SA358969155_SMC_SR_A018s1Female never_used Serum Y Control
SA358970147_SMC_SR_A010s1Female never_used Serum Y Control
SA358971141_SMC_SR_A004s1Female never_used Serum Y Control
SA358972159_SMC_SR_A022s1Female never_used Serum Y Control
SA358973184_SMC_EN_A048s1Female never_used Serum Y Control
SA358974099_SMC_IIRN_p38s2Female previous Serum N CD
SA358975101_SMC_IIRN_p38s4Female previous Serum N CD
SA358976144_SMC_SR_A007s1Female previous Serum Y CD
SA358977100_SMC_IIRN_p38s3Female previous Serum Y CD
SA358978140_SMC_SR_A002s1Female previous Serum Y Control
SA358979027_SMC_IIRN_p11s3Male current Serum N CD
SA358980105_SMC_IIRN_p41s4Male current Serum N CD
SA358981104_SMC_IIRN_p41s3Male current Serum N CD
SA358982103_SMC_IIRN_p41s2Male current Serum N CD
SA358983028_SMC_IIRN_p11s4Male current Serum N CD
SA358984053_SMC_IIRN_p16s2Male current Serum N CD
SA358985025_SMC_IIRN_p11s1Male current Serum N CD
SA358986052_SMC_IIRN_p16s1Male current Serum N CD
SA358987054_SMC_IIRN_p16s3Male current Serum N CD
SA358988055_SMC_IIRN_p16s4Male current Serum N CD
SA358989136_SMC_CL_A311s2Male current Serum N Control
SA358990135_SMC_CL_A311s1Male current Serum N Control
SA358991191_SMC_SR_A036s1Male current Serum Y CD
SA358992026_SMC_IIRN_p11s2Male current Serum Y CD
SA358993102_SMC_IIRN_p41s1Male current Serum Y CD
SA358994157_SMC_SR_A020s1Male current Serum Y CD
SA358995161_SMC_SR_A024s1Male current Serum Y CD
SA358996146_SMC_SR_A009s1Male current Serum Y Control
SA358997037_SMC_IIRN_p13s4Male never_used Serum N CD
SA358998035_SMC_IIRN_p13s2Male never_used Serum N CD
SA358999033_SMC_IIRN_p12s5Male never_used Serum N CD
SA359000029_SMC_IIRN_p12s1Male never_used Serum N CD
SA359001031_SMC_IIRN_p12s3Male never_used Serum N CD
SA359002004_SMC_IIRN_p3s4Male never_used Serum N CD
SA359003080_SMC_IIRN_p29s5Male never_used Serum N CD
SA359004096_SMC_IIRN_p37s3Male never_used Serum N CD
SA359005081_SMC_IIRN_p29s6Male never_used Serum N CD
SA359006097_SMC_IIRN_p37s4Male never_used Serum N CD
SA359007083_SMC_IIRN_p29s8Male never_used Serum N CD
SA359008039_SMC_IIRN_p13s6Male never_used Serum N CD
SA359009076_SMC_IIRN_p29s1Male never_used Serum N CD
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Collection:

Collection ID:CO003426
Collection Summary:Samples were centrifuged at 16,000g for 10min, and 40μl of the supernatant was transferred into a sterile tube, containing 960μl extraction mix composed of methanol, acetonitrile, and water (5:3:2). The (1:25) diluted samples were vortexed for 10min and centrifuged at 16,000g for 10min, and 100μl were transferred into a LC-MS vial. The vials were stored at -80c until submission for LC-MS metabolomics analysis.
Sample Type:Blood (serum)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003442
Treatment Summary:Samples were centrifuged at 16,000g for 10min, and 40μl of the supernatant was transferred into a sterile tube, containing 960μl extraction mix composed of methanol, acetonitrile, and water (5:3:2). The (1:25) diluted samples were vortexed for 10min and centrifuged at 16,000g for 10min, and 100μl were transferred into a LC-MS vial. The vials were stored at -80c until submission for LC-MS metabolomics analysis.

Sample Preparation:

Sampleprep ID:SP003440
Sampleprep Summary:Samples were centrifuged at 16,000g for 10min, and 40μl of the supernatant was transferred into a sterile tube, containing 960μl extraction mix composed of methanol, acetonitrile, and water (5:3:2). The (1:25) diluted samples were vortexed for 10min and centrifuged at 16,000g for 10min, and 100μl were transferred into a LC-MS vial. The vials were stored at -80c until submission for LC-MS metabolomics analysis.

Combined analysis:

Analysis ID AN005424
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Dionex
Column SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units normalized metabolite percentage per sample

Chromatography:

Chromatography ID:CH004113
Chromatography Summary:The UPLC setup consisted of ZIC-pHILIC column (SeQuant; 150 mm × 2.1 mm, 5 μm; Merck). Extracts were injected, and the compounds were separated with mobile phase gradient, starting at 20% aqueous (20 mM ammonium carbonate adjusted to pH 9.2 with 0.1% of 25% ammonium hydroxide) and 80% organic (acetonitrile) and terminated with 20% acetonitrile. Flow rate and column temperature were maintained at 0.2 ml/min and 45 °C, respectively, for a total run time of 27 min.
Instrument Name:Thermo Dionex
Column Name:SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
Column Temperature:45
Flow Gradient:0-2min: 80% B; 17min: 20% B; 19 min: 20% B; 21min: 80% B; 27min: 80% B
Flow Rate:0.2mL/min
Solvent A:100% Water; 20mM ammonium carbonate; 0.25% ammonium hydroxide
Solvent B:100% Acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS005150
Analysis ID:AN005424
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Orbitrap Q-Exactive Mass Spectrometer (Thermo Fisher Scientific) was used. The resolution was set to 35,000 at a 200 mass/charge ratio (m/z) with electrospray ionization and polarity switching mode to enable both positive and negative ions across a mass range of 67–1000 m/z. The raw data files generated by UPLC-MS/MS were processed using the MassLynx software (v4.1, Waters, Milford, MA, USA) to perform peak integration, calibration, and quantitation for each metabolite.
Ion Mode:UNSPECIFIED
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