Summary of Study ST003313

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 IDST003313
Study TitleIntegrative analysis of serum and fecal metabolome and the microbiome that herald Crohn Disease flare - feces
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 fecal metabolomics samples.
Institute
Sheba hospital
Last NameBraun
First NameTzipi
AddressSheba hospital, Ramat Gan, Ramat Gan, 52621, Israel
Emailzipik0@gmail.com
Phone97235305000
Submit Date2024-06-19
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:SU003434
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Sex Smoking Sample source Dx
SA359112132_28_IIRN_Female_CD_2017Female current Feces CD
SA359113123_15_IIRN_Female_CD_2016Female current Feces CD
SA359114116_42_IIRN_Female_CD_2016Female current Feces CD
SA359115230_24_IIRN_Female_CD_2015Female current Feces CD
SA359116160_24_IIRN_Female_CD_2016Female current Feces CD
SA359117219_28_IIRN_Female_CD_2017Female current Feces CD
SA359118209_24_IIRN_Female_CD_2017Female current Feces CD
SA359119168_28_IIRN_Female_CD_2015Female current Feces CD
SA359120201_24_IIRN_Female_CD_2015Female current Feces CD
SA359121290_28_IIRN_Female_CD_2016Female current Feces CD
SA35912267_24_IIRN_Female_CD_2017Female current Feces CD
SA35912362_28_IIRN_Female_CD_2018Female current Feces CD
SA359124138_15_IIRN_Female_CD_2015Female current Feces CD
SA35912582_15_IIRN_Female_CD_2016Female current Feces CD
SA359126131_15_IIRN_Female_CD_2016Female current Feces CD
SA35912773_42_IIRN_Female_CD_2016Female current Feces CD
SA359128139_42_IIRN_Female_CD_2015Female current Feces CD
SA35912987_42_IIRN_Female_CD_2015Female current Feces CD
SA35913098_15_IIRN_Female_CD_2016Female current Feces CD
SA35913155_28_IIRN_Female_CD_2015Female current Feces CD
SA359132212_10_IIRN_Female_CD_2015Female current Feces CD
SA359133148_28_IIRN_Female_CD_2016Female current Feces CD
SA359134171_44_IIRN_Female_CD_2016Female never_used Feces CD
SA359135169_S046_SOURCE_Female_CD_2020Female never_used Feces CD
SA359136162_20_IIRN_Female_CD_2016Female never_used Feces CD
SA359137172_22_IIRN_Female_CD_2016Female never_used Feces CD
SA35913897_27_IIRN_Female_CD_2018Female never_used Feces CD
SA359139137_31_IIRN_Female_CD_2017Female never_used Feces CD
SA359140130_14_IIRN_Female_CD_2016Female never_used Feces CD
SA359141115_23_IIRN_Female_CD_2016Female never_used Feces CD
SA359142113_33_IIRN_Female_CD_2015Female never_used Feces CD
SA359143100_43_IIRN_Female_CD_2015Female never_used Feces CD
SA359144175_5_IIRN_Female_CD_2015Female never_used Feces CD
SA35914581_9_IIRN_Female_CD_2016Female never_used Feces CD
SA35914679_14_IIRN_Female_CD_2017Female never_used Feces CD
SA35914777_31_IIRN_Female_CD_2010Female never_used Feces CD
SA35914868_23_IIRN_Female_CD_2017Female never_used Feces CD
SA35914960_20_IIRN_Female_CD_2016Female never_used Feces CD
SA35915050_23_IIRN_Female_CD_2015Female never_used Feces CD
SA359151174_5_IIRN_Female_CD_2018Female never_used Feces CD
SA359152208_S054_SOURCE_Female_CD_NIFemale never_used Feces CD
SA359153177_S001_SOURCE_Female_CD_2019Female never_used Feces CD
SA359154267_44_IIRN_Female_CD_2016Female never_used Feces CD
SA359155126_5_IIRN_Female_CD_2016Female never_used Feces CD
SA35915634_27_IIRN_Female_CD_2017Female never_used Feces CD
SA359157166_27_IIRN_Female_CD_2017Female never_used Feces CD
SA359158108_14_IIRN_Female_CD_2017Female never_used Feces CD
SA359159133_14_IIRN_Female_CD_2016Female never_used Feces CD
SA359160294_20_IIRN_Female_CD_2015Female never_used Feces CD
SA359161289_27_IIRN_Female_CD_2015Female never_used Feces CD
SA359162288_20_IIRN_Female_CD_2017Female never_used Feces CD
SA359163285_31_IIRN_Female_CD_2016Female never_used Feces CD
SA359164282_S042_SOURCE_Female_CD_2020Female never_used Feces CD
SA359165281_5_IIRN_Female_CD_2017Female never_used Feces CD
SA359166272_20_IIRN_Female_CD_2016Female never_used Feces CD
SA359167262_9_IIRN_Female_CD_2016Female never_used Feces CD
SA359168178_44_IIRN_Female_CD_2015Female never_used Feces CD
SA359169259_23_IIRN_Female_CD_2015Female never_used Feces CD
SA359170254_14_IIRN_Female_CD_2017Female never_used Feces CD
SA359171252_27_IIRN_Female_CD_2017Female never_used Feces CD
SA359172246_31_IIRN_Female_CD_2016Female never_used Feces CD
SA359173243_14_IIRN_Female_CD_2015Female never_used Feces CD
SA359174237_31_IIRN_Female_CD_2016Female never_used Feces CD
SA359175222_27_IIRN_Female_CD_2016Female never_used Feces CD
SA359176216_43_IIRN_Female_CD_2015Female never_used Feces CD
SA35917748_31_IIRN_Female_CD_2015Female never_used Feces CD
SA359178195_27_IIRN_Female_CD_2015Female never_used Feces CD
SA359179192_5_IIRN_Female_CD_2018Female never_used Feces CD
SA359180188_5_IIRN_Female_CD_2017Female never_used Feces CD
SA35918149_14_IIRN_Female_CD_2015Female never_used Feces CD
SA359182214_5_IIRN_Female_CD_2016Female never_used Feces CD
SA35918345_33_IIRN_Female_CD_2015Female never_used Feces CD
SA35918427_5_IIRN_Female_CD_2015Female never_used Feces CD
SA359185251_5_IIRN_Female_CD_2016Female never_used Feces CD
SA359186225_43_IIRN_Female_CD_2016Female never_used Feces CD
SA359187145_43_IIRN_Female_CD_2016Female never_used Feces CD
SA35918813_43_IIRN_Female_CD_2017Female never_used Feces CD
SA359189187_43_IIRN_Female_CD_2017Female never_used Feces CD
SA359190245_S011_SOURCE_Female_CD_2019Female never_used Feces CD
SA359191229_9_IIRN_Female_CD_2015Female never_used Feces CD
SA35919243_9_IIRN_Female_CD_2016Female never_used Feces CD
SA359193197_9_IIRN_Female_CD_2017Female never_used Feces CD
SA35919408_20_IIRN_Female_CD_2015Female never_used Feces CD
SA35919525_44_IIRN_Female_CD_2015Female never_used Feces CD
SA359196158_23_IIRN_Female_CD_2017Female never_used Feces CD
SA35919731_31_IIRN_Female_CD_2017Female never_used Feces CD
SA35919832_S055_SOURCE_Female_CD_NIFemale never_used Feces CD
SA35919942_23_IIRN_Female_CD_2016Female never_used Feces CD
SA3592003_SMC_FC_A304s1_ControlFemale never_used Feces Control
SA359201185_S047_SOURCE_Female_Control_NIFemale never_used Feces Control
SA359202271_A308_Lab_Control_Female_Control_2020Female never_used Feces Control
SA35920309_A303_Lab_Control_Female_Control_2019Female never_used Feces Control
SA3592045_SMC_FC_A305s1_ControlFemale never_used Feces Control
SA3592054_SMC_FC_A304s2_ControlFemale never_used Feces Control
SA359206118_A305_Lab_Control_Female_Control_2019Female never_used Feces Control
SA359207112_A302_Lab_Control_Female_Control_2019Female never_used Feces Control
SA359208248_A303_Lab_Control_Female_Control_2019Female never_used Feces Control
SA359209196_A304_Lab_Control_Female_Control_2020Female never_used Feces Control
SA359210125_S028_SOURCE_Female_Control_2019Female never_used Feces Control
SA359211146_A302_Lab_Control_Female_Control_2019Female never_used Feces Control
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 294

Collection:

Collection ID:CO003427
Collection Summary:Extraction solution (ES: 75% methanol and 25% water and six internal standards) was mixed with fecal smear, sonicated for 10 min, centrifuged at 14,000g for 10min at 4°C, and stored at -80c until submission for LC-MS metabolomics analysis.
Sample Type:Feces
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003443
Treatment Summary:Extraction solution (ES: 75% methanol and 25% water and six internal standards) was mixed with fecal smear, sonicated for 10 min, centrifuged at 14,000g for 10min at 4°C, and stored at -80c until submission for LC-MS metabolomics analysis.

Sample Preparation:

Sampleprep ID:SP003441
Sampleprep Summary:Extraction solution (ES: 75% methanol and 25% water and six internal standards) was mixed with fecal smear, sonicated for 10 min, centrifuged at 14,000g for 10min at 4°C, and stored at -80c until submission for LC-MS metabolomics analysis.

Combined analysis:

Analysis ID AN005425
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 percentage of metabolites per sample

Chromatography:

Chromatography ID:CH004114
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:0-2 min: 80%B; 17 min: 20%B; 19 min: 20%B; 21min: 80%B; 27min: 80%B
Flow Rate:0.2mL/min
Solvent A:100% Water; 20 mM ammonium carbonate; 0.25% ammonium hydroxide
Solvent B:100% Acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS005151
Analysis ID:AN005425
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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