Summary of Study ST003161

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 PR001966. The data can be accessed directly via it's Project DOI: 10.21228/M8KX6R 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	ST003161
Study Title	Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort
Study Summary	Crohn disease (CD) burden has increased with globalization/urbanization, and the rapid rise is attributed to environmental changes rather than genetic drift. The Study Of Urban and Rural CD Evolution (SOURCE, n=380) has considered diet-omics domains simultaneously to detect complex interactions and identify potential beneficial and pathogenic factors linked with rural-urban transition and CD. We characterize exposures, diet, ileal transcriptomics, metabolomics, and microbiome in newly diagnosed CD patients and controls in rural and urban China and Israel. We show that time spent by rural residents in urban environments is linked with changes in gut microbial composition and metabolomics, which mirror those seen in CD. Ileal transcriptomics highlights personal metabolic and immune gene expression modules, that are directly linked to potential protective dietary exposures (coffee, manganese, vitamin D), fecal metabolites, and the microbiome. Bacteria-associated metabolites are primarily linked with host immune modules, whereas diet-linked metabolites are associated with host epithelial metabolic functions.
Institute	Sheba hospital
Last Name	Braun
First Name	Tzipi
Address	Sheba hospital, Ramat Gan, Ramat Gan, 52621, Israel
Email	zipik0@gmail.com
Phone	97235305000
Submit Date	2024-04-03
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	Other
Release Date	2024-04-16
Release Version	1

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Project:

Project ID:	PR001966
Project DOI:	doi: 10.21228/M8KX6R
Project Title:	Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort
Project Summary:	Crohn disease (CD) burden has increased with globalization/urbanization, and the rapid rise is attributed to environmental changes rather than genetic drift. The Study Of Urban and Rural CD Evolution (SOURCE, n=380) has considered diet-omics domains simultaneously to detect complex interactions and identify potential beneficial and pathogenic factors linked with rural-urban transition and CD. We characterize exposures, diet, ileal transcriptomics, metabolomics, and microbiome in newly diagnosed CD patients and controls in rural and urban China and Israel. We show that time spent by rural residents in urban environments is linked with changes in gut microbial composition and metabolomics, which mirror those seen in CD. Ileal transcriptomics highlights personal metabolic and immune gene expression modules, that are directly linked to potential protective dietary exposures (coffee, manganese, vitamin D), fecal metabolites, and the microbiome. Bacteria-associated metabolites are primarily linked with host immune modules, whereas diet-linked metabolites are associated with host epithelial metabolic functions.
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:	SU003280
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	Sample source	Gender	Diagnosis
SA342822	025_FC_S042_SOURCE_Female_CD	Feces	Female	CD
SA342823	009_FC_S016_SOURCE_Female_CD	Feces	Female	CD
SA342824	027_FC_S045_SOURCE_Female_CD	Feces	Female	CD
SA342825	005_FC_S011_SOURCE_Female_CD	Feces	Female	CD
SA342826	037_FC_S063_SOURCE_Female_CD	Feces	Female	CD
SA342827	004_FC_S007_SOURCE_Female_CD	Feces	Female	CD
SA342828	001_FC_S002_SOURCE_Female_Control	Feces	Female	Control
SA342829	017_FC_S030_SOURCE_Female_Control	Feces	Female	Control
SA342830	029_FC_S050_SOURCE_Female_Control	Feces	Female	Control
SA342831	035_FC_S061_SOURCE_Female_Control	Feces	Female	Control
SA342832	016_FC_S028_SOURCE_Female_Control	Feces	Female	Control
SA342833	028_FC_S047_SOURCE_Female_Control	Feces	Female	Control
SA342834	019_FC_S032_SOURCE_Female_Control	Feces	Female	Control
SA342835	007_FC_S014_SOURCE_Female_Control	Feces	Female	Control
SA342836	010_FC_S018_SOURCE_Female_Control	Feces	Female	Control
SA342837	012_FC_S022_SOURCE_Female_Control	Feces	Female	Control
SA342838	002_FC_S004_SOURCE_Female_Control	Feces	Female	Control
SA342839	032_FC_S056_SOURCE_Male_CD	Feces	Male	CD
SA342840	031_FC_S052_SOURCE_Male_CD	Feces	Male	CD
SA342841	034_FC_S060_SOURCE_Male_CD	Feces	Male	CD
SA342842	011_FC_S020_SOURCE_Male_CD	Feces	Male	CD
SA342843	023_FC_S040_SOURCE_Male_CD	Feces	Male	CD
SA342844	020_FC_S033_SOURCE_Male_CD	Feces	Male	CD
SA342845	022_FC_S036_SOURCE_Male_CD	Feces	Male	CD
SA342846	013_FC_S024_SOURCE_Male_CD	Feces	Male	CD
SA342847	014_FC_S025_SOURCE_Male_CD	Feces	Male	CD
SA342848	021_FC_S035_SOURCE_Male_CD	Feces	Male	CD
SA342849	006_FC_S012_SOURCE_Male_Control	Feces	Male	Control
SA342850	033_FC_S057_SOURCE_Male_Control	Feces	Male	Control
SA342851	036_FC_S062_SOURCE_Control	Feces	Male	Control
SA342852	003_FC_S006_SOURCE_Male_Control	Feces	Male	Control
SA342853	026_FC_S044_SOURCE_Male_Control	Feces	Male	Control
SA342854	018_FC_S031_SOURCE_Male_Control	Feces	Male	Control
SA342855	024_FC_S041_SOURCE_Male_Control	Feces	Male	Control
SA342856	015_FC_S026_SOURCE_Male_Control	Feces	Male	Control
SA342857	008_FC_S015_SOURCE_Male_Control	Feces	Male	Control
SA342858	030_FC_S051_SOURCE_Male_Control	Feces	Male	Control

Showing results 1 to 37 of 37

Showing results 1 to 37 of 37

Collection:

Collection ID:	CO003273
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 10 min at 4 °C, and stored at -80c until submission for LC-MS metabolomics analysis
Sample Type:	Feces

Treatment:

Treatment ID:	TR003289
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 10 min at 4 °C, and stored at -80c until submission for LC-MS metabolomics analysis

Sample Preparation:

Sampleprep ID:	SP003287
Sampleprep Summary:	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 UPLC setup consisted of ZIC-pHILIC column (SeQuant; 150 mm × 2.1 mm, 5 μm; Merck). Stool 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.

Sampleprep ID:

SP003287

Sampleprep Summary:

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 UPLC setup consisted of ZIC-pHILIC column (SeQuant; 150 mm × 2.1 mm, 5 μm; Merck). Stool 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.

Combined analysis:

Analysis ID	AN005186
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	TSS normalized values

Chromatography:

Chromatography ID:	CH003923
Instrument Name:	Thermo Dionex
Column Name:	SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
Column Temperature:	45
Flow Gradient:	0-2 min: 80%B B; 17 min: 20%B; 19 min: 20%B; 21min: 80%B; 27min: 80%B
Flow Rate:	0.2 ml/min
Solvent A:	100% Water; 20 mM ammonium carbonate; 0.1% of 25% ammonium hydroxide (pH 9.2)
Solvent B:	100% Acetonitrile
Chromatography Type:	HILIC

MS:

MS ID:	MS004919
Analysis ID:	AN005186
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	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