Summary of Study ST000923

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 PR000639. The data can be accessed directly via it's Project DOI: 10.21228/M82T15 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 IDST000923
Study TitleLongitudinal Metabolomics of the Human Microbiome in Inflammatory Bowel Disease
Study SummaryA number of factors contribute to the complex array of small molecules that occur in stool; including diet, gut flora, and gut function. Comprehensive profiling of the stool metabolome therefore can provide detailed phenotypic information on health status, metabolic interactions between the host and the microbiome, and interactions among gut microbes. Here, we applied metabolomics to characterize stool samples collected longitudinally from inflammatory bowel disease (IBD) patients and non-IBD controls who participated in the Integrative Human Microbiome Project (iHMP). A total of 546 stool samples were analyzed using a platform comprised of four complementary liquid chromatography tandem mass spectrometry (LC-MS) methods designed to measure polar metabolites and lipids. Each method used high resolution/accurate mass (HRAM) profiling to measure both metabolites of confirmed identity and yet to be identified metabolite peaks. 81,867 de-isotoped LC-MS peaks were measured, out of which 597 were annotated based on confirmation with authentic reference standards. Pooled stool extracts inserted and analyzed throughout the analysis queues to evaluate analytical reproducibility showed a median coefficient of variation of 5.1% among known metabolites and 24.2% across all 81,867 features. Owing to differences in water content and heterogeneity among stool samples, total median scaling was used to standardize the metabolomics data. In addition to being accessible at the Metabolomics Workbench repository, these metabolomics data will be incorporated into a multi’omic database (https://www.hmpdacc.org/ihmp/) that will enable the study of associations between the gut microbiome and IBD.
Institute
Broad Institute of MIT and Harvard
Last NameAvila-Pacheco
First NameJulian
Address415 Main Street
Emailjravilap@broadinstitute.org
Phone617-714-8264
Submit Date2017-11-14
Num Groups3
Total Subjects546
Num Males276
Num Females270
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2018-02-07
Release Version1
Julian Avila-Pacheco Julian Avila-Pacheco
https://dx.doi.org/10.21228/M82T15
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000639
Project DOI:doi: 10.21228/M82T15
Project Title:Longitudinal Multiomics of the Human Microbiome in Inflammatory Bowel Disease
Project Summary:The Inflammatory Bowel Disease (IBD) Multi'omics Database (IBDMDB) includes multi’omics measurements from over 100 subjects, sampled biweekly over up to a year in both adult and pediatric patients with IBD (Crohn’s disease and ulcerative colitis), along with non-IBD controls. Data types include fecal metagenomes, metatranscriptomes, metabolomes, and proteomes, as well as host genetics, intestinal biopsy transcriptomes, epigenetics, and 16S amplicon profiles. Subjects’ medical histories and demographics are collected at baseline and medication, diet, and disease activity profiled longitudinally.
Institute:Broad Institute of MIT and Harvard
Last Name:Avila-Pacheco
First Name:Julian
Address:415 Main Street, Rm 7175, Cambridge, MA, 02142, USA
Email:jravilap@broadinstitute.org
Phone:6177148264
Funding Source:NIDDK 8U54DK102557
Contributors:Courtney Dennis, Kerry Pierce, Kevin Bullock, Amy Deik, Clary Clish, Curtis Huttenhower, Ramnik Xavier, Hera Vlamakis, Tiffany Poon, Eric Franzosa, Jason Lloyd-Price, Cesar Arze, Melanie Schirmer, Elizabeth Andrews

Subject:

Subject ID:SU000961
Subject Type:Human stool
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Diagnosis sex
SA054705SM-7EWUSCD Female
SA054706SM-7F43PCD Female
SA054707SM-7GCHKCD Female
SA054708SM-7E5EHCD Female
SA054709SM-7DGV5CD Female
SA054710SM-7CRX2CD Female
SA054711SM-7D34KCD Female
SA054712SM-7D34OCD Female
SA054713SM-7DN3VCD Female
SA054714SM-7GFUXCD Female
SA054715SM-7IL1SCD Female
SA054716SM-AGUN1CD Female
SA054717SM-7IWESCD Female
SA054718SM-7IWF5CD Female
SA054719SM-7IL1KCD Female
SA054720SM-7IKZFCD Female
SA054721SM-7HAI4CD Female
SA054722SM-7HNM8CD Female
SA054723SM-B4A4GCD Female
SA054724SM-7CP3GCD Female
SA054725SM-CE6ZHCD Female
SA054726SM-72PHSCD Female
SA054727SM-72XGSCD Female
SA054728SM-74Y93CD Female
SA054729SM-76CATCD Female
SA054730SM-72PGNCD Female
SA054731SM-71WY2CD Female
SA054732SM-6ZT2VCD Female
SA054733SM-6ZT3WCD Female
SA054734SM-71WXHCD Female
SA054735SM-76ENWCD Female
SA054736SM-76EO1CD Female
SA054737SM-7AK5UCD Female
SA054738SM-7AK5YCD Female
SA054739SM-7AMIHCD Female
SA054740SM-7BF22CD Female
SA054741SM-7AA21CD Female
SA054742SM-7AA1SCD Female
SA054743SM-76EODCD Female
SA054744SM-77M5KCD Female
SA054745SM-CH32HCD Female
SA054746SM-7K1UWCD Female
SA054747SM-7K1V5CD Female
SA054748SM-9ZA5VCD Female
SA054749SM-9ZE8TCD Female
SA054750SM-9ZJIICD Female
SA054751SM-9ZK9FCD Female
SA054752SM-9YTMACD Female
SA054753SM-APR9QCD Female
SA054754SM-9W3B4CD Female
SA054755SM-9W7VZCD Female
SA054756SM-ARMC7CD Female
SA054757SM-A12KLCD Female
SA054758SM-A375PCD Female
SA054759SM-ACTNECD Female
SA054760SM-ADICOCD Female
SA054761SM-AFSIOCD Female
SA054762SM-AADKWCD Female
SA054763SM-A9J9NCD Female
SA054764SM-A5A1VCD Female
SA054765SM-A61QGCD Female
SA054766SM-AIG8MCD Female
SA054767SM-9VWCQCD Female
SA054768SM-9VWC6CD Female
SA054769SM-7R3ACCD Female
SA054770SM-9KOMOCD Female
SA054771SM-AVR79CD Female
SA054772SM-AVPGZCD Female
SA054773SM-7NSP1CD Female
SA054774SM-AXQRHCD Female
SA054775SM-7K1V9CD Female
SA054776SM-7K1W8CD Female
SA054777SM-7K1WGCD Female
SA054778SM-9NBF6CD Female
SA054779SM-9O9R1CD Female
SA054780SM-9SIJ5CD Female
SA054781SM-9U262CD Female
SA054782SM-9UW5SCD Female
SA054783SM-9RTUZCD Female
SA054784SM-9RTURCD Female
SA054785SM-9PJ1ICD Female
SA054786SM-9QMNLCD Female
SA054787SM-9QMORCD Female
SA054788SM-6ZKY3CD Female
SA054789SM-B2OQ7CD Female
SA054790SM-6WJN1CD Female
SA054791SM-6X9WACD Female
SA054792SM-6SSMYCD Female
SA054793SM-6SF6TCD Female
SA054794SM-6MYZ2CD Female
SA054795SM-6OLSCCD Female
SA054796SM-6X9WMCD Female
SA054797SM-6X9WUCD Female
SA054798SM-6XTSQCD Female
SA054799SM-6XTSUCD Female
SA054800SM-6XRKGCD Female
SA054801SM-6XJTFCD Female
SA054802SM-6XJTBCD Female
SA054803SM-6MSSOCD Female
SA054804SM-6KUCHCD Female
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Collection:

Collection ID:CO000955
Collection Summary:Stool samples were collected by subjects in tubes containing 5 ml of 100% Ethanol and shipped to collection sites. A portion of each stool sample (40-100 mg) and the entire volume of ethanol preservative were stored in 15 mL centrifuge tubes at -80 °C until all samples were collected.
Sample Type:Stool
Additives:Ethanol

Treatment:

Treatment ID:TR000975
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP000968
Sampleprep Summary:Samples were thawed on ice and then centrifuged (4 ˚C, 5,000 x g) for 5 minutes. Ethanol was evaporated using a gentle stream of nitrogen gas using a nitrogen evaporator (TurboVap LV; Biotage, Charlotte, NC) and stored at -80 ˚C until all samples in the study had been dried. Aqueous homogenates were generated by sonicating each sample in 900 μl of H2O using an ultrasonic probe homogenizer (Branson Sonifier 250) set to a duty cycle of 25% and output control of 2 for 3 minutes. Samples were kept on ice during the homogenization process. The homogenate for each sample was aliquoted into two 10 μL and two 30 μL in 1.5mL centrifuge tubes for LC-MS sample preparation and 30 μL of homogenate from each sample were transferred into a 50 mL conical tube on ice to create a pooled reference sample. The pooled reference mixture was mixed by vortexing and then aliquoted (100 μL per aliquot) into 1.5 mL centrifuge tubes. Aliquots and reference sample aliquots were stored at -80 °C until LC-MS analyses were conducted. Pairs of pooled reference samples were inserted into the queue at intervals of approximately 20 samples in order to assess analytical variance and as a reference to standardize within and across batches by “nearest neighbor” scaling.

Combined analysis:

Analysis ID AN001513 AN001514 AN001515 AN001516
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Shimadzu Nexera X2 Shimadzu Nexera X2 Shimadzu Nexera X2 Shimadzu Nexera X2
Column Atlantis HILIC (Waters; Milford,MA) Luna NH2 (Phenomenex; Torrance,CA) Waters ACQUITY UPLC BEH C18 Waters ACQUITY UPLC BEH C8 (1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE NEGATIVE NEGATIVE POSITIVE
Units abundance abundance abundance abundance

Chromatography:

Chromatography ID:CH001066
Chromatography Summary:LC-MS samples were prepared from stool homogenates (10 μL) via protein precipitation with the addition of nine volumes of 74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (valine-d8, Isotec; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants injected directly onto a 150 x 2 mm Atlantis HILIC column (Waters; Milford, MA). The column was eluted isocratically at a flow rate of 250 μL/min with 5% mobile phase A (10 mM ammonium formate and 0.1% formic acid in water) for 1 minute followed by a linear gradient to 40% mobile phase B (acetonitrile with 0.1% formic acid) over 10 minutes.
Instrument Name:Shimadzu Nexera X2
Column Name:Atlantis HILIC (Waters; Milford,MA)
Flow Gradient:The column was eluted isocratically with 5% A for 1 minute followed by a linear gradient to 40% B over 10 minutes.
Flow Rate:250 µL/min
Solvent A:100% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:HILIC
  
Chromatography ID:CH001067
Chromatography Summary:LC-MS samples were prepared from stool homogenates (30 μL) via protein precipitation with the addition of four volumes of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C) and the supernatants were injected directly onto a 150 x 2.0 mm Luna NH2 column (Phenomenex; Torrance, CA). The column was eluted at a flow rate of 400 μL/min with initial conditions of 10% mobile phase A (20 mM ammonium acetate and 20 mM ammonium hydroxide in water) and 90% mobile phase B (10 mM ammonium hydroxide in 75:25 v/v acetonitrile/methanol) followed by a 10 min linear gradient to 100% mobile phase A.
Instrument Name:Shimadzu Nexera X2
Column Name:Luna NH2 (Phenomenex; Torrance,CA)
Flow Gradient:The column was eluted with initial conditions of 10% mobile phase A and 90% mobile phase B followed by a 10 min linear gradient to 100% mobile phase A.
Flow Rate:400 µL/min
Solvent A:100% water; 20 mM ammonium acetate; mM ammonium hydroxide
Solvent B:75% acetonitrile/25% methanol; 10 mM ammonium hydroxide
Chromatography Type:HILIC
  
Chromatography ID:CH001068
Chromatography Summary:Stool homogenates (30 μL) were extracted using 90 μL of methanol containing PGE2-d4 as an internal standard (Cayman Chemical Co.; Ann Arbor, MI) and centrifuged (10 min, 9,000 x g, 4°C). The supernatants (10 μL) were injected onto a 150 x 2.1 mm ACQUITY BEH C18 column (Waters; Milford, MA). The column was eluted isocratically at a flow rate of 450 μL/min with 20% mobile phase A (0.01% formic acid in water) for 3 minutes followed by a linear gradient to 100% mobile phase B (0.01% acetic acid in acetonitrile) over 12 minutes.
Instrument Name:Shimadzu Nexera X2
Column Name:Waters ACQUITY UPLC BEH C18
Flow Gradient:The column was eluted isocratically at a flow rate of 450 µL/min with 20% A for 3 minutes followed by a linear gradient to 100% B over 12 minutes.
Flow Rate:450 µL/min
Solvent A:100% water; 0.01% formic acid
Solvent B:100% acetonitrile; 0.01% acetic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH001069
Chromatography Summary:Lipids (polar and nonpolar) were extracted from stool homogenates (10 μL) using 190 μL of isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL). After centrifugation (10 min, 9,000 x g, ambient temperature), supernatants (10 μL) were injected directly onto a 100 x 2.1 mm ACQUITY BEH C8 column (1.7 μm; Waters; Milford, MA). The column was eluted at a flow rate of 450 μL/min isocratically for 1 minute at 80% mobile phase A (95:5:0.1 vol/vol/vol 10 mM ammonium acetate/methanol/acetic acid), followed by a linear gradient to 80% mobile-phase B (99.9:0.1 vol/vol methanol/acetic acid) over 2 minutes, a linear gradient to 100% mobile phase B over 7 minutes, and then 3 minutes at 100% mobile-phase B.
Instrument Name:Shimadzu Nexera X2
Column Name:Waters ACQUITY UPLC BEH C8 (1.7um)
Flow Gradient:The column was eluted isocratically for 1 minute at 80% mobile phase A, followed by a linear gradient to 80% mobile-phase B over 2 minutes, a linear gradient to 100% mobile phase B over 7 minutes, and then 3 minutes at 100% mobile-phase B.
Flow Rate:450 µL/min
Solvent A:95% water/5% methanol; 0.1% acetic acid; 10 mM ammonium acetate
Solvent B:100% methanol; 0.1% acetic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS001396
Analysis ID:AN001513
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
Scanning Range:70-800
  
MS ID:MS001397
Analysis ID:AN001514
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
Scanning Range:60-750
  
MS ID:MS001398
Analysis ID:AN001515
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
Scanning Range:70-850
  
MS ID:MS001399
Analysis ID:AN001516
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
Scanning Range:200-1100
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