Summary of Study ST000923

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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 ( that will enable the study of associations between the gut microbiome and IBD.
Broad Institute of MIT and Harvard
Last NameAvila-Pacheco
First NameJulian
Address415 Main Street
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 application/zip

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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
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