Summary of Study ST001000

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 PR000677. The data can be accessed directly via it's Project DOI: 10.21228/M85H44 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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001000
Study TitleGut microbiome structure and metabolic activity in inflammatory bowel disease
Study SummaryThe inflammatory bowel diseases (IBD), which include Crohn’s disease (CD) and ulcerative colitis (UC), are multifactorial, chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome -- the molecular interface between host and microbiota -- are less-well understood. To address this gap, we performed untargeted LC-MS metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n=155) and validation (n=65) cohorts of CD, UC, and non-IBD control subjects. Metabolomic and metagenomic profiles were broadly correlated with fecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant (DA) in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While >50% of DA metabolite features were uncharacterized, many could be assigned putative roles through metabolomic “guilt-by-association” (covariation with known metabolites). DA species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between DA species and well-characterized DA metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome-metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.
Institute
Broad Institute of MIT and Harvard
DepartmentMetabolomics Platform
Last NameAvila-Pacheco
First NameJulian
Address415 Main Street
Emailjravilap@broadinstitute.org
Phone617-714-8264
Submit Date2018-07-09
Num Groups3
Total Subjects220
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2019-04-17
Release Version1
Julian Avila-Pacheco Julian Avila-Pacheco
https://dx.doi.org/10.21228/M85H44
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Combined analysis:

Analysis ID AN001878 AN001879 AN001880 AN001881
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 Waters 150 x 2 mm Atlantis HILIC Phenomenex Luna NH2 (150 x 2.1mm,3um) Waters 150 x 2 mm ACQUITY T3 Waters Acquity BEH C8 (100 x 2.1mm,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 Orbitrap Thermo Q Exactive Orbitrap Thermo Exactive Plus Orbitrap
Ion Mode POSITIVE NEGATIVE NEGATIVE POSITIVE
Units abundance abundance abundance abundance

MS:

MS ID:MS001734
Analysis ID:AN001878
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Detailed acquisition and data processing methods available in Fransoza et al. (2019) DOI 10.1038/s41564-018-0306-4
Ion Mode:POSITIVE
  
MS ID:MS001735
Analysis ID:AN001879
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Detailed acquisition and data processing methods available in Fransoza et al. (2019) DOI 10.1038/s41564-018-0306-4
Ion Mode:NEGATIVE
  
MS ID:MS001736
Analysis ID:AN001880
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Detailed acquisition and data processing methods available in Fransoza et al. (2019) DOI 10.1038/s41564-018-0306-4
Ion Mode:NEGATIVE
  
MS ID:MS001737
Analysis ID:AN001881
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Detailed acquisition and data processing methods available in Fransoza et al. (2019) DOI 10.1038/s41564-018-0306-4
Ion Mode:POSITIVE
  logo