Summary of Study ST001671

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 PR001074. The data can be accessed directly via it's Project DOI: 10.21228/M8W11P This work is supported by NIH grant, U2C- DK119886.

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Study IDST001671
Study TitleA gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism
Study SummaryGut microbes modulate host phenotypes and are associated with numerous health effects in humans, ranging from cancer immunotherapy response to metabolic disease and obesity. However, difficulty in accurate and high-throughput functional analysis of human gut microbes has hindered defining mechanistic connections between individual microbial strains and host phenotypes. One key way the gut microbiome influences host physiology is through the production of small molecules1–3, yet progress in elucidating this chemical interplay has been hindered by limited tools calibrated to detect products of anaerobic biochemistry in the gut. Here we construct a microbiome-focused, integrated mass-spectrometry pipeline to accelerate the identification of microbiota-dependent metabolites (MDMs) in diverse sample types. We report the metabolic profiles of 178 gut microbe strains using our library of 833 metabolites. Leveraging this metabolomics resource we establish deviations in the relationships between phylogeny and metabolism, use machine learning to discover novel metabolism in Bacteroides, and employ comparative genomics-based discovery of candidate biochemical pathways. MDMs can be detected in diverse body fluids in gnotobiotic and conventional mice and traced back to corresponding metabolomic profiles of cultured bacteria. Collectively, our microbiome-focused metabolomics pipeline and interactive metabolomics profile explorer are a powerful tool for characterizing microbe and microbe-host interactions.
Institute
Stanford University
DepartmentMicrobiology and Immunology
LaboratoryJustin Sonnenburg
Last NameVan Treuren
First NameWill
AddressSherman Fairchild Building, 299 Campus Drive, Stanford CA, 94305
Emailwdwvt@stanford.edu
Phone7209370980
Submit Date2021-01-20
Raw Data AvailableYes
Raw Data File Type(s)raw
Analysis Type DetailLC-MS
Release Date2021-06-01
Release Version1
Will Van Treuren Will Van Treuren
https://dx.doi.org/10.21228/M8W11P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Subject:

Subject ID:SU001748
Subject Type:Bacteria
Subject Species:Bacteria
Subject Comments:178 bacterial strains
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