Summary of project PR001074
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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Project ID: | PR001074 |
| Project DOI: | doi: 10.21228/M8W11P |
| Project Title: | A gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism |
| Project Summary: | Gut 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 |
| Department: | Microbiology and Immunology |
| Laboratory: | Justin Sonnenburg |
| Last Name: | Van Treuren |
| First Name: | Will |
| Address: | Sherman Fairchild Building, 299 Campus Drive, Stanford CA, 94305 |
| Email: | wdwvt@stanford.edu |
| Phone: | 7209370980 |
| Contributors: | Shuo Han1,*, Will Van Treuren1,2,*, Curt R. Fischer3, 4, Bryan D. Merrill1,2, Leah Guthrie1, Brian C. DeFelice4, Lalla A. Fall3,5, Dylan Dodd1,5,^, Michael A. Fischbach4,6,^, and Justin L. Sonnenburg1,4,7,^. |
Summary of all studies in project PR001074
| Study ID | Study Title | Species | Institute | Analysis(* : Contains Untargted data) | Release Date | Version | Samples | Download(* : Contains raw data) |
|---|---|---|---|---|---|---|---|---|
| ST001671 | A gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism | Bacteria | Stanford University | MS | 2021-06-01 | 1 | 1049 | Not available |
| ST001683 | A gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism. | Mus musculus | Stanford University | MS | 2021-05-17 | 1 | 268 | Uploaded data (18.1G)* |
| ST001688 | A gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism (part-II) | Bacteria | Stanford University | MS | 2021-05-17 | 1 | 1049 | Uploaded data (69.5G)* |
