Summary of Study ST001683
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
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.
| Study ID | ST001683 |
| Study Title | A gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism. |
| Study 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 molecules 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 & Immunology |
| Laboratory | Justin Sonnenburg |
| Last Name | Han |
| First Name | Shuo |
| Address | 299 Campus Drive, Stanford, CA, 94305-5124, USA |
| shuohan@stanford.edu | |
| Phone | - |
| Submit Date | 2021-02-06 |
| Publications | not published, status to be updated |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-05-17 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN002747 | AN002748 | AN002749 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Agilent qTOF 6545 | Agilent qTOF 6545 | Agilent qTOF 6545 |
| Column | Waters Acquity BEH (100 x 2.1mm,1.7um) | Waters Acquity BEH (100 x 2.1mm,1.7um) | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | QTOF | QTOF | QTOF |
| MS instrument name | Agilent qTOF 6545 | Agilent qTOF 6545 | Agilent qTOF 6545 |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE |
| Units | Raw ion count (peak area) | Raw ion count (peak area) | Raw ion count (peak area) |
Chromatography:
| Chromatography ID: | CH002029 |
| Chromatography Summary: | Published C18 reveres phase methods were implemented with minor modifications. The C18 positive method (ESI+) used mobile phase solvents (LC-MS grade) consisting of 0.1% formic acid (Fisher) in water (A) and 0.1% formic acid in methanol (B). The gradient profile was from 0.5% B to 70% B in 4 minutes, from 70% B to 98% B in 0.5 minutes, and holding at 98% B for 0.9 minute before returning to 0.5% B in 0.2 minutes. The flow rate was 350 µL per minute. The sample injection volume was 5 µL. LC separations were made at 40oC on separate columns fitted with a Vanguard pre-column of the same composition: Waters Acquity BEH 1.7 µm particle size, 2.1 mm id x 100 mm length (C18). Data were collected at a mass range of 70-1000 m/z at an acquisition rate of 2 spectra per second. Specific ion source parameters included Fragmentor (140V), Gas Temp (250oC), Sheath Gas Temp (200oC), and VCap (4000V). |
| Instrument Name: | Agilent qTOF 6545 |
| Column Name: | Waters Acquity BEH (100 x 2.1mm,1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0.5% B to 70% B in 4 minutes, from 70% B to 98% B in 0.5 minutes, and holding at 98% B for 0.9 minute before returning to 0.5% B in 0.2 minutes. |
| Flow Rate: | 350 µL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002030 |
| Chromatography Summary: | Published C18 reverse phase methods were implemented with minor modifications. The C18 negative method (ESI-) used mobile phase solvents (LC-MS grade) consisting of 6.5 mM ammonium bicarbonate (Sigma) in water at pH 8 (A) and 6.5 mM ammonium bicarbonate in 95:5 v/v methanol:water (B). The gradient profile was from 0.5% B to 70% B in 4 minutes, from 70% B to 98% B in 0.5 minutes, and holding at 98% B for 0.9 minute before returning to 0.5% B in 0.2 minutes. The flow rate was 350 µL per minute. The sample injection volume was 5 µL. LC separations were made at 40oC on separate columns fitted with a Vanguard pre-column of the same composition: Waters Acquity BEH 1.7 µm particle size, 2.1 mm id x 100 mm length. Data were collected at a mass range of 70-1000 m/z at an acquisition rate of 2 spectra per second. Specific ion source parameters included Fragmentor (140V), Gas Temp (250oC), Sheath Gas Temp (200oC), and VCap (4000V). |
| Instrument Name: | Agilent qTOF 6545 |
| Column Name: | Waters Acquity BEH (100 x 2.1mm,1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0.5% B to 70% B in 4 minutes, from 70% B to 98% B in 0.5 minutes, and holding at 98% B for 0.9 minute before returning to 0.5% B in 0.2 minutes. |
| Flow Rate: | 350 µL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002031 |
| Chromatography Summary: | Published HILIC method was implemented with minor modifications. The HILIC (Hydrophilic Interaction Liquid Chromatography) positive method (ESI+) used mobile phase solvents (LC-MS grade) consisting of 0.125% formic acid and 10 mM ammonium formate (Sigma) in water at pH 3 (A) and 0.125% formic acid in 10 mM ammonium formate in 95:5 v/v acetonitrile:water (B). The gradient profile was held at 100% B for 2 minutes, from 100% B to 70% B in 5 minutes, holding at 70% B for 0.7 minute, from 70% B to 40% B for 1.3 minutes, holding at 40% B for 0.5 minutes, from 40% B to 30% B for 0.75 minutes, before returning to 100% B for 2.5 minutes and holding at 100% B for 4 minutes. The flow rate was 400 µL per minute. The sample injection volume was 3 µL. LC separations were made at 40oC on separate columns fitted with a Vanguard pre-column of the same composition dedicated to each analytical method: Waters Acquity BEH Amide 1.7 µm particle size, 2.1 mm id x 150 mm length. Data were collected at a mass range of 70-1000 m/z at an acquisition rate of 2 spectra per second. Specific ion source parameters included Fragmentor (140V), Gas Temp (250oC), Sheath Gas Temp (200oC), and VCap (4000V). |
| Instrument Name: | Agilent qTOF 6545 |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | The gradient profile was held at 100% B for 2 minutes, from 100% B to 70% B in 5 minutes, holding at 70% B for 0.7 minute, from 70% B to 40% B for 1.3 minutes, holding at 40% B for 0.5 minutes, from 40% B to 30% B for 0.75 minutes, before returning to 100% B for 2.5 minutes and holding at 100% B for 4 minutes. |
| Flow Rate: | 400 µL/min |
| Solvent A: | 100% water; 0.125% formic acid; 10 mM ammonium formate, pH 3 |
| Solvent B: | 95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate |
| Chromatography Type: | HILIC |
