Summary of Study ST003919
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 PR002452. The data can be accessed directly via it's Project DOI: 10.21228/M8PR93 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 | ST003919 |
| Study Title | An anaerobic pathogen operates oxidative metabolism to colonize the inflamed intestine |
| Study Type | untargeted metabolomics analysis |
| Study Summary | To colonize the densely populated large intestine and cause disease, enteric pathogens must deploy their virulence factors to establish distinct nutrient niches. While facultative anaerobes exploit inflammation-induced oxygenation to gain a competitive advantage, how obligate anaerobic pathogens construct nutrient niches for colonization remains poorly understood. Here we show that enterotoxigenic Bacteroides fragilis (ETBF) an obligate anaerobe implicated in colitis and colorectal cancer, uses its virulence factor, Bacteroides fragilis toxin (BFT), to reprogram intestinal epithelial cell metabolism. BFT activates pro-tumorigenic signaling and hijacks the host bile acid recycling pathway, inducing a metabolic shift in the epithelium from oxidative phosphorylation to glycolysis. This shift increases intestinal lactate and oxygen, nutrients that fuel ETBF’s own oxidative metabolism. These findings reveal an unexpected strategy by which an obligate anaerobe generates and exploits an oxidative niche in the inflamed gut, redefining how microbial virulence factors shape host metabolism to promote pathogen persistence. |
| Institute | Vanderbilt University |
| Department | Chemistry |
| Laboratory | Center for Innovative Technology |
| Last Name | CODREANU |
| First Name | SIMONA Gabriela |
| Address | 1234 STEVENSON CENTER LANE |
| SIMONA.CODREANU@VANDERBILT.EDU | |
| Phone | 16158758422 |
| Submit Date | 2025-05-09 |
| Num Groups | 2 |
| Total Subjects | 8 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-11-09 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002452 |
| Project DOI: | doi: 10.21228/M8PR93 |
| Project Title: | An anaerobic pathogen operates oxidative metabolism to colonize the inflamed intestine |
| Project Type: | Untargeted Metabolomics analysis |
| Project Summary: | In contrast to the facultative pathogens, ETBF is canonically classified as an obligate anaerobe that is susceptible to oxygen toxicity and reliant on anaerobic fermentation for energy production. How ETBF successfully colonizes the inflamed gut, an environment enriched in oxygen and inflammatory mediators46, has remained unclear. Here, we demonstrate that ETBF leverages its virulence factor BFT to reprogram epithelial cell metabolism, thereby reshaping the gut nutritional landscape. This reprogramming leads to increased levels of lactate and oxygen, which fuel ETBF's unique oxidative metabolism, challenging the long-standing view of B. fragilis as strictly anaerobic. Our findings uncover a novel mechanism by which an obligate anaerobe reshapes its environment to establish an oxidative metabolic niche and promote its own expansion in the inflamed gut. |
| Institute: | Vanderbilt University |
| Department: | Chemistry |
| Laboratory: | Center for Innovative Technology |
| Last Name: | CODREANU |
| First Name: | SIMONA Gabriela |
| Address: | 1234 STEVENSON CENTER LANE |
| Email: | SIMONA.CODREANU@VANDERBILT.EDU |
| Phone: | 6158758422 |
Subject:
| Subject ID: | SU004054 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Gender: | Not applicable |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | genotype |
|---|---|---|---|
| SA443865 | 8_01 | Fecal Content | Control |
| SA443866 | 8_02 | Fecal Content | Control |
| SA443867 | 8_03 | Fecal Content | Control |
| SA443868 | 8_04 | Fecal Content | Control |
| SA443869 | 9_01 | Fecal Content | Tumor |
| SA443870 | 9_02 | Fecal Content | Tumor |
| SA443871 | 9_03 | Fecal Content | Tumor |
| SA443872 | 9_04 | Fecal Content | Tumor |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO004047 |
| Collection Summary: | Notably, ETBF-infected ApcMin mice develop colonic tumors within weeks, well before small intestinal adenomas are clinically evident or detectable. Untargeted metabolomic profiling was performed on intestinal contents from ETBF-infected mice twelve weeks post-infection. |
| Collection Protocol Filename: | Fecal_Samples.pdf |
| Sample Type: | Feces |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004063 |
| Treatment Summary: | Notably, ETBF-infected ApcMin mice develop colonic tumors within weeks, well before small intestinal adenomas are clinically evident or detectable. ApcMin mice were colonized with the ETBF strains and received a single dose of tributyrin or a mock control. Samples were collected 12 weeks post-inoculation. Twelve weeks post-infection, we assessed colonic tumor incidence. These findings support a model in which ETBF-induced tumorigenesis is potentiated by its capacity to exploit oxygen and engage in oxidative metabolism, suggesting a link between microbial respiration and cancer promotion in the gut. |
| Treatment Protocol Filename: | Fecal_Samples.pdf |
| Treatment Compound: | tributyrin |
Sample Preparation:
| Sampleprep ID: | SP004060 |
| Sampleprep Summary: | Samples were stored at -80°C until analyzed via Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS and LC-HRMS/MS)-based metabolomics in the Vanderbilt Center for Innovative Technology (CIT) using previously described methods (PMID: 34068340 PMID: 27955696 PMID: 29774083). Briefly, frozen mouse intestinal content samples (n=8, 4 biological replicates for each sample groups) were lysed in 1000 µl ice-cold lysis buffer (1:1:2,v:v:v, acetonitrile: methanol: ammonium bicarbonate 0.1M - pH 8.0) and sonicated individually using a probe tip sonicator at 50% power (10 pulses). Homogenized samples were normalized by weight to the smallest amount of tissue sample to an equal amount per sample. Proteins were precipitated from individual samples by addition of 800 µL of ice-cold methanol followed by overnight incubation at -80°C. Precipitated proteins were pelleted by centrifugation (15k rpm, 15 min) and metabolite extracts were dried down in vacuo. Individual extracts were reconstituted in 100 µl of acetonitrile/water (3:97, v/v) with 0.1% formic acid containing heavy-labeled carnitine-D9, tryptophan-D3, valine-D8, and inosine-4N15, and centrifuged for 5 min at 10,000 rpm to remove insoluble material. A pooled quality control sample (QC) was prepared by pooling equal volumes of individual samples. The pooled QC sample was used for column conditioning (8 injections prior to sample analysis), retention time alignment and to assess mass spectrometry instrument reproducibility throughout the sample set and to determine sample acceptance. |
| Sampleprep Protocol Filename: | Metabolomics_Methods.pdf |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -80℃ |
Chromatography:
| Chromatography ID: | CH004883 |
| Chromatography Summary: | RPLC positive - hydrophobic compounds |
| Methods Filename: | Metabolomics_Methods.pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Hypersil GOLD aQ (100 x 2.1mm,1.9um) |
| Column Temperature: | 40 |
| Flow Gradient: | Linear gradient from 0-1 min 1% B, 1-10min 35%B, 10-15min 70%B, 15-19min 99%B, 19-25min 99%B, 25-25.5min 1%B, 25.5-30min 1%B |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; |
| Solvent B: | 80% Acetonitrile; 20% water; 0.1% formic acid; |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006435 |
| Analysis Type: | MS |
| Analysis Protocol File: | Metabolomics_Methods.pdf |
| Chromatography ID: | CH004883 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003919_AN006435_Results.txt |
| Units: | Peak intensity |
