Summary of Study ST003796
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 PR002371. The data can be accessed directly via it's Project DOI: 10.21228/M8582Z 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 | ST003796 |
| Study Title | Short-term alterations in dietary amino acids override host genetic susceptibility and reveal mechanisms of Salmonella Typhimurium small intestine colonization |
| Study Type | untargeted metabolomics analysis |
| Study Summary | Herein, we find that alterations in dietary amino acid influence the susceptibility of genetically resistant CBA/J mice to infection by S. Tm. Interestingly, increased susceptibility is not due to the overall inability of the murine host to handle infection or differences in host transcriptome. Significant reductions in microbial diversity of the small intestine impact the ability of the small intestine microbiota to prevent colonization and expansion of the pathogen. Using this model, we identified small intestine-relevant metabolic pathways necessary for S. Tm expansion, such as using Fructosyl-Asparagine, which enables expansion in the terminal ileum. |
| 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 | 6158758422 |
| Submit Date | 2025-03-17 |
| Num Groups | 3 |
| Total Subjects | 18 |
| Num Males | 9 |
| Num Females | 9 |
| Study Comments | Significant reductions in microbial diversity of the small intestine impact the ability of the small intestine microbiota to prevent colonization and expansion of the pathogen. |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-09-17 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002371 |
| Project DOI: | doi: 10.21228/M8582Z |
| Project Title: | Short-term alterations in dietary amino acids override host genetic susceptibility and reveal mechanisms of Salmonella Typhimurium small intestine colonization |
| Project Type: | Untargeted Metabolomics analysis |
| Project Summary: | In addition to individual genetics, environmental factors, i.e., short-term dietary changes, may influence host susceptibility to gastrointestinal infection. Herein, we developed a model in which CBA/J mice, a genetically resistant strain that tolerates intestinal colonization by the enteric pathogen Salmonella Typhimurium (S. Tm), rapidly succumb to infectious gastroenteritis after exposure to a L-amino acids (AA) rich diet. In mice, S. Tm-gastroenteritis is restricted to the cecum (large intestine), limiting their use to understand S. Tm small intestine (ileum) colonization, a feature of human Salmonellosis. Surprisingly, CBA mice fed AA diet demonstrated enhanced S. Tm ileal colonization and mortality. Using germ-free mice and ileal-fecal slurry transplant, we found that diet-dependent S. Tm ileal colonization to be microbiota-dependent. Mechanistically, S. Tm relied on Fructosyl-asparagine utilization to expand in the ileum during infection. We demonstrate how AA-based diet overrides host genetics by altering the gut microbiota’s ability to prevent S. Tm ileal colonization. |
| 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: | SU003930 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 6-7 weeks old for all CBA/J |
| Gender: | Male and female |
| Animal Animal Supplier: | Jackson Laboratories |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Treatment |
|---|---|---|---|
| SA413069 | Diet2_AA_08 | CBA/J mice | AA Diet |
| SA413070 | Diet2_AA_12 | CBA/J mice | AA Diet |
| SA413071 | Diet2_AA_11 | CBA/J mice | AA Diet |
| SA413072 | Diet2_AA_09 | CBA/J mice | AA Diet |
| SA413073 | Diet2_AA_10 | CBA/J mice | AA Diet |
| SA413074 | Diet2_AA_07 | CBA/J mice | AA Diet |
| SA413075 | Diet2_CA_13 | CBA/J mice | Casein Diet |
| SA413076 | Diet2_CA_14 | CBA/J mice | Casein Diet |
| SA413077 | Diet2_CA_15 | CBA/J mice | Casein Diet |
| SA413078 | Diet2_CA_16 | CBA/J mice | Casein Diet |
| SA413079 | Diet2_CA_17 | CBA/J mice | Casein Diet |
| SA413080 | Diet2_CA_18 | CBA/J mice | Casein Diet |
| SA413081 | Diet2_CH_06 | CBA/J mice | Chow |
| SA413082 | Diet2_CH_05 | CBA/J mice | Chow |
| SA413083 | Diet2_CH_02 | CBA/J mice | Chow |
| SA413084 | Diet2_CH_04 | CBA/J mice | Chow |
| SA413085 | Diet2_CH_03 | CBA/J mice | Chow |
| SA413086 | Diet2_CH_01 | CBA/J mice | Chow |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO003923 |
| Collection Summary: | Both sexes were equally represented in each experimental group. Animals were randomly assigned into cages and treatment groups 3 days prior to experimentation. Unless stated otherwise, a minimum of 5 mice were used based on variability observed in previous experiments. All mice were monitored daily, and cage bedding changed every two weeks. At the end of the experiments, mice were humanely euthanized using carbon dioxide inhalation. Animals that had to be euthanized for humane reasons prior to reaching the predetermined time point were excluded from the analysis. Small intestinal content from mice was collected following a diet switch and maintenance for two days without infection (n=18, 6 per diet) prior to sacrifice, snap-frozen, and stored at -80°C. |
| Collection Protocol Filename: | Mouse_Sample_Preparation.pdf |
| Sample Type: | Feces |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003939 |
| Treatment Summary: | For the aspartate-free diet experiments, Groups (n=5) of 6-7 weeks old CBA mice were fed control diet A20073101 (Research Diets) or aspartate-free diet A20073102 (Research Diets) beginning 48h before S. Tm infection and were kept on the diets throughout the experiment. |
| Treatment Protocol Filename: | Mouse_Sample_Preparation.pdf |
Sample Preparation:
| Sampleprep ID: | SP003936 |
| Sampleprep Summary: | Frozen mouse intestinal content samples 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). Isotopically labeled standards (phenylalanine and biotin) were added to each sample to determine sample process variability as previously described ). Homogenized samples were normalized by weight to the smallest amount of tissue sample such that each sample contained an equal amount of intestinal content into a 200 µL final volume of lysate. Proteins were precipitated from individual samples by the addition of 800 µL of ice-cold methanol followed by overnight incubation at -80°C. Precipitated proteins were pelleted by centrifugation (10k rpm, 10 min) and metabolite extracts were dried down in vacuo and stored at -80°C. Samples were reconstituted in 100 µL H2O, and 100 µL MeOH with vortex mixing after each addition. Samples were incubated at room temperature for 10 min followed by liquid-liquid extraction. For liquid-liquid extraction (LLE), 800 µL MTBE was added with vortex mixing for 30 sec followed by incubation on ice for 10 min and centrifugation at 15k rpm for 15 min at 4°C. The lower (hydrophilic) fraction was transferred into a new Eppendorf tube, dried in vacuo, and stored at -80°C until further use. |
| Sampleprep Protocol Filename: | Untargeted_metabolomics.pdf |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -80℃ |
| Sample Resuspension: | Prior to mass spectrometry analysis, individual hydrophilic extracts were reconstituted in 100 µL acetonitrile/water (80:20, v/v) containing isotopically labeled standards, tryptophan, inosine, valine, and carnitine, and centrifuged for 5 min at 10,000 rpm to remove insoluble material. |
Chromatography:
| Chromatography ID: | CH004732 |
| Methods Filename: | Untargeted_metabolomics.pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters XBridge BEH Amide (100 x 2.1mm,2.5um) |
| Column Temperature: | 30℃ |
| Flow Gradient: | 30 min; 0-1 min 95%B, 1-12 min 95-45%B, 12-15 min 45%B, 15-26 min 45-95%B, 26-30 min 95%B |
| Flow Rate: | 0.20 mL/min |
| Solvent A: | 90% Water/10% Acetonitrile; 5mM Ammonium Formate, 0.1% Formic Acid |
| Solvent B: | 90% acetonitrile/10% water; 5mM Ammonium Formate, 0.1% Formic Acid |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN006241 |
| Analysis Type: | MS |
| Analysis Protocol File: | Untargeted_metabolomics.pdf |
| Chromatography ID: | CH004732 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003796_AN006241_Results.txt |
| Units: | peak intensity |
