Summary of Study ST003346

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 PR002080. The data can be accessed directly via it's Project DOI: 10.21228/M8RJ9N This work is supported by NIH grant, U2C- DK119886.

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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.

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Study IDST003346
Study TitleFast Targeted Metabolomics for Analyzing Metabolic Diversity of Bacterial Indole Derivatives - fecal samples
Study TypeMS quantitative analysis
Study SummaryWe explored the metabolic diversity of indole derivatives as potential biomarkers for ME/CFS by analyzing fecal samples from patients and healthy controls using the fast-targeted metabolomics method. An AdaBoost-LOOCV model achieved moderate classification success. Our findings suggest that the local indole diversity of tryptophan degradation is a promising biomarker for differentiating bacterial strains and classifying ME/CFS samples. The fast-targeted metabolomics method and data analysis enable accurate and precise quantitative measurements of metabolic diversity in indole derivatives, facilitating the study of microbial contributions to ME/CFS and other immune-related conditions.
Institute
University of Connecticut
DepartmentChemistry
LaboratoryYao Lab
Last NameTian
First NameHuidi
Address55 N. Eagleville Road, Unit 3060, Storrs CT 06269
Emailhuidi.tian@uconn.edu
Phone8606341143
Submit Date2024-07-22
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-10-05
Release Version1
Huidi Tian Huidi Tian
https://dx.doi.org/10.21228/M8RJ9N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002080
Project DOI:doi: 10.21228/M8RJ9N
Project Title:Fast Targeted Metabolomics for Analyzing Metabolic Diversity of Bacterial Indole Derivatives
Project Type:Bacteria supernatant
Project Summary:Disruptions in microbial metabolite interactions due to gut microbiome dysbiosis and metabolomic shifts may contribute to Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and other immune-related conditions. The aryl hydrocarbon receptor (AhR), activated upon binding various tryptophan metabolites, modulates host immune responses. This study investigates whether the metabolic diversity—the concentration distribution—of bacterial indole pathway metabolites can differentiate bacterial strains and classify ME/CFS samples. A fast-targeted liquid chromatography-parallel reaction monitoring method with a 4-minute cycle time was developed for large-scale analysis. This method revealed significant metabolic diversity in indole derivatives among B. uniformis strains cultured from human isolates. Principal component analysis identified two major components (PC1, 68.9%; PC2, 18.7%), accounting for 87.6% of the variance and distinguishing two distinct B. uniformis clusters. The metabolic diversity between clusters was particularly evident in the contributions of indole-3-acrylate and indole-3-aldehyde. We explored the metabolic diversity of indole derivatives as potential biomarkers for ME/CFS by analyzing fecal samples from patients and healthy controls using the fast-targeted metabolomics method. An AdaBoost-LOOCV model achieved moderate classification success. Our findings suggest that the local indole diversity of tryptophan degradation is a promising biomarker for differentiating bacterial strains and classifying ME/CFS samples. The fast-targeted metabolomics method and data analysis enable accurate and precise quantitative measurements of metabolic diversity in indole derivatives, facilitating the study of microbial contributions to ME/CFS and other immune-related conditions.
Institute:University of Connecticut
Department:Chemistry
Laboratory:Yao Lab
Last Name:Tian
First Name:Huidi
Address:55 N. Eagleville Road, Unit 3060, Storrs CT 06269
Email:huidi.tian@uconn.edu
Phone:8606341143
Funding Source:NIH

Subject:

Subject ID:SU003467
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Condition
SA364989FECAL_D6_2Control
SA364990FECAL_D3_3Control
SA364991FECAL_D4_1Control
SA364992FECAL_D4_2Control
SA364993FECAL_D4_3Control
SA364994FECAL_D5_1Control
SA364995FECAL_D5_2Control
SA364996FECAL_D5_3Control
SA364997FECAL_D6_1Control
SA364998FECAL_D6_3Control
SA364999FECAL_D3_1Control
SA365000FECAL_D7_1Control
SA365001FECAL_D7_2Control
SA365002FECAL_D7_3Control
SA365003FECAL_D8_1Control
SA365004FECAL_D8_2Control
SA365005FECAL_D8_3Control
SA365006FECAL_D9_1Control
SA365007FECAL_D9_2Control
SA365008FECAL_D3_2Control
SA365009FECAL_D2_3Control
SA365010FECAL_D10_1Control
SA365011FECAL_C10_3Control
SA365012FECAL_C8_1Control
SA365013FECAL_C8_2Control
SA365014FECAL_C8_3Control
SA365015FECAL_C9_1Control
SA365016FECAL_C9_2Control
SA365017FECAL_C9_3Control
SA365018FECAL_C10_1Control
SA365019FECAL_C10_2Control
SA365020FECAL_C11_1Control
SA365021FECAL_D2_2Control
SA365022FECAL_C11_2Control
SA365023FECAL_C11_3Control
SA365024FECAL_C12_1Control
SA365025FECAL_C12_2Control
SA365026FECAL_C12_3Control
SA365027FECAL_D1_1Control
SA365028FECAL_D1_2Control
SA365029FECAL_D1_3Control
SA365030FECAL_D2_1Control
SA365031FECAL_D9_3Control
SA365032FECAL_D10_2Control
SA365033FECAL_C7_2Control
SA365034FECAL_E9_2Control
SA365035FECAL_E6_3Control
SA365036FECAL_E7_1Control
SA365037FECAL_E7_2Control
SA365038FECAL_E7_3Control
SA365039FECAL_E8_1Control
SA365040FECAL_E8_2Control
SA365041FECAL_E8_3Control
SA365042FECAL_E9_1Control
SA365043FECAL_E9_3Control
SA365044FECAL_E6_1Control
SA365045FECAL_E10_1Control
SA365046FECAL_E10_2Control
SA365047FECAL_E10_3Control
SA365048FECAL_E11_1Control
SA365049FECAL_E11_2Control
SA365050FECAL_E11_3Control
SA365051FECAL_E12_1Control
SA365052FECAL_E12_2Control
SA365053FECAL_E12_3Control
SA365054FECAL_E6_2Control
SA365055FECAL_E5_3Control
SA365056FECAL_D10_3Control
SA365057FECAL_E1_3Control
SA365058FECAL_D11_1Control
SA365059FECAL_D11_2Control
SA365060FECAL_D11_3Control
SA365061FECAL_D12_1Control
SA365062FECAL_D12_2Control
SA365063FECAL_D12_3Control
SA365064FECAL_E1_1Control
SA365065FECAL_E1_2Control
SA365066FECAL_E2_1Control
SA365067FECAL_E5_2Control
SA365068FECAL_E2_2Control
SA365069FECAL_E2_3Control
SA365070FECAL_E3_1Control
SA365071FECAL_E3_2Control
SA365072FECAL_E3_3Control
SA365073FECAL_E4_1Control
SA365074FECAL_E4_2Control
SA365075FECAL_E4_3Control
SA365076FECAL_E5_1Control
SA365077FECAL_C7_3Control
SA365078FECAL_C7_1Control
SA365079FECAL_A1_2MECFS
SA365080FECAL_A12_1MECFS
SA365081FECAL_A9_2MECFS
SA365082FECAL_A9_3MECFS
SA365083FECAL_A10_1MECFS
SA365084FECAL_A10_2MECFS
SA365085FECAL_A10_3MECFS
SA365086FECAL_A11_1MECFS
SA365087FECAL_A11_2MECFS
SA365088FECAL_A11_3MECFS
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Collection:

Collection ID:CO003460
Collection Summary:Fecal samples from 10 healthy cohorts and 10 ME/CFS patients were lyophilized overnight. Sixty 1.5 mL centrifuge tubes were weighed and labeled. Each sample was homogenized and approximately 20 mg was aliquoted into a centrifuge tube in triplicates. The tubes were weighed again to obtain the exact mass. Ice-cold 50% methanol was added to each tube in a ratio of 600 µL extraction solvent per 25 mg fecal sample. Approximately ten 2 mm zirconium beads were added to each tube, and the samples were homogenized for 10 minutes at 30 Hz. The resulting solutions were centrifuged at 12,000 g for 10 minutes. The supernatants were filtered with a 0.22 µm filter. The resulting solution was dried by Speedvac and reconstituted in 2% acetonitrile at five times the concentration for further analysis.
Sample Type:Feces
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003476
Treatment Summary:No treatment.

Sample Preparation:

Sampleprep ID:SP003474
Sampleprep Summary:The supernatants were processed by solid phase extraction and dried for LC-MS. Solid phase extraction in plate format: High-throughput reversed-phase SPE was performed using a Targa C18 (Higgins Analytical, The Nest Group) 96-well plate format. Each well was conditioned with 200 µL of methanol three times with centrifugation at 600 × g for 2 minutes, followed by equilibration with 200 µL of water (2 minutes at 800 × g) three times. The samples were loaded into each prepared well with centrifugation at 800 × g for 2 minutes. After loading, each well was washed with 200 µL of water five times. The sample was eluted with 200 µL of 80% acetonitrile in water (v/v), and the eluates were collected in a 96-deep well plate (800 × g for 2 minutes). The resulting solution was dried and reconstituted with 2% acetonitrile for further analysis.
Processing Storage Conditions:4℃
Extract Storage:-80℃

Chromatography:

Chromatography ID:CH004164
Chromatography Summary:Targeted quantitation of selected indole compounds was performed on a quadrupole orbitrap mass spectrometer (Exploris 480, Thermo Fisher Scientific) with an H-ESI ionization source in positive ion mode. The front-end separation utilized a reversed-phase column (CORTECS UPLC T3, 2.1 x 50 mm, 1.6 μm particle size, Waters). The autosampler temperature was maintained at 4.0 °C, and the column oven temperature was set at 40.0 °C. The sample injection volume was 5 µL. The mobile phase flow rate was 1 mL/min. Solvent A was 0.1% FA in water, and solvent B was 0.1% FA in MeCN. The gradient (% for Solvent B at runtime) was as follows: 1% from -1.5 to 0 minutes for equilibration, 1% from 0 to 0.2 minutes, 65% at 1.7 minutes, 90% from 1.8 to 2.2 minutes, and 1% from 2.3 to 2.5 minutes.
Instrument Name:Thermo Vanquish
Column Name:Waters CORTECS UPLC T3 (50 x 2.1mm, 1.6um)
Column Pressure:8000 psi
Column Temperature:40
Flow Gradient:1% from -1.5 to 0 minutes for equilibration, 1% from 0 to 0.2 minutes, 65% at 1.7 minutes, 90% from 1.8 to 2.2 minutes, and 1% from 2.3 to 2.5 minutes.
Flow Rate:1 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN005481
Laboratory Name:Yao Lab
Analysis Type:MS
Analysis Protocol File:HT_Targeted_MS_method.pdf
Operator Name:Huidi Tian
Detector Type:Orbitrap
Chromatography ID:CH004164
Num Factors:2
Num Metabolites:5
Units:uM
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