Summary of Study ST003344

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.

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	ST003344
Study Title	Fast Targeted Metabolomics for Analyzing Metabolic Diversity of Bacterial Indole Derivatives - gut bacterial cultures
Study Type	MS quantitative analysis
Study Summary	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.
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
Submit Date	2024-07-22
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-10-05
Release Version	1

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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:	SU003465
Subject Type:	Bacteria
Subject Species:	Bacteroides uniformis
Species Group:	Bacteria

Factors:

Subject type: Bacteria; Subject species: Bacteroides uniformis (Factor headings shown in green)

mb_sample_id	local_sample_id	Condition
SA364739	BUni_E3_1	Control
SA364740	BUni_D9_3	Control
SA364741	BUni_E1_2	Control
SA364742	BUni_E1_3	Control
SA364743	BUni_E2_1	Control
SA364744	BUni_E2_2	Control
SA364745	BUni_E2_3	Control
SA364746	BUni_E3_2	Control
SA364747	BUni_D9_1	Control
SA364748	BUni_E3_3	Control
SA364749	BUni_E4_1	Control
SA364750	BUni_E4_2	Control
SA364751	BUni_E4_3	Control
SA364752	BUni_E5_1	Control
SA364753	BUni_E5_2	Control
SA364754	BUni_E5_3	Control
SA364755	BUni_D9_2	Control
SA364756	BUni_D8_3	Control
SA364757	BUni_E6_2	Control
SA364758	BUni_D2_2	Control
SA364759	BUni_C9_2	Control
SA364760	BUni_C9_3	Control
SA364761	BUni_D1_1	Control
SA364762	BUni_D1_2	Control
SA364763	BUni_D1_3	Control
SA364764	BUni_D2_1	Control
SA364765	BUni_D2_3	Control
SA364766	BUni_D8_2	Control
SA364767	BUni_D3_1	Control
SA364768	BUni_D3_2	Control
SA364769	BUni_D3_3	Control
SA364770	BUni_D7_1	Control
SA364771	BUni_D7_2	Control
SA364772	BUni_D7_3	Control
SA364773	BUni_D8_1	Control
SA364774	BUni_E6_1	Control
SA364775	BUni_E6_3	Control
SA364776	BUni_C8_3	Control
SA364777	BUni_G7_1	Control
SA364778	BUni_G2_1	Control
SA364779	BUni_G2_2	Control
SA364780	BUni_G2_3	Control
SA364781	BUni_G3_1	Control
SA364782	BUni_G3_2	Control
SA364783	BUni_G3_3	Control
SA364784	BUni_G7_2	Control
SA364785	BUni_G1_2	Control
SA364786	BUni_G7_3	Control
SA364787	BUni_G8_1	Control
SA364788	BUni_G8_2	Control
SA364789	BUni_G8_3	Control
SA364790	BUni_G9_1	Control
SA364791	BUni_G9_2	Control
SA364792	BUni_G9_3	Control
SA364793	BUni_G1_3	Control
SA364794	BUni_G1_1	Control
SA364795	BUni_E7_1	Control
SA364796	BUni_E9_3	Control
SA364797	BUni_E7_2	Control
SA364798	BUni_E7_3	Control
SA364799	BUni_E8_1	Control
SA364800	BUni_E8_2	Control
SA364801	BUni_E8_3	Control
SA364802	BUni_E9_1	Control
SA364803	BUni_E9_2	Control
SA364804	BUni_F4_1	Control
SA364805	BUni_F6_3	Control
SA364806	BUni_F4_2	Control
SA364807	BUni_F4_3	Control
SA364808	BUni_F5_1	Control
SA364809	BUni_F5_2	Control
SA364810	BUni_F5_3	Control
SA364811	BUni_F6_1	Control
SA364812	BUni_F6_2	Control
SA364813	BUni_C9_1	Control
SA364814	BUni_E1_1	Control
SA364815	BUni_C8_2	Control
SA364816	BUni_B1_1	Control
SA364817	BUni_B3_2	Control
SA364818	BUni_B3_1	Control
SA364819	BUni_B2_3	Control
SA364820	BUni_B2_2	Control
SA364821	BUni_B2_1	Control
SA364822	BUni_B1_3	Control
SA364823	BUni_B1_2	Control
SA364824	BUni_A9_3	Control
SA364825	BUni_C4_1	Control
SA364826	BUni_C8_1	Control
SA364827	BUni_A9_1	Control
SA364828	BUni_A8_3	Control
SA364829	BUni_A8_2	Control
SA364830	BUni_A8_1	Control
SA364831	BUni_A7_3	Control
SA364832	BUni_A7_2	Control
SA364833	BUni_A7_1	Control
SA364834	BUni_B3_3	Control
SA364835	BUni_A9_2	Control
SA364836	BUni_C7_3	Control
SA364837	BUni_C6_3	Control
SA364838	BUni_C4_2	Control

Showing page 1 of 3 Results: 1 2 3 Next Showing results 1 to 100 of 216

Collection:

Collection ID:	CO003458
Collection Summary:	Bacterial strains were cultured from the microbiota of healthy volunteers or ME/CFS patients at Jackson Laboratory for Genomic Medicine (Farmington, CT). The derived bacteria were cultured overnight in tryptic soy broth (TSB) media or TSB media supplemented with vitamin K (0.1 mg/L) and hemin (5 mg/L) to saturation under anaerobic or aerobic conditions at 37℃, as appropriate. OD600 was used to estimate cell density, and 1 mL of cells were pelleted. The supernatant was filtered through a 0.22-µm filter to prepare cell-free culture supernatants, which were then stored at -80℃.
Sample Type:	Bacterial cells
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR003474
Treatment Summary:	No treatment.

Sample Preparation:

Sampleprep ID:	SP003472
Sampleprep Summary:	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:	CH004162
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:	AN005479
Laboratory Name:	Yao Lab
Analysis Type:	MS
Analysis Protocol File:	HT_Targeted_MS_method.pdf
Operator Name:	Huidi Tian
Detector Type:	Orbitrap
Chromatography ID:	CH004162
Num Factors:	2
Num Metabolites:	6
Units:	uM