Summary of Study ST004210

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 PR002653. The data can be accessed directly via it's Project DOI: 10.21228/M8QN9C 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.

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Study IDST004210
Study TitleStool Metabolomics Profiling in Men Who Have Sex with Men Before HIV-1 Infection
Study SummaryThis study includes Men who have Sex with Men (MSM) enrolled in the Multicenter AIDS Cohort study (MACS) between 1984-1985. All participants were HIV-1-negative during their first MACS clinic visit, when samples were collected. Metabolic profiles are compared between those who were infected with HIV-1 by their second study clinic visit approximately 6 months later (termed Pre-HIV) and those who remained HIV-negative (termed Non-HIV) at their second MACS clinic visit. Data Availability : Access to individual-level data from the MACS/WIHS Combined Cohort Study Data (MWCCS) may be obtained upon review and approval of a MWCCS concept sheet. Links and instructions for online concept sheet submission are on the study website (http://mwccs.org/). Once the concept sheet is approved, please contact Dr. Yue Chen (cheny@pitt.edu) to obtain the metadata.
Institute
National Institute of Environmental Health Sciences
Last NameFouladi
First NameFarnaz
Address111 T.W. Alexander Drive, Durham, NC 27709
Emailfarnaz.fouladi@nih.gov
Phone984-287-4663
Submit Date2025-02-28
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-10-12
Release Version1
Farnaz Fouladi Farnaz Fouladi
https://dx.doi.org/10.21228/M8QN9C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002653
Project DOI:doi: 10.21228/M8QN9C
Project Title:A taxon-specific measurement of disruption in a multi-modal study of microbiomes and metabolomes reveals system-wide dysbiosis preceding HIV-1 infection
Project Summary:The microbiome is important in immune responses and inflammation in HIV-1 infection. Hence, a deeper understanding of the microbiome prior to HIV-1 infection is potentially important for HIV-1 prevention strategies. Using stool, oral washes, and plasma biospecimens obtained from HIV-1 negative men who have sex with men (MSM), we found several differences in microbial ecologies, gene functions, and metabolites between MSM who became HIV-1 infected approximately 6 months later and those who remained HIV-1 uninfected. The HIV-1 infected MSM had an enrichment of enzymes involved in purine metabolism, lower amino acid metabolism, and higher oxidative stress before the infection. Using a novel taxon-specific measure of DISruption in COrrelations (DISCO) with various data modalities, we identified several gut and oral species with disrupted correlations prior to HIV-1 infection. Application of DISCO to external datasets revealed that Prevotella spp. are consistently disrupted in their correlations across multiple cohorts prior to or following HIV-1 infection.
Institute:National Institute of Environmental Health Sciences
Last Name:Fouladi
First Name:Farnaz
Address:111 T.W. Alexander Drive, Durham, NC 27709
Email:farnaz.fouladi@nih.gov
Phone:984-287-4663

Subject:

Subject ID:SU004362
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Sample source Group
SA485220372Stool A
SA4852215Stool A
SA4852221Stool A
SA48522312Stool A
SA48522414Stool A
SA48522518Stool A
SA48522620Stool A
SA48522724Stool A
SA485228179Stool A
SA48522921Stool A
SA48523028Stool A
SA48523132Stool A
SA485232180Stool A
SA485233181Stool A
SA485234158Stool A
SA48523534Stool A
SA48523638Stool A
SA485237284Stool A
SA485238320Stool A
SA485239285Stool A
SA485240195Stool A
SA485241289Stool A
SA48524248Stool A
SA48524347Stool A
SA485244288Stool A
SA48524549Stool A
SA485246260Stool A
SA485247198Stool A
SA485248156Stool A
SA485249356Stool A
SA485250131Stool A
SA485251117Stool A
SA485252122Stool A
SA485253123Stool A
SA485254173Stool A
SA485255177Stool A
SA485256125Stool A
SA485257178Stool A
SA485258129Stool A
SA485259247Stool A
SA485260246Stool A
SA485261130Stool A
SA485262250Stool A
SA485263136Stool A
SA485264154Stool A
SA485265253Stool A
SA485266255Stool A
SA485267134Stool A
SA485268133Stool A
SA485269139Stool A
SA485270140Stool A
SA485271257Stool A
SA485272144Stool A
SA485273143Stool A
SA485274145Stool A
SA485275152Stool A
SA485276153Stool A
SA48527753Stool A
SA48527857Stool A
SA485279170Stool A
SA485280138Stool A
SA485281172Stool A
SA485282368Stool A
SA485283369Stool A
SA485284370Stool A
SA485285126Stool A
SA485286124Stool A
SA485287371Stool A
SA485288352Stool A
SA485289251Stool A
SA485290132Stool A
SA485291256Stool A
SA485292350Stool A
SA485293354Stool A
SA485294248Stool A
SA485295142Stool A
SA485296141Stool A
SA485297146Stool A
SA485298147Stool A
SA485299148Stool A
SA485300150Stool A
SA485301149Stool A
SA485302155Stool A
SA485303160Stool A
SA485304159Stool A
SA485305157Stool A
SA485306161Stool A
SA485307351Stool A
SA485308110Stool A
SA48530965Stool A
SA48531084Stool A
SA485311361Stool A
SA485312360Stool A
SA48531370Stool A
SA48531469Stool A
SA48531574Stool A
SA48531676Stool A
SA48531778Stool A
SA485318355Stool A
SA48531981Stool A
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Collection:

Collection ID:CO004355
Collection Summary:Stool samples were collected from participants during their first Multicenter AIDS Cohort Study (MACS) clinic visit and were preserved at −80°C without additives or preservatives. Stools were sampled in 20 ml screw-capped glass vials at home and delivered to the clinic within one day by the participants. (Chen et al 2021, Microbiome)
Sample Type:Stool

Treatment:

Treatment ID:TR004371
Treatment Summary:This study includes Men who have Sex with Men (MSM) enrolled in the Multicenter AIDS Cohort study (MACS). All participants were HIV-1-negative during their first MACS clinic visit when samples were collected. This study compares gut, plasma, and oral metabolic profiles between those who became infected with HIV-1 by their second study clinic visit approximately 6 months later (termed Pre-HIV) and those who remained HIV-negative (termed Non-HIV) at their second MACS clinic visit.

Sample Preparation:

Sampleprep ID:SP004368
Sampleprep Summary:Sample were thawed on ice and weigh about 100 mg sample into tube, added with 800 μL 80% methanol. All samples were vortexed 30 s, ground 90 s at 65 Hz, followed by sonication for 30 min, 4°C. Then each sample was kept at -20°C for 1 h, vortexed for 30 s and kept at 4°C for 30 min. After that, samples were centrifuged at 12,000 rpm and 4°C for 15 min. All the supernatant was transferred to a new tube, keep at -20°C for 1 h, centrifuged at 12,000 rpm and 4°C for 15 min. Finally, 200 μL of supernatant into vial and 5 μL of 0.14 mg/mL DL-o-Chlorophenylalanine as internal standard filtered through a 0.22 μm filter for LC-MS analysis.

Chromatography:

Chromatography ID:CH005316
Instrument Name:Waters Acquity
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1 mm, 1.8 μm)
Column Temperature:40°C
Flow Gradient:0-1.0 min, 5% B; 1.0-12.5 min, 5%-95% B; 12.5-13.5 min, 95% B; 13.5-13.6 min, 95%-5% B; 13.6-16 min, 5% B
Flow Rate:0.3 mL/min
Solvent A:100% Water; 0.05% Formic acid
Solvent B:100% Acetonitrile
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN007002
Analysis Type:MS
Chromatography ID:CH005316
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST004210_AN007002_Results.txt
Units:Peak area
  
Analysis ID:AN007003
Analysis Type:MS
Chromatography ID:CH005316
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST004210_AN007003_Results.txt
Units:Peak area
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