Summary of Study ST004209

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 IDST004209
Study TitleOral 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 Date2025-09-17
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:SU004361
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
SA48498394Oral wash A
SA48498450Oral wash A
SA48498570Oral wash A
SA48498674Oral wash A
SA48498777Oral wash A
SA48498880Oral wash A
SA48498982Oral wash A
SA48499083Oral wash A
SA48499186Oral wash A
SA48499288Oral wash A
SA48499392Oral wash A
SA48499493Oral wash A
SA48499599Oral wash A
SA484996373Oral wash A
SA484997101Oral wash A
SA484998103Oral wash A
SA484999106Oral wash A
SA485000107Oral wash A
SA485001109Oral wash A
SA485002118Oral wash A
SA485003120Oral wash A
SA485004125Oral wash A
SA485005127Oral wash A
SA485006128Oral wash A
SA485007129Oral wash A
SA485008135Oral wash A
SA48500939Oral wash A
SA485010370Oral wash A
SA485011153Oral wash A
SA485012332Oral wash A
SA485013300Oral wash A
SA485014303Oral wash A
SA485015306Oral wash A
SA485016307Oral wash A
SA485017309Oral wash A
SA485018311Oral wash A
SA485019318Oral wash A
SA485020322Oral wash A
SA485021323Oral wash A
SA485022325Oral wash A
SA485023327Oral wash A
SA485024328Oral wash A
SA485025336Oral wash A
SA485026368Oral wash A
SA485027338Oral wash A
SA485028342Oral wash A
SA485029344Oral wash A
SA485030347Oral wash A
SA485031350Oral wash A
SA485032351Oral wash A
SA485033352Oral wash A
SA485034355Oral wash A
SA485035356Oral wash A
SA485036359Oral wash A
SA485037363Oral wash A
SA485038367Oral wash A
SA485039147Oral wash A
SA485040154Oral wash A
SA485041294Oral wash A
SA485042345Oral wash A
SA485043283Oral wash A
SA485044296Oral wash A
SA485045301Oral wash A
SA485046304Oral wash A
SA485047312Oral wash A
SA485048316Oral wash A
SA485049317Oral wash A
SA485050320Oral wash A
SA485051330Oral wash A
SA485052333Oral wash A
SA485053335Oral wash A
SA485054340Oral wash A
SA485055349Oral wash A
SA485056269Oral wash A
SA485057357Oral wash A
SA485058358Oral wash A
SA485059360Oral wash A
SA485060361Oral wash A
SA485061362Oral wash A
SA485062365Oral wash A
SA485063366Oral wash A
SA485064369Oral wash A
SA485065371Oral wash A
SA485066372Oral wash A
SA485067374Oral wash A
SA485068375Oral wash A
SA485069271Oral wash A
SA485070264Oral wash A
SA485071156Oral wash A
SA485072215Oral wash A
SA485073168Oral wash A
SA485074176Oral wash A
SA485075180Oral wash A
SA485076188Oral wash A
SA485077189Oral wash A
SA485078191Oral wash A
SA485079193Oral wash A
SA485080196Oral wash A
SA485081197Oral wash A
SA485082200Oral wash A
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Collection:

Collection ID:CO004354
Collection Summary:Oral wash samples obtained from participants during their first Multicenter AIDS Cohort Study (MACS) clinic visit and were preserved at −80°C without additives or preservatives(Chen et al 2021, Microbiome)
Sample Type:Saliva

Treatment:

Treatment ID:TR004370
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:SP004367
Sampleprep Summary:Sample were thawed on ice and transfer 200 μL sample into tube, added with 300 μL methanol. All samples were vortexed 30 s, and 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:CH005315
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:AN007000
Analysis Type:MS
Chromatography ID:CH005315
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST004209_AN007000_Results.txt
Units:Peak area
  
Analysis ID:AN007001
Analysis Type:MS
Chromatography ID:CH005315
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST004209_AN007001_Results.txt
Units:Peak area
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