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

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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.

Combined analysis:

Analysis ID AN007000 AN007001
Chromatography ID CH005315 CH005315
MS ID MS006697 MS006698
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters ACQUITY UPLC HSS T3 (100 x 2.1 mm,1.8 μm) Waters ACQUITY UPLC HSS T3 (100 x 2.1 mm,1.8 μm)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Focus Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

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

MS:

MS ID:MS006697
Analysis ID:AN007000
Instrument Name:Thermo Q Exactive Focus
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The electrospray ionization positive mode was operated using following conditions: heater temperature of 300°C, sheath gas flow rate of 45 arb, aux gas flow rate of 15 arb, sweep gas flow rate of 1 arb, spray voltage of 3.0 KV, capillary temperature of 350°C and S-Lens RF level set constant at 30%.The full scan was performed 70-1050 m/z at the resolution of 70,000 fwhm, automatic gain control (AGC) target of 3×106, maximum injection time of 100 ms and spectrum data type of centroid. Significant features were identified using data-dependent MS2. Settings for dd-MS2 data acquisition was as follows, resolution of 17,500 fwhm, AGC target of 1×105, maximum injection time of 50 ms, isolation window of 1.7 m/z, loop count of 10, and normalized collision energy (NCE) was set at 15, 30 and 45 eV, spectrum data type of centroid. The Compound Discoverer 3.1 (CD3.1, Thermo Fisher) software was used to process raw data generated by the UPLC-MS via peak alignment, peak picking, and identification of each metabolite. After analysis, these data were matched with the mzCloud, mzVault databases to obtain accurate identification results. The data was further processed by Progenesis QI to provide strong support for identifying metabolites accurately.
Ion Mode:POSITIVE
  
MS ID:MS006698
Analysis ID:AN007001
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The electrospray ionization positive mode was operated using following conditions: heater temperature of 300°C, sheath gas flow rate of 45 arb, aux gas flow rate of 15 arb, sweep gas flow rate of 1 arb, spray voltage of 3.2 KV, capillary temperature of 350°C and S-Lens RF level set constant at 60%.The full scan was performed 70-1050 m/z at the resolution of 70,000 fwhm, automatic gain control (AGC) target of 3×106, maximum injection time of 100 ms and spectrum data type of centroid. Significant features were identified using data-dependent MS2. Settings for dd-MS2 data acquisition was as follows, resolution of 17,500 fwhm, AGC target of 1×105, maximum injection time of 50 ms, isolation window of 1.7 m/z, loop count of 10, and normalized collision energy (NCE) was set at 15, 30 and 45 eV, spectrum data type of centroid. The Compound Discoverer 3.1 (CD3.1, Thermo Fisher) software was used to process raw data generated by the UPLC-MS via peak alignment, peak picking, and identification of each metabolite. After analysis, these data were matched with the mzCloud, mzVault databases to obtain accurate identification results. The data was further processed by Progenesis QI to provide strong support for identifying metabolites accurately.
Ion Mode:NEGATIVE
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