Summary of Study ST004208

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 ID	ST004208
Study Title	Plasma Metabolomics Profiling in Men Who Have Sex with Men Before HIV-1 Infection
Study Summary	This 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 Name	Fouladi
First Name	Farnaz
Address	111 T.W. Alexander Drive, Durham, NC 27709
Email	farnaz.fouladi@nih.gov
Phone	984-287-4663
Submit Date	2025-09-17
Raw Data Available	Yes
Raw Data File Type(s)	mzML, raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2025-10-12
Release Version	1

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:	SU004360
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
SA484748	92	Plasma	A
SA484749	375	Plasma	A
SA484750	39	Plasma	A
SA484751	50	Plasma	A
SA484752	70	Plasma	A
SA484753	74	Plasma	A
SA484754	77	Plasma	A
SA484755	80	Plasma	A
SA484756	82	Plasma	A
SA484757	83	Plasma	A
SA484758	86	Plasma	A
SA484759	88	Plasma	A
SA484760	93	Plasma	A
SA484761	370	Plasma	A
SA484762	94	Plasma	A
SA484763	99	Plasma	A
SA484764	101	Plasma	A
SA484765	103	Plasma	A
SA484766	106	Plasma	A
SA484767	107	Plasma	A
SA484768	109	Plasma	A
SA484769	118	Plasma	A
SA484770	125	Plasma	A
SA484771	127	Plasma	A
SA484772	128	Plasma	A
SA484773	129	Plasma	A
SA484774	372	Plasma	A
SA484775	369	Plasma	A
SA484776	147	Plasma	A
SA484777	328	Plasma	A
SA484778	295	Plasma	A
SA484779	299	Plasma	A
SA484780	301	Plasma	A
SA484781	304	Plasma	A
SA484782	307	Plasma	A
SA484783	308	Plasma	A
SA484784	310	Plasma	A
SA484785	312	Plasma	A
SA484786	319	Plasma	A
SA484787	323	Plasma	A
SA484788	324	Plasma	A
SA484789	326	Plasma	A
SA484790	329	Plasma	A
SA484791	365	Plasma	A
SA484792	333	Plasma	A
SA484793	337	Plasma	A
SA484794	339	Plasma	A
SA484795	343	Plasma	A
SA484796	345	Plasma	A
SA484797	348	Plasma	A
SA484798	351	Plasma	A
SA484799	352	Plasma	A
SA484800	353	Plasma	A
SA484801	357	Plasma	A
SA484802	358	Plasma	A
SA484803	361	Plasma	A
SA484804	135	Plasma	A
SA484805	153	Plasma	A
SA484806	290	Plasma	A
SA484807	350	Plasma	A
SA484808	284	Plasma	A
SA484809	302	Plasma	A
SA484810	305	Plasma	A
SA484811	313	Plasma	A
SA484812	317	Plasma	A
SA484813	318	Plasma	A
SA484814	321	Plasma	A
SA484815	331	Plasma	A
SA484816	334	Plasma	A
SA484817	341	Plasma	A
SA484818	346	Plasma	A
SA484819	355	Plasma	A
SA484820	270	Plasma	A
SA484821	359	Plasma	A
SA484822	360	Plasma	A
SA484823	362	Plasma	A
SA484824	363	Plasma	A
SA484825	364	Plasma	A
SA484826	367	Plasma	A
SA484827	368	Plasma	A
SA484828	371	Plasma	A
SA484829	373	Plasma	A
SA484830	374	Plasma	A
SA484831	376	Plasma	A
SA484832	377	Plasma	A
SA484833	272	Plasma	A
SA484834	265	Plasma	A
SA484835	154	Plasma	A
SA484836	216	Plasma	A
SA484837	156	Plasma	A
SA484838	168	Plasma	A
SA484839	176	Plasma	A
SA484840	180	Plasma	A
SA484841	188	Plasma	A
SA484842	189	Plasma	A
SA484843	191	Plasma	A
SA484844	193	Plasma	A
SA484845	196	Plasma	A
SA484846	197	Plasma	A
SA484847	200	Plasma	A

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Collection:

Collection ID:	CO004353
Collection Summary:	Plasma samples obtained from participants during their first Multicenter AIDS Cohort Study (MACS) clinic visit and stored at -80 ° C (Wade et al 2015, AIDS.
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR004369
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.

Treatment ID:

TR004369

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:	SP004366
Sampleprep Summary:	Sample were thawed on ice and transfer 100 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 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.
Sampleprep Protocol Filename:	Untargeted_Metabolomics_Analysis_Report_Creative_Proteomics_CPLC02082301_370_Plasma.pdf

Chromatography:

Chromatography ID:	CH005314
Instrument Name:	Waters ACQUITY
Column Name:	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:	AN006998
Analysis Type:	MS
Chromatography ID:	CH005314
Has Mz:	1
Has Rt:	1
Rt Units:	Minutes
Results File:	ST004208_AN006998_Results.txt
Units:	Peak area

Analysis ID:	AN006999
Analysis Type:	MS
Chromatography ID:	CH005314
Has Mz:	1
Has Rt:	1
Rt Units:	Minutes
Results File:	ST004208_AN006999_Results.txt
Units:	Peak area