#METABOLOMICS WORKBENCH NReisdorphLab_20191022_142639 DATATRACK_ID:1834 STUDY_ID:ST001268 ANALYSIS_ID:AN002105 PROJECT_ID:PR000853
VERSION             	1
CREATED_ON             	October 23, 2019, 9:39 am
#PROJECT
PR:PROJECT_TITLE                 	Integrating microbiome and metabolome data to annotate metabolite origins
PR:PROJECT_SUMMARY               	Untargeted metabolomics of host-associated samples has yielded insights into
PR:PROJECT_SUMMARY               	mechanisms by which microbes modulate health. However, data interpretation is
PR:PROJECT_SUMMARY               	challenged by the complexity of origins of the small molecules measured, which
PR:PROJECT_SUMMARY               	can come from the host, microbes that live within the host, or from other
PR:PROJECT_SUMMARY               	exposures such as diet or the environment. We address this challenge through
PR:PROJECT_SUMMARY               	development of AMON: Annotation of Metabolite Origins via Networks. AMON is an
PR:PROJECT_SUMMARY               	open-source bioinformatics application that can be used to annotate which
PR:PROJECT_SUMMARY               	compounds in the metabolome could have been produced by bacteria present or the
PR:PROJECT_SUMMARY               	host, to evaluate pathway enrichment of host verses microbial metabolites, and
PR:PROJECT_SUMMARY               	to visualize which compounds may have been produced by host versus microbial
PR:PROJECT_SUMMARY               	enzymes in KEGG pathway maps.
PR:INSTITUTE                     	University of Colorado ST:INSTITUTE                     	University of Colorado, Denver
PR:DEPARTMENT                    	Anschutz Medical Campus
PR:LAST_NAME                     	Reisdorph
PR:FIRST_NAME                    	Nichole
PR:ADDRESS                       	12850 East Montview Blvd, Aurora, CO, 80045, USA
PR:EMAIL                         	nichole.reisdorph@ucdenver.edu
PR:PHONE                         	3037249234
PR:FUNDING_SOURCE                	NIH
#STUDY
ST:STUDY_TITLE                   	Metabolome data to annotate metabolite origins
ST:STUDY_SUMMARY                 	Plasma metabolomics from HIV subjects and controls was incorporated with
ST:STUDY_SUMMARY                 	microbiome data to develop Annotation of Metabolite Origins via Networks (AMON).
ST:INSTITUTE                     	University of Colorado Denver|Anschutz Medical Campus
ST:DEPARTMENT                    	Anschutz Medical Campus
ST:LAST_NAME                     	Reisdorph
ST:FIRST_NAME                    	Nichole
ST:ADDRESS                       	12850 East Montview Blvd, Aurora, CO, 80045, USA
ST:EMAIL                         	nichole.reisdorph@ucdenver.edu
ST:PHONE                         	3037249234
ST:TOTAL_SUBJECTS                	63
#SUBJECT
SU:SUBJECT_TYPE                  	Human
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
SU:GENDER                        	Male and female
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	-	GLD001	HIV:Positive	status=Chronic; treatment=untreated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=24; sex=Male; race=White; ethnicity=hispanic; height(cm)=175; weight (kg)=74; BMI (kg/m2)=24.2; cd4_value=741; viral_load_value=2530; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD002	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=Yes; vaccine=No; MSM=Yes; receptive_anal_sex_frequency=NA; age=23; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=168; weight (kg)=55; BMI (kg/m2)=19.5; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=NA; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD003	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=54; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=162; weight (kg)=69.6; BMI (kg/m2)=26.5; cd4_value=619; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=NA; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD004	HIV:Positive	status=Chronic; treatment=untreated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=24; sex=Male; race=White; ethnicity=hispanic; height(cm)=46; weight (kg)=170; BMI (kg/m2)=15.9; cd4_value=322; viral_load_value=492; cd4_nadir=-; antibiotics_past_6_months=Yes; antibiotic_1=azithromycin 7/2014 infection; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD005	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=Female; receptive_anal_sex_frequency=NA; age=31; sex=Female; race=White; ethnicity=non-hispanic; height(cm)=177; weight (kg)=95; BMI (kg/m2)=30.3; cd4_value=831; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=Yes; antibiotic_1=clindamycin; arv_AEI=no; arv_II=no; arv_NNRTI=yes; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD006	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=Female; receptive_anal_sex_frequency=Never; age=40; sex=Female; race=White; ethnicity=hispanic; height(cm)=170; weight (kg)=81; BMI (kg/m2)=28; cd4_value=1417; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=yes; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD007	HIV:Positive	status=Chronic; treatment=untreated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=35; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=172; weight (kg)=61.9; BMI (kg/m2)=21; cd4_value=478; viral_load_value=32500; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD008	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=Yes; vaccine=No; MSM=Yes; receptive_anal_sex_frequency=NA; age=35; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=185; weight (kg)=84.4; BMI (kg/m2)=25; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD009	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=46; sex=Male; race=Black/African American; ethnicity=non-hispanic; height(cm)=176; weight (kg)=82.2; BMI (kg/m2)=26.5; cd4_value=819; viral_load_value=28; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=yes; arv_PI=yes; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD010	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=Yes; vaccine=No; MSM=Yes; receptive_anal_sex_frequency=NA; age=50; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=187.5; weight (kg)=103; BMI (kg/m2)=29; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD011	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=Yes; vaccine=Yes; MSM=Yes; receptive_anal_sex_frequency=NA; age=31; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=181; weight (kg)=82.6; BMI (kg/m2)=25.2; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD012	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=Yes; vaccine=Yes; MSM=Yes; receptive_anal_sex_frequency=NA; age=31; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=189; weight (kg)=80.9; BMI (kg/m2)=22.6; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD013	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=Yes; vaccine=Yes; MSM=Yes; receptive_anal_sex_frequency=NA; age=33; sex=Male; race=White; ethnicity=hispanic; height(cm)=173; weight (kg)=86.9; BMI (kg/m2)=29; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD014	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=Female; receptive_anal_sex_frequency=NA; age=61; sex=Female; race=White; ethnicity=non-hispanic; height(cm)=165; weight (kg)=62.5; BMI (kg/m2)=23; cd4_value=576; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=yes
SUBJECT_SAMPLE_FACTORS           	-	GLD016	HIV:Positive	status=Chronic; treatment=untreated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=33; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=183; weight (kg)=86; BMI (kg/m2)=25.7; cd4_value=403; viral_load_value=24200; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD017	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=Yes; vaccine=No; MSM=Yes; receptive_anal_sex_frequency=NA; age=39; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=184; weight (kg)=85.1; BMI (kg/m2)=25.1; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD018	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=Yes; vaccine=Yes; MSM=Yes; receptive_anal_sex_frequency=NA; age=38; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=173; weight (kg)=84.4; BMI (kg/m2)=28.2; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD019	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=48; sex=Male; race=Black/African American; ethnicity=non-hispanic; height(cm)=186; weight (kg)=80; BMI (kg/m2)=23.1; cd4_value=177; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=yes; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD020	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=54; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=172; weight (kg)=74.9; BMI (kg/m2)=25.3; cd4_value=1200; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=yes
SUBJECT_SAMPLE_FACTORS           	-	GLD021	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=59; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=166; weight (kg)=67.5; BMI (kg/m2)=24.5; cd4_value=578; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=yes; arv_PI=yes; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD022	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=56; sex=Male; race=White; ethnicity=hispanic; height(cm)=173; weight (kg)=82; BMI (kg/m2)=27.4; cd4_value=545; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=yes; arv_PI=yes; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD023	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=50; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=177; weight (kg)=71.2; BMI (kg/m2)=22.7; cd4_value=510; viral_load_value=5314; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=yes; arv_PI=yes; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD026	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=52; sex=Male; race=Black/African American; ethnicity=non-hispanic; height(cm)=181; weight (kg)=88; BMI (kg/m2)=26.9; cd4_value=838; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=yes; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD027	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=Yes; receptive_anal_sex_frequency=Never; age=50; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=179; weight (kg)=93; BMI (kg/m2)=29; cd4_value=648; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD028	HIV:Positive	status=Chronic; treatment=untreated; high_risk=HIV_pos; vaccine=No; MSM=Yes; receptive_anal_sex_frequency=Never; age=37; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=185; weight (kg)=87; BMI (kg/m2)=25.4; cd4_value=598; viral_load_value=159; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD029	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=44; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=183; weight (kg)=96.9; BMI (kg/m2)=28.9; cd4_value=1114; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=yes
SUBJECT_SAMPLE_FACTORS           	-	GLD030	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=37; sex=Male; race=White; ethnicity=hispanic; height(cm)=167; weight (kg)=71.9; BMI (kg/m2)=25.8; cd4_value=998; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=Yes; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD031	HIV:Positive	status=Chronic; treatment=untreated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=50; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=171; weight (kg)=88.4; BMI (kg/m2)=30.2; cd4_value=447; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD032	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=Yes; vaccine=No; MSM=Yes; receptive_anal_sex_frequency=NA; age=45; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=171; weight (kg)=69.4; BMI (kg/m2)=23.7; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=NA; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD036	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=47; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=182; weight (kg)=66.7; BMI (kg/m2)=20.1; cd4_value=334; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=Yes; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=yes; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD037	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=Yes; receptive_anal_sex_frequency=< 1 time per week; age=57; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=195; weight (kg)=89.9; BMI (kg/m2)=23.6; cd4_value=659; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=Yes; antibiotic_1=PCN; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD039	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=Female; receptive_anal_sex_frequency=NA; age=60; sex=Female; race=White; ethnicity=non-hispanic; height(cm)=163; weight (kg)=63.5; BMI (kg/m2)=23.9; cd4_value=924; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD040	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=45; sex=Male; race=Black/African American; ethnicity=non-hispanic; height(cm)=153; weight (kg)=56; BMI (kg/m2)=23.9; cd4_value=431; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD041	HIV:Positive	status=Chronic; treatment=untreated; high_risk=HIV_pos; vaccine=No; MSM=Yes; receptive_anal_sex_frequency=< 1 time per week; age=44; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=178; weight (kg)=63.5; BMI (kg/m2)=20; cd4_value=616; viral_load_value=518000; cd4_nadir=-; antibiotics_past_6_months=Yes; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD042	HIV:Positive	status=Chronic; treatment=untreated; high_risk=HIV_pos; vaccine=No; MSM=No; receptive_anal_sex_frequency=Never; age=51; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=180; weight (kg)=86.7; BMI (kg/m2)=26.8; cd4_value=551; viral_load_value=3880; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD043	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=Female; receptive_anal_sex_frequency=NA; age=60; sex=Female; race=White; ethnicity=hispanic; height(cm)=152; weight (kg)=72; BMI (kg/m2)=31.2; cd4_value=1058; viral_load_value=-; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=yes; arv_PI=yes; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD044	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=51; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=178; weight (kg)=83.2; BMI (kg/m2)=26.3; cd4_value=908; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD045	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=unknown; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=33; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=191; weight (kg)=96.4; BMI (kg/m2)=26.4; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD046	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=unknown; vaccine=Yes; MSM=unknown; receptive_anal_sex_frequency=NA; age=39; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=188; weight (kg)=105.5; BMI (kg/m2)=29.8; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD047	HIV:Positive	status=Chronic; treatment=untreated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=23; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=190; weight (kg)=73; BMI (kg/m2)=20.2; cd4_value=291; viral_load_value=62800; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD048	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=unknown; vaccine=Yes; MSM=unknown; receptive_anal_sex_frequency=NA; age=28; sex=Male; race=White; ethnicity=hispanic; height(cm)=174; weight (kg)=67.7; BMI (kg/m2)=22.4; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD049	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=unknown; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=48; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=177; weight (kg)=79.7; BMI (kg/m2)=25.4; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD050	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=60; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=192; weight (kg)=107.5; BMI (kg/m2)=29.2; cd4_value=950; viral_load_value=-; cd4_nadir=-; antibiotics_past_6_months=Yes; antibiotic_1=Amoxicillin; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=yes; arv_PI=yes; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD051	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=unknown; vaccine=Yes; MSM=unknown; receptive_anal_sex_frequency=NA; age=41; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=176; weight (kg)=77.1; BMI (kg/m2)=24.9; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD053	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=62; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=177; weight (kg)=68; BMI (kg/m2)=21.7; cd4_value=545; viral_load_value=-; cd4_nadir=-; antibiotics_past_6_months=Yes; antibiotic_1=Amoxicillin; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=yes; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD054	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=Female; receptive_anal_sex_frequency=NA; age=63; sex=Female; race=White; ethnicity=hispanic; height(cm)=167; weight (kg)=85; BMI (kg/m2)=30.4; cd4_value=187; viral_load_value=-; cd4_nadir=-; antibiotics_past_6_months=Yes; antibiotic_1=Bactrim; arv_AEI=yes; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD055	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=48; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=179; weight (kg)=86.6; BMI (kg/m2)=27; cd4_value=550; viral_load_value=10; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=yes; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD056	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=Yes; vaccine=No; MSM=Yes; receptive_anal_sex_frequency=NA; age=46; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=179; weight (kg)=95.9; BMI (kg/m2)=29.9; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD057	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=58; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=176; weight (kg)=72.5; BMI (kg/m2)=23.4; cd4_value=240; viral_load_value=-; cd4_nadir=-; antibiotics_past_6_months=Yes; antibiotic_1=NA; arv_AEI=yes; arv_II=no; arv_NNRTI=no; arv_NRTI=yes; arv_PI=yes; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD060	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=No; vaccine=No; MSM=Female; receptive_anal_sex_frequency=NA; age=38; sex=Female; race=Asian; ethnicity=non-hispanic; height(cm)=176; weight (kg)=96; BMI (kg/m2)=30; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD061	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=No; vaccine=No; MSM=No; receptive_anal_sex_frequency=Never; age=59; sex=Male; race=White; ethnicity=hispanic; height(cm)=173; weight (kg)=74.5; BMI (kg/m2)=24.9; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD062	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=No; vaccine=No; MSM=No; receptive_anal_sex_frequency=Never; age=33; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=178; weight (kg)=95; BMI (kg/m2)=30; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD063	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=No; vaccine=No; MSM=No; receptive_anal_sex_frequency=Never; age=37; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=188; weight (kg)=94; BMI (kg/m2)=26.6; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD065	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=No; vaccine=No; MSM=Female; receptive_anal_sex_frequency=Never; age=28; sex=Female; race=White; ethnicity=non-hispanic; height(cm)=159; weight (kg)=50.3; BMI (kg/m2)=20; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD066	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=No; vaccine=No; MSM=No; receptive_anal_sex_frequency=Never; age=22; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=166; weight (kg)=62.6; BMI (kg/m2)=22.7; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD069	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=48; sex=Male; race=Black/African American; ethnicity=non-hispanic; height(cm)=188; weight (kg)=102; BMI (kg/m2)=28.9; cd4_value=1150; viral_load_value=20; cd4_nadir=-; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=no; arv_PE=yes
SUBJECT_SAMPLE_FACTORS           	-	GLD070	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=No; vaccine=No; MSM=Female; receptive_anal_sex_frequency=Never; age=29; sex=Female; race=Other; ethnicity=hispanic; height(cm)=155; weight (kg)=54.8; BMI (kg/m2)=22.8; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD071	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=No; vaccine=No; MSM=Female; receptive_anal_sex_frequency=Never; age=26; sex=Female; race=White; ethnicity=hispanic; height(cm)=166; weight (kg)=55.7; BMI (kg/m2)=20.2; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=NA; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD072	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=62; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=176; weight (kg)=62.6; BMI (kg/m2)=20.2; cd4_value=361.53; viral_load_value=-; cd4_nadir=600; antibiotics_past_6_months=Yes; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=yes; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD073	HIV:Positive	status=Chronic; treatment=untreated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=38; sex=Male; race=Black/African American; ethnicity=non-hispanic; height(cm)=186; weight (kg)=75.1; BMI (kg/m2)=21.7; cd4_value=766.64; viral_load_value=522935; cd4_nadir=766.64; antibiotics_past_6_months=Yes; antibiotic_1=pencillin; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD074	HIV:Negative	status=Negative; treatment=HIV_neg; high_risk=No; vaccine=No; MSM=No; receptive_anal_sex_frequency=Never; age=28; sex=Male; race=White; ethnicity=hispanic; height(cm)=172; weight (kg)=87.3; BMI (kg/m2)=29.4; cd4_value=NA; viral_load_value=NA; cd4_nadir=NA; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=no; arv_NNRTI=no; arv_NRTI=no; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD079	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=63; sex=Male; race=White; ethnicity=non-hispanic; height(cm)=177.8; weight (kg)=72.8; BMI (kg/m2)=23; cd4_value=190; viral_load_value=-; cd4_nadir=13; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=yes; arv_NRTI=yes; arv_PI=no; arv_PE=no
SUBJECT_SAMPLE_FACTORS           	-	GLD080	HIV:Positive	status=Chronic; treatment=treated; high_risk=HIV_pos; vaccine=No; MSM=unknown; receptive_anal_sex_frequency=NA; age=43; sex=Male; race=White; ethnicity=hispanic; height(cm)=172.7; weight (kg)=83.5; BMI (kg/m2)=28; cd4_value=922.32; viral_load_value=-; cd4_nadir=390; antibiotics_past_6_months=No; antibiotic_1=NA; arv_AEI=no; arv_II=yes; arv_NNRTI=no; arv_NRTI=yes; arv_PI=yes; arv_PE=no
#COLLECTION
CO:COLLECTION_SUMMARY            	During a clinic visit, blood was drawn from HIV positive individuals and
CO:COLLECTION_SUMMARY            	controls as previously described as part of a larger study of differences in the
CO:COLLECTION_SUMMARY            	fecal microbiome in HIV positive and high risk populations [Caporaso JG, et al.
CO:COLLECTION_SUMMARY            	QIIME allows analysis of high-throughput community sequencing data. Nat Methods.
CO:COLLECTION_SUMMARY            	2010;7:335–6. doi:10.1038/nmeth.f.303].
CO:SAMPLE_TYPE                   	Blood (plasma)
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	Three cohorts based on HIV status: (1) HIV-1 infection untreated; (2) chronic
TR:TREATMENT_SUMMARY             	HIV-1 infection on long-term ART; (3) healthy controls (HIV-negative individuals
TR:TREATMENT_SUMMARY             	both high and low risk for contracting HIV).
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	100 µL of plasma spiked with internal standards underwent a protein crash with
SP:SAMPLEPREP_SUMMARY            	400 µL ice cold methanol. The supernatant was dried under nitrogen. Methyl
SP:SAMPLEPREP_SUMMARY            	tert-butyl ether (MTBE) and water were added to extract the hydrophobic and
SP:SAMPLEPREP_SUMMARY            	hydrophilic compounds, respectively. The upper hydrophobic layer was transferred
SP:SAMPLEPREP_SUMMARY            	to a new tube and the lower hydrophilic layer was re-extracted with MTBE. The
SP:SAMPLEPREP_SUMMARY            	upper hydrophobic layer was combined, dried under nitrogen and reconstituted in
SP:SAMPLEPREP_SUMMARY            	200 µL of methanol. The hydrophilic layer was dried under nitrogen, underwent a
SP:SAMPLEPREP_SUMMARY            	second protein crash with water and ice-cold methanol (1:4 water-methanol). The
SP:SAMPLEPREP_SUMMARY            	supernatant was removed, dried by SpeedVac at 45 °C and reconstituted in 100
SP:SAMPLEPREP_SUMMARY            	µL of 5% acetonitrile in water. Both fractions were stored at -80 °C until
SP:SAMPLEPREP_SUMMARY            	LCMS analysis.
SP:PROCESSING_STORAGE_CONDITIONS 	On ice
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Gradient was as follows: 0–1 minutes 30–70% B, 1–7.92 minutes 70–100% B,
CH:CHROMATOGRAPHY_SUMMARY        	7.92–10.4 minutes 100% B, 10.4–10.5 minutes 100–30% B, 10.5–15.1 minutes
CH:CHROMATOGRAPHY_SUMMARY        	30% B.
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Agilent 1290
CH:COLUMN_NAME                   	Agilent Zorbax RRHD SB-C18 (100 x 2.1mm, 1.8um)
CH:FLOW_RATE                     	0.7 mL/min
CH:COLUMN_TEMPERATURE            	60 °C
CH:SOLVENT_A                     	water with 0.1% formic acid
CH:SOLVENT_B                     	60:36:4 isopropyl alcohol:acetonitrile:water with 0.1% formic acid
CH:INJECTION_TEMPERATURE         	4 °C
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Agilent 6520 QTOF
MS:INSTRUMENT_TYPE               	QTOF
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	Scan range 50-1700 m/z, scan rate 2.2 spectra/sec, gas temp 300C, gas flow 12
MS:MS_COMMENTS                   	L/min, nebulizer 30 psig, Vcap 4000 V, fragmentor 120 V. Data processed with
MS:MS_COMMENTS                   	Profinder B.08 using small molecule chromatographic extraction.
MS:MS_RESULTS_FILE               	ST001268_AN002105_Results.txt	UNITS:Abundance	Has m/z:Neutral masses	Has RT:Yes	RT units:Minutes
#END