#METABOLOMICS WORKBENCH NReisdorphLab_20191022_142639 DATATRACK_ID:1834 STUDY_ID:ST001268 ANALYSIS_ID:AN002107 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 elution was as follows: 0–2 minutes 100% B, 2–2.1 minutes 100–90% CH:CHROMATOGRAPHY_SUMMARY B, 2.1–8.6 minutes 90–50% B, 8.6–8.7 minutes 50–0% B, 8.7–14.7 minutes CH:CHROMATOGRAPHY_SUMMARY 0% B, 14.7–14.8 minutes 0–100% B, 14.8–24.8 minutes 100% B. CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 1290 CH:COLUMN_NAME Phenomenex Kinetex HILIC 100A (50 x 2.1 mm, 2.6um) CH:FLOW_RATE 0.6 mL/min CH:COLUMN_TEMPERATURE 20 °C CH:SOLVENT_A 50% ACN with pH 5.8 ammonium acetate CH:SOLVENT_B 90% ACN with pH 5.8 ammonium acetate CH:INJECTION_TEMPERATURE 4 °C #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6550 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Scan range 75-1700 m/z, scan rate 2.0 spectra/sec, gas temp 225C, gas flow 18 MS:MS_COMMENTS L/min, nebulizer 45 psig, Vcap 3500 V, fragmentor 360 V. Data processed with MS:MS_COMMENTS Profinder B.08 using small molecule chromatographic extraction. MS:MS_RESULTS_FILE ST001268_AN002107_Results.txt UNITS:Abundance Has m/z:Neutral masses Has RT:Yes RT units:Minutes #END