Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Joan Chuks, Fiddyhamma

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: HIV infection , Methamphetamine dependence [X]Human immunodeficiency virus disease,[X]Human immunodeficiency virus disease (disorder),[X]Unspecified human immunodeficiency virus [HIV] disease,[X]Unspecified human immunodeficiency virus [HIV] disease (disorder),HIV - Human immunodeficiency virus infection,HIV INFECT,HIV Infection,HIV infection,HIV Infections,HIV infectious disease,HTLV III INFECT,HTLV III Infections,HTLV III LAV INFECT,HTLV III LAV Infections,HTLV WIII INFECTIONS,HTLV WIII LAV INFECTIONS,HTLV-III Infection,HTLV-III Infections,HTLV-III-LAV Infection,HTLV-III-LAV Infections,HUMAN IMMUNO VIRUS DIS,human immunodeficiency virus,Human immunodeficiency virus [HIV] disease,HUMAN IMMUNOdeficiency VIRUS [HIV] INFECTION,Human immunodeficiency virus caused disease or disorder,Human immunodeficiency virus disease,Human immunodeficiency virus disease (disorder),Human immunodeficiency virus disease or disorder,Human immunodeficiency virus infection,Human immunodeficiency virus infection (disorder),Human immunodeficiency virus infection, NOS,Human immunodeficiency virus infectious disease,human immunodeficiency virus infectious disease,Infection, HIV,Infection, HTLV-III,Infection, HTLV-III-LAV,Infections, HIV,Infections, HTLV-III,Infections, HTLV-III-LAV,LYMPHOTROPIC VIRUS TYPE III INFECTIONS HUMAN T,T LYMPHOTROPIC VIRUS TYPE III INFECT HUMAN,T Lymphotropic Virus Type III Infections, Human,T-Lymphotropic Virus Type III Infections, Human,Unspecified human immunodeficiency virus [HIV] disease (disorder),hIV infection,Amphetamine-Related Disorders,metamphetamine addiction,metamphetamine dependence,Methamphetamine dependence,methamphetamine dependence

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HIV-positive non-MA users

Group 1 name Corresponds to the case (exposed) group for case-control studies: HIV-positive MA users

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: HIV-positive Men who have sex with men (MSM) who self-reported methamphetamine (MA) use in the past six months

Group 0 sample size Number of subjects in the control (unexposed) group: 81

Group 1 sample size Number of subjects in the case (exposed) group: 101

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: Negative Binomial Regression

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.1

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, alcohol drinking, ethnic group, smoking behavior, antibiotic, cannabis use, HIV/AIDS pre-exposure prophylaxis, receptive anal intercourse frequency, antiretroviral therapy, homelessness, sexually transmitted infection, substance use, number of sex partners

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): Claregrieve1, WikiWorks

Source: Text, Supplementary Table S2, Figure 3

Description: Differential abundance of bacterial genera between HIV+ methamphetamine users and non-users

Abundance in Group 1: increased abundance in HIV-positive MA users

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Actinomyces
Mannheimia
Negativicoccus
Streptobacillus

Revision editor(s): Claregrieve1, WikiWorks

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Joan Chuks, Fiddyhamma

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Methamphetamine dependence Amphetamine-Related Disorders,metamphetamine addiction,metamphetamine dependence,Methamphetamine dependence,methamphetamine dependence

Group 0 name Corresponds to the control (unexposed) group for case-control studies: non-users

Group 1 name Corresponds to the case (exposed) group for case-control studies: Methamphetamine users

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: MSM who self-reported methamphetamine (MA) use in the past six months

Group 0 sample size Number of subjects in the control (unexposed) group: 225

Group 1 sample size Number of subjects in the case (exposed) group: 156

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, alcohol drinking, ethnic group, smoking behavior, antibiotic, cannabis use, HIV/AIDS pre-exposure prophylaxis, receptive anal intercourse frequency, homelessness, number of sex partners, sexually transmitted infection, substance use, antiretroviral therapy

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): WikiWorks

Source: Text, Supplementary Table S2

Description: Differential abundance of bacterial genera between MA users and non-users

Abundance in Group 1: increased abundance in Methamphetamine users

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Murdochiella
Haemophilus
Eubacterium
Veillonella
Dietzia
Streptococcus
Parvimonas
Finegoldia
Corynebacterium
Fusobacterium
Peptoniphilus
Porphyromonas
Peptostreptococcus
Anaerococcus
Mogibacterium

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): WikiWorks

Source: Text, Supplementary Table S2

Description: Differential abundance of bacterial genera between MA users and non-users

Abundance in Group 1: decreased abundance in Methamphetamine users

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Butyricicoccus
Faecalibacterium
Alloprevotella

Revision editor(s): WikiWorks

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Joan Chuks, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: MSM who did not test positive on MA urine drug screening

Group 1 name Corresponds to the case (exposed) group for case-control studies: MSM who tested positive on MA urine drug screening

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: MSM who tested positive for methamphetamine (MA) use in a urine drug screening

Group 0 sample size Number of subjects in the control (unexposed) group: 329

Group 1 sample size Number of subjects in the case (exposed) group: 52

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, alcohol drinking, ethnic group, smoking behavior, antibiotic, cannabis use, HIV/AIDS pre-exposure prophylaxis, receptive anal intercourse frequency, homelessness, antiretroviral therapy, substance use, sexually transmitted infection, number of sex partners

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Supplementary Figure S6, Results within text (Page 5, under subheading "Dose-response analysis of bacterial counts on increasing frequency of MA use"

Description: Sensitivity analysis using urine toxicology screening to define MA use

Abundance in Group 1: increased abundance in MSM who tested positive on MA urine drug screening

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Anaerococcus
Corynebacterium
Dietzia
Eubacterium
Finegoldia
Fusobacterium
Mogibacterium
Murdochiella
Peptoniphilus
Peptostreptococcus
Porphyromonas

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): WikiWorks

Source: Text, Supplementary Figure 4-6

Description: Sensitivity analysis using urine toxicology screening to define MA use

Abundance in Group 1: decreased abundance in MSM who tested positive on MA urine drug screening

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Faecalibacterium
Clostridium
Lactobacillus
Oligosphaera
Succinivibrio

Revision editor(s): WikiWorks

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Joan Chuks, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HIV-positive men who have sex with men who did not test positive in a methamphetamine drug screening

Group 1 name Corresponds to the case (exposed) group for case-control studies: HIV-positive men who have sex with men who tested positive in a methamphetamine drug screening

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: HIV-positive Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening

Group 0 sample size Number of subjects in the control (unexposed) group: 81

Group 1 sample size Number of subjects in the case (exposed) group: 21

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, alcohol drinking, ethnic group, smoking behavior, antibiotic, cannabis use, HIV/AIDS pre-exposure prophylaxis, receptive anal intercourse frequency, antiretroviral therapy, homelessness, number of sex partners, sexually transmitted infection, substance use

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/5

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): Claregrieve1, WikiWorks

Source: Text, Supplementary Figure 4-6

Description: Differential microbial abundance between MA+ and MA- stratified by HIV (Using urine toxicology screening to define MA use in HIV-positive MSM)

Abundance in Group 1: increased abundance in HIV-positive men who have sex with men who tested positive in a methamphetamine drug screening

NCBI	Quality Control	Links
Streptobacillus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/5

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): Claregrieve1, WikiWorks

Source: Text, Supplementary Figure 4-6

Description: Differential microbial abundance between MA+ and MA- in HIv+ patients (Using urine toxicology screening to define MA use in HIV-positive MSM)

Abundance in Group 1: decreased abundance in HIV-positive men who have sex with men who tested positive in a methamphetamine drug screening

NCBI	Quality Control	Links
Oxalobacter

Revision editor(s): Claregrieve1, WikiWorks

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Joan Chuks, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HIV-negative MSM who did not test positive in a MA drug screening

Group 1 name Corresponds to the case (exposed) group for case-control studies: HIV-negative MSM who tested positive in a MA drug screening

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: HIV-negative Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening

Group 0 sample size Number of subjects in the control (unexposed) group: 248

Group 1 sample size Number of subjects in the case (exposed) group: 31

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, alcohol drinking, ethnic group, smoking behavior, antibiotic, cannabis use, HIV/AIDS pre-exposure prophylaxis, receptive anal intercourse frequency, homelessness, number of sex partners, sexually transmitted infection, antiretroviral therapy, substance use

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/5

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

Source: Supplementary Figure S6

Description: Differential microbial abundance between MA+ and MA- in HIV- men

Abundance in Group 1: increased abundance in HIV-negative MSM who tested positive in a MA drug screening

NCBI	Quality Control	Links
Clostridium

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

Signature 2