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

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: 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

Needs review

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

Needs review

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

Needs review

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

NCBI	Quality Control	Links
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

Needs review

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

Needs review

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

NCBI	Quality Control	Links
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

Needs review

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