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

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 3 July 2022
study design
cross-sectional observational, not case-control
Citation
PMID
URI
Authors
Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM, Gorbach PM
Journal
Scientific reports
Year
2019
Methamphetamine (MA) use is a major public health problem in the United States, especially among people living with HIV (PLWH). Many MA-induced neurotoxic effects are mediated by inflammation and gut microbiota may play a role in this process, yet the effects of MA on the microbiome have not been adequately explored. Therefore, we performed 16S rRNA gene sequencing on rectal swab samples from 381 men who have sex with men, 48% of whom were PLWH and 41% of whom used MA. We compared microbiome composition between MA users and non-users while testing for potential interactions with HIV and controlling for numerous confounders using inverse probability of treatment weighting. We found that MA use explained significant variation in overall composition (R2 = 0.005, p = 0.008) and was associated with elevated Finegoldia, Parvimonas, Peptoniphilus, and Porphyromonas and reduced Butyricicoccus and Faecalibacterium, among others. Genera including Actinomyces and Streptobacillus interacted with HIV status, such that they were increased in HIV+ MA users. Finegoldia and Peptoniphilus increased with increasing frequency of MA use, among others. In summary, MA use was associated with a microbial imbalance favoring pro-inflammatory bacteria, including some with neuroactive potential and others that have previously been associated with poor HIV outcomes.

Experiment 1


Reviewed Marked as Reviewed by Claregrieve1 on 3 July 2022

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): LGeistlinger, WikiWorks743, WikiWorks753, Claregrieve1

Subjects

Location of subjects Country from which study subjects were recruited
United States of America
Host species Species from which microbiome was sampled (if applicable)
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
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),Amphetamine-Related Disorders,metamphetamine addiction,metamphetamine 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 Experimental technique used for quantifying microbial abundance
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 Statistical test or computational tool used for differential abundance testing
"Zero-inflated negative binomial regression" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values for the "Statistical test" property.Zero-inflated 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, cannabis use, "homelessness in past six months" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.homelessness in past six months, "number of receptive anal intercourse acts in past month (RAI)" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.number of receptive anal intercourse acts in past month (RAI), "number of anal sex partners in past six months" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.number of anal sex partners in past six months, "indicator for RAI in past the past seven days" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.indicator for RAI in past the past seven days, "indicator for a positive sexually transmitted infection (STI) test" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.indicator for a positive sexually transmitted infection (STI) test, "use of antibiotics in the past month" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.use of antibiotics in the past month, "type of anti-retroviral therapy" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.type of anti-retroviral therapy, "pre-exposure prophylaxis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.pre-exposure prophylaxis, "cocaine use" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.cocaine 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 3 July 2022

Curated date: 2020-10-22

Curator: Michael Lutete

Revision editor(s): WikiWorks743, Claregrieve1

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

NCBI Links
Actinomyces
Mannheimia
Negativicoccus
Streptobacillus

Revision editor(s): WikiWorks743, Claregrieve1

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 3 July 2022

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, LGeistlinger, WikiWorks743, Claregrieve1

Subjects

Location of subjects Country from which study subjects were recruited
United States of America
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
methamphetamine dependence Amphetamine-Related Disorders,metamphetamine addiction,metamphetamine 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

Sequencing type Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
"Zero-inflated negative binomial regression" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values for the "Statistical test" property.Zero-inflated 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, cannabis use, "homelessness in past six months" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.homelessness in past six months, "number of receptive anal intercourse acts in past month (RAI)" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.number of receptive anal intercourse acts in past month (RAI), "number of anal sex partners in past six months" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.number of anal sex partners in past six months, "indicator for RAI in past the past seven days" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.indicator for RAI in past the past seven days, "indicator for a positive sexually transmitted infection (STI) test" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.indicator for a positive sexually transmitted infection (STI) test, "use of antibiotics in the past month" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.use of antibiotics in the past month, "type of anti-retroviral therapy" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.type of anti-retroviral therapy, "pre-exposure prophylaxis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.pre-exposure prophylaxis, "cocaine use" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.cocaine 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 3 July 2022

Curated date: 2020-10-22

Curator: Michael Lutete

Revision editor(s): WikiWorks743

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

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

Revision editor(s): WikiWorks743

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 3 July 2022

Curated date: 2020-10-22

Curator: Michael Lutete

Revision editor(s): WikiWorks743

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 Links
Butyricicoccus
Faecalibacterium
Alloprevotella

Revision editor(s): WikiWorks743

Experiment 3


Reviewed Marked as Reviewed by Claregrieve1 on 3 July 2022

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, LGeistlinger, WikiWorks743, Claregrieve1

Subjects

Location of subjects Country from which study subjects were recruited
United States of America
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
methamphetamine dependence Amphetamine-Related Disorders,metamphetamine addiction,metamphetamine dependence,methamphetamine dependence
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

Sequencing type Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
"Zero-inflated negative binomial regression" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values for the "Statistical test" property.Zero-inflated 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, cannabis use, "homelessness in past six months" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.homelessness in past six months, "number of receptive anal intercourse acts in past month (RAI)" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.number of receptive anal intercourse acts in past month (RAI), "number of anal sex partners in past six months" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.number of anal sex partners in past six months, "indicator for RAI in past the past seven days" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.indicator for RAI in past the past seven days, "indicator for a positive sexually transmitted infection (STI) test" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.indicator for a positive sexually transmitted infection (STI) test, "use of antibiotics in the past month" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.use of antibiotics in the past month, "type of anti-retroviral therapy" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.type of anti-retroviral therapy, "pre-exposure prophylaxis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.pre-exposure prophylaxis, "cocaine use" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.cocaine 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 3 July 2022

Curated date: 2020-11-03

Curator: Michael Lutete

Revision editor(s): WikiWorks743

Source: Text, Supplementary Figure 4-6

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

NCBI Links
Murdochiella
Dietzia
Eubacterium
Finegoldia
Peptoniphilus
Porphyromonas
Fusobacterium
Mogibacterium
Peptostreptococcus
Corynebacterium
Anaerococcus

Revision editor(s): WikiWorks743

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 3 July 2022

Curated date: 2020-11-03

Curator: Michael Lutete

Revision editor(s): WikiWorks743

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 Links
Faecalibacterium
Clostridium
Lactobacillus
Oligosphaera
Succinivibrio

Revision editor(s): WikiWorks743

Experiment 4


Reviewed Marked as Reviewed by Claregrieve1 on 3 July 2022

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): LGeistlinger, WikiWorks743, WikiWorks753, Claregrieve1

Subjects

Location of subjects Country from which study subjects were recruited
United States of America
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
methamphetamine dependence Amphetamine-Related Disorders,metamphetamine addiction,metamphetamine dependence,methamphetamine dependence
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

Sequencing type Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
"Zero-inflated negative binomial regression" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values for the "Statistical test" property.Zero-inflated 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, cannabis use, "homelessness in past six months" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.homelessness in past six months, "number of receptive anal intercourse acts in past month (RAI)" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.number of receptive anal intercourse acts in past month (RAI), "number of anal sex partners in past six months" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.number of anal sex partners in past six months, "indicator for RAI in past the past seven days" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.indicator for RAI in past the past seven days, "indicator for a positive sexually transmitted infection (STI) test" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.indicator for a positive sexually transmitted infection (STI) test, "use of antibiotics in the past month" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.use of antibiotics in the past month, "type of anti-retroviral therapy" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.type of anti-retroviral therapy, "pre-exposure prophylaxis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.pre-exposure prophylaxis, "cocaine use" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.cocaine 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 5 July 2022

Curated date: 2020-11-03

Curator: Michael Lutete

Revision editor(s): WikiWorks743, Claregrieve1

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 Links
Streptobacillus

Revision editor(s): WikiWorks743, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 5 July 2022

Curated date: 2020-11-03

Curator: Michael Lutete

Revision editor(s): WikiWorks743, Claregrieve1

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 Links
Oxalobacter

Revision editor(s): WikiWorks743, Claregrieve1

Experiment 5


Needs review

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): LGeistlinger, WikiWorks743, WikiWorks753, Claregrieve1

Subjects

Location of subjects Country from which study subjects were recruited
United States of America
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
methamphetamine dependence Amphetamine-Related Disorders,metamphetamine addiction,metamphetamine dependence,methamphetamine dependence
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

Sequencing type Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
"Zero-inflated negative binomial regression" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values for the "Statistical test" property.Zero-inflated 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, cannabis use, "homelessness in past six months" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.homelessness in past six months, "number of receptive anal intercourse acts in past month (RAI)" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.number of receptive anal intercourse acts in past month (RAI), "number of anal sex partners in past six months" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.number of anal sex partners in past six months, "indicator for RAI in past the past seven days" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.indicator for RAI in past the past seven days, "indicator for a positive sexually transmitted infection (STI) test" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.indicator for a positive sexually transmitted infection (STI) test, "use of antibiotics in the past month" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.use of antibiotics in the past month, "type of anti-retroviral therapy" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.type of anti-retroviral therapy, "pre-exposure prophylaxis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.pre-exposure prophylaxis, "cocaine use" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Confounders controlled for" property.cocaine 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 5 July 2022

Curated date: 2020-11-03

Curator: Michael Lutete

Revision editor(s): WikiWorks743, Claregrieve1

Source: Text, Supplementary Figure 4-6

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 Links
Clostridium

Revision editor(s): WikiWorks743, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 5 July 2022

Curated date: 2020-11-03

Curator: Michael Lutete

Revision editor(s): WikiWorks743, Claregrieve1

Source: Text, Supplementary Figure 4-6

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

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

NCBI Links
Barnesiella
Granulicatella
Sneathia
Streptobacillus
Subdoligranulum

Revision editor(s): WikiWorks743, Claregrieve1