Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
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 2022/07/3
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): LGeistlinger, WikiWorks743, WikiWorks753, Claregrieve1
Subjects
- Location of subjects
- 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
- 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, cannabis use, Confounders controlled for: "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.homelessness in past six months, Confounders controlled for: "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.number of receptive anal intercourse acts in past month (RAI), Confounders controlled for: "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.number of anal sex partners in past six months, Confounders controlled for: "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.indicator for RAI in past the past seven days, Confounders controlled for: "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.indicator for a positive sexually transmitted infection (STI) test, Confounders controlled for: "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.use of antibiotics in the past month, Confounders controlled for: "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.type of anti-retroviral therapy, Confounders controlled for: "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.pre-exposure prophylaxis, Confounders controlled for: "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.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 2022/07/3
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 2022/07/3
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, LGeistlinger, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- 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
- 16S
- 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, cannabis use, Confounders controlled for: "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.homelessness in past six months, Confounders controlled for: "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.number of receptive anal intercourse acts in past month (RAI), Confounders controlled for: "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.number of anal sex partners in past six months, Confounders controlled for: "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.indicator for RAI in past the past seven days, Confounders controlled for: "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.indicator for a positive sexually transmitted infection (STI) test, Confounders controlled for: "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.use of antibiotics in the past month, Confounders controlled for: "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.type of anti-retroviral therapy, Confounders controlled for: "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.pre-exposure prophylaxis, Confounders controlled for: "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.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 2022/07/3
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
Revision editor(s): WikiWorks743
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
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 2022/07/3
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, LGeistlinger, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- 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
- 16S
- 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, cannabis use, Confounders controlled for: "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.homelessness in past six months, Confounders controlled for: "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.number of receptive anal intercourse acts in past month (RAI), Confounders controlled for: "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.number of anal sex partners in past six months, Confounders controlled for: "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.indicator for RAI in past the past seven days, Confounders controlled for: "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.indicator for a positive sexually transmitted infection (STI) test, Confounders controlled for: "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.use of antibiotics in the past month, Confounders controlled for: "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.type of anti-retroviral therapy, Confounders controlled for: "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.pre-exposure prophylaxis, Confounders controlled for: "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.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 2022/07/3
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 2022/07/3
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 2022/07/3
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): LGeistlinger, WikiWorks743, WikiWorks753, Claregrieve1
Subjects
- Location of subjects
- 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
- 16S
- 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, cannabis use, Confounders controlled for: "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.homelessness in past six months, Confounders controlled for: "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.number of receptive anal intercourse acts in past month (RAI), Confounders controlled for: "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.number of anal sex partners in past six months, Confounders controlled for: "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.indicator for RAI in past the past seven days, Confounders controlled for: "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.indicator for a positive sexually transmitted infection (STI) test, Confounders controlled for: "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.use of antibiotics in the past month, Confounders controlled for: "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.type of anti-retroviral therapy, Confounders controlled for: "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.pre-exposure prophylaxis, Confounders controlled for: "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.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 2022/07/5
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 2022/07/5
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
- 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
- 16S
- 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, cannabis use, Confounders controlled for: "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.homelessness in past six months, Confounders controlled for: "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.number of receptive anal intercourse acts in past month (RAI), Confounders controlled for: "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.number of anal sex partners in past six months, Confounders controlled for: "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.indicator for RAI in past the past seven days, Confounders controlled for: "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.indicator for a positive sexually transmitted infection (STI) test, Confounders controlled for: "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.use of antibiotics in the past month, Confounders controlled for: "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.type of anti-retroviral therapy, Confounders controlled for: "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.pre-exposure prophylaxis, Confounders controlled for: "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.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 2022/07/5
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 2022/07/5
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
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