Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men/Experiment 4

From BugSigDB


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
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 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
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, 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 ControlLinks
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 ControlLinks
Oxalobacter

Revision editor(s): Claregrieve1, WikiWorks