Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men/Experiment 3

From BugSigDB


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): LGeistlinger, Claregrieve1, WikiWorks

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
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
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

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

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

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

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

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): WikiWorks

Source: Text, Supplementary Figure 4-6

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

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

NCBI Quality ControlLinks
Faecalibacterium
Clostridium
Lactobacillus
Oligosphaera
Succinivibrio

Revision editor(s): WikiWorks