Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men/Experiment 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
- 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, 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
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 Control | Links |
|---|---|---|
| Anaerococcus | ||
| Corynebacterium | ||
| Dietzia | ||
| Eubacterium | ||
| Finegoldia | ||
| Fusobacterium | ||
| Mogibacterium | ||
| Murdochiella | ||
| Peptoniphilus | ||
| Peptostreptococcus | ||
| Porphyromonas |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
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
