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
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
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 | Quality Control | Links |
---|---|---|
Faecalibacterium | ||
Clostridium | ||
Lactobacillus | ||
Oligosphaera | ||
Succinivibrio |
Revision editor(s): WikiWorks