Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis/Experiment 2

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Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, LGeistlinger, Chikamso, Victoria

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

HIV/AIDS pre-exposure prophylaxis AIDS pre-exposure prophylaxis,HIV pre-exposure prophylaxis,HIV/AIDS pre-exposure prophylaxis,hIV/AIDS pre-exposure prophylaxis

Group 0 name Corresponds to the control (unexposed) group for case-control studies

HIV-negative MSM not on PrEP

Group 1 name Corresponds to the case (exposed) group for case-control studies

HIV-negative MSM on PrEP

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) on HIV pre-exposure prophylaxis (PrEP)

Group 0 sample size Number of subjects in the control (unexposed) group

37

Group 1 sample size Number of subjects in the case (exposed) group

37

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

raw counts

Statistical test

Zero-inflated negative binomial regression Statistical test: "Zero-inflated negative binomial regression" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Yes

Matched on Factors on which subjects have been matched on in a case-control study

age, alcohol drinking, drug dependence, ethnic group, nicotine dependence, obesity, anal intercourse, marijuana, race

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

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Mark reviewed

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Needs review

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): WikiWorks

Source: Figure 2, Text

Description: Pre-exposure prophylaxis use associates with differential abundance of specific bacterial genera

Abundance in Group 1: increased abundance in HIV-negative MSM on PrEP

NCBI	Quality Control	Links
Streptococcus

Revision editor(s): WikiWorks