Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Fulcher JA, Li F, Cook RR, Zabih S, Louie A, Okochi H, Tobin NH, Gandhi M, Shoptaw S, Gorbach PM, Aldrovandi GM
Journal
Open forum infectious diseases
Year
2019
Keywords:
men who have sex with men (MSM), pre-exposure prophylaxis (PrEP), rectal microbiome
Background: Oral daily tenofovir (TFV) disoproxil fumarate/emtricitabine (TDF/FTC) for human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) is highly effective for HIVprevention, yet long-term effects are not fully understood. We investigated the effects of PrEP on the rectal microbiome in a cohort of men who have sex with men (MSM). Methods: This cross-sectional analysis included HIV-negative MSM either on PrEP (n = 37) or not (n = 37) selected from an ongoing cohort using propensity score matching. Rectal swabs were used to examine microbiome composition using 16S ribosomal ribonucleic acid gene sequencing, and associations between PrEP use and microbiota abundance were examined. Hair specimens were used to quantify TFV and FTC exposure over the past 6 weeks on a subset of participants (n = 15). Results: Pre-exposure prophylaxis use was associated with a significant increase in Streptococcus abundance (adjusted P = .015). Similar associations were identified using least absolute shrinkage and selection operator (LASSO) regression, confirming the increase in Streptococcus and also showing increased Mitsuokella, Fusobacterium, and decreased Escherichia/Shigella. Increased Fusobacterium was significantly associated with increasing TFV exposure. Conclusions: Oral TDF/FTC for PrEP is associated with rectal microbiome changes compared to well matched controls, specifically increased Streptococcus and Fusobacterium abundance. This study highlights the need for future investigations of the role of microbiome changes on HIV susceptibility and effectiveness of PrEP.
Experiment 1
Needs review
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- 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
- Statistical test
- LASSO regression Statistical test: "LASSO regression" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, ethnic group, nicotine dependence, obesity, anal intercourse, marijuana, race, Matched on: "methamphetaime dependence" 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.methamphetaime dependence, Matched on: "alcohol consumption" 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.alcohol consumption
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
Needs review
Source: Figure 1, 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 | ||
Fusobacterium | ||
Mitsuokella |
Revision editor(s): WikiWorks
Signature 2
Needs review
Source: Figure 1, Figure 2, Text
Description: Pre-exposure prophylaxis use associates with differential abundance of specific bacterial genera
Abundance in Group 1: decreased abundance in HIV-negative MSM on PrEP
NCBI | Quality Control | Links |
---|---|---|
Escherichia | ||
Shigella |
Revision editor(s): WikiWorks
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Zero-inflated negative binomial regression Statistical test: "Zero-inflated negative binomial regression" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
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
Needs review
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
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