HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases
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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 Uniform resource identifier for web resources.
Authors
Vujkovic-Cvijin I, Sortino O, Verheij E, Sklar J, Wit FW, Kootstra NA, Sellers B, Brenchley JM, Ananworanich J, Loeff MSV, Belkaid Y, Reiss P, Sereti I
Journal
Nature communications
Year
2020
Loss of gut mucosal integrity and an aberrant gut microbiota are proposed mechanisms contributing to chronic inflammation and increased morbidity and mortality during antiretroviral-treated HIV disease. Sexual practice has recently been uncovered as a major source of microbiota variation, potentially confounding prior observations of gut microbiota alterations among persons with HIV (PWH). To overcome this and other confounding factors, we examine a well-powered subset of AGEhIV Cohort participants comprising antiretroviral-treated PWH and seronegative controls matched for age, body-mass index, sex, and sexual practice. We report significant gut microbiota differences in PWH regardless of sex and sexual practice including Gammaproteobacteria enrichment, Lachnospiraceae and Ruminococcaceae depletion, and decreased alpha diversity. Men who have sex with men (MSM) exhibit a distinct microbiota signature characterized by Prevotella enrichment and increased alpha diversity, which is linked with receptive anal intercourse in both males and females. Finally, the HIV-associated microbiota signature correlates with inflammatory markers including suPAR, nadir CD4 count, and prevalence of age-associated noncommunicable comorbidities.
Statistical test
Fisher's Exact Test Mann-Whitney (Wilcoxon) PERMANOVA
Experiment 1
Subjects
- Location of subjects
- Netherlands
- 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
- Gut wall Digestive tract wall,Wall of alimentary tract,Wall of digestive tract,Wall of gut,Gut wall
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gut microbiome measurement gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV-seronegative controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PWH
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- PWH: Persons with HIV ( PWH-F: Female PWH, PWH-MSM: Men who have sex with men PWH, PWH-MSW: None MSM group)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 71
- Group 1 sample size Number of subjects in the case (exposed) group
- 71
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina, Non-quantitative PCR
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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, sex, "body-mass index" 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 for the "Matched on" property.body-mass index
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- "sexual practices" 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 for the "Confounders controlled for" property.sexual practices
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. 1
Description: Gut microbiota composition differs between PWH and uninfected controls.
Abundance in Group 1: increased abundance in PWH
NCBI | Links |
---|---|
Desulfovibrionaceae | |
Enterobacteriaceae |
Revision editor(s): Tso ure
Signature 2
Source: Fig. 1c
Description: Gut microbiota composition differs between PWH and uninfected controls.
Abundance in Group 1: decreased abundance in PWH
NCBI | Links |
---|---|
Lachnospiraceae | |
RuminococcaceaeRuminococcaceae |
Revision editor(s): Tso ure
Signature 3
Source: Fig. 3
Description: Sexual practice exerts major impact on gut microbiota composition (MSM/MSW)
Abundance in Group 1: increased abundance in PWH
NCBI | Links |
---|---|
Coriobacteriaceae | |
Erysipelotrichaceae | |
Lachnospiraceae | |
Prevotellaceae |
Revision editor(s): Tso ure
Signature 4
Source: Fig. 3
Description: Sexual practice exerts major impact on gut microbiota composition(MSM/MSW)
Abundance in Group 1: decreased abundance in PWH
NCBI | Links |
---|---|
Bacteroides | |
Rikenellaceae | |
Akkermansia muciniphila |
Revision editor(s): Tso ure
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