Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection
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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
Dinh DM, Volpe GE, Duffalo C, Bhalchandra S, Tai AK, Kane AV, Wanke CA, Ward HD
Journal
The Journal of infectious diseases
Year
2015
Keywords:
HIV, dysbiosis, inflammation, microbial translocation, microbiota
BACKGROUND: Despite effective antiretroviral therapy (ART), patients with chronic human immunodeficiency virus (HIV) infection have increased microbial translocation and systemic inflammation. Alterations in the intestinal microbiota may play a role in microbial translocation and inflammation. METHODS: We profiled the fecal microbiota by pyrosequencing the gene encoding 16S ribosomal RNA (rRNA) and measured markers of microbial translocation and systemic inflammation in 21 patients who had chronic HIV infection and were receiving suppressive ART (cases) and 16 HIV-uninfected controls. RESULTS: The fecal microbial community composition was significantly different between cases and controls. The relative abundance of Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae, Erysipelotrichi, Erysipelotrichales, Erysipelotrichaceae, and Barnesiella was significantly enriched in cases, whereas that of Rikenellaceae and Alistipes was depleted. The plasma soluble CD14 level (sCD14) was significantly higher and the endotoxin core immunoglobulin M (IgM) level lower in cases, compared with controls. There were significant positive correlations between the relative abundances of Enterobacteriales and Enterobacteriaceae and the sCD14 level; the relative abundances of Gammaproteobacteria, Enterobacteriales, and Enterobacteriaceae and the interleukin 1β (IL-1β) level; the relative abundances of Enterobacteriales and Enterobacteriaceae and the interferon γ level; and the relative abundances of Erysipelotrichi and Barnesiella and the TNF-α level. There were negative correlations between endotoxin core IgM and IL-1β levels. CONCLUSIONS: Patients who have chronic HIV infection and are receiving suppressive ART display intestinal dysbiosis associated with increased microbial translocation and significant associations between specific taxa and markers of microbial translocation and systemic inflammation. This was an exploratory study, the findings of which need to be confirmed.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-10-28
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antiviral drug Response to antiviral drug,response to antiviral drug
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV-uninfected controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic HIV-infected cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with HIV infection receiving suppressive ART and had an undetectable plasma HIV RNA levels
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-10-28
Source: Figure 3A-B
Description: Differential abundance of microbiota between cases and controls using LEfSe.
Abundance in Group 1: increased abundance in Chronic HIV-infected cases
| NCBI | Quality Control | Links |
|---|---|---|
| Barnesiella | ||
| Enterobacterales | ||
| Enterobacteriaceae | ||
| Erysipelotrichaceae | ||
| Erysipelotrichales | ||
| Erysipelotrichia | ||
| Gammaproteobacteria | ||
| Pseudomonadota |
Revision editor(s): Agatha, KateRasheed
Signature 4
Reviewed Marked as Reviewed by Svetlana up on 2024-10-28
Source: Figure 3A-B
Description: Differential abundance of microbiota between cases and controls using LEfSe.
Abundance in Group 1: decreased abundance in Chronic HIV-infected cases
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Rikenellaceae |
Revision editor(s): Agatha, KateRasheed
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-10-28
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-10-28
Source: Figure 3C
Description: Differential abundance of microbiota between cases and controls using Mann-Whitney.
Abundance in Group 1: decreased abundance in Chronic HIV-infected cases
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Rikenellaceae |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-10-28
Source: Figure 3C
Description: Differential abundance of microbiota between cases and controls using Mann-Whitney.
Abundance in Group 1: increased abundance in Chronic HIV-infected cases
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Gammaproteobacteria | ||
| Enterobacteriaceae | ||
| Erysipelotrichia | ||
| Erysipelotrichales | ||
| Enterobacterales | ||
| Erysipelotrichaceae | ||
| Barnesiella |
Revision editor(s): KateRasheed
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