Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome
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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
Monaco CL, Gootenberg DB, Zhao G, Handley SA, Ghebremichael MS, Lim ES, Lankowski A, Baldridge MT, Wilen CB, Flagg M, Norman JM, Keller BC, Luévano JM, Wang D, Boum Y, Martin JN, Hunt PW, Bangsberg DR, Siedner MJ, Kwon DS, Virgin HW
Journal
Cell host & microbe
Year
2016
Keywords:
AIDS, AIDS enteropathy, HIV, adenovirus, microbiome, systemic inflammation, virome
Human immunodeficiency virus (HIV) infection is associated with increased intestinal translocation of microbial products and enteropathy as well as alterations in gut bacterial communities. However, whether the enteric virome contributes to this infection and resulting immunodeficiency remains unknown. We characterized the enteric virome and bacterial microbiome in a cohort of Ugandan patients, including HIV-uninfected or HIV-infected subjects and those either treated with anti-retroviral therapy (ART) or untreated. Low peripheral CD4 T cell counts were associated with an expansion of enteric adenovirus sequences and this increase was independent of ART treatment. Additionally, the enteric bacterial microbiome of patients with lower CD4 T counts exhibited reduced phylogenetic diversity and richness with specific bacteria showing differential abundance, including increases in Enterobacteriaceae, which have been associated with inflammation. Thus, immunodeficiency in progressive HIV infection is associated with alterations in the enteric virome and bacterial microbiome, which may contribute to AIDS-associated enteropathy and disease progression.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-12
Subjects
- Location of subjects
- Uganda
- 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
- Human immunodeficiency virus AIDS virus,HIV,Human immunodeficiency virus,human immunodeficiency virus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV - uninfected
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CD4 T cell counts < 200 (CD4 < 200)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- CD4 T cell counts < 200 (CD4 < 200) refers to HIV infected patients who had significantly higher levels of circulating sCD14 than both HIV-negative subjects and HIV-infected subjects with CD4 > 200.
- 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
- 25
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
- DESeq2
- 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
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-12
Source: Table S5, Tab 1
Description: Differentially abundant bacterial taxa in subjects with CD4 < 200 compared to HIV-negative subjects.
Abundance in Group 1: increased abundance in CD4 T cell counts < 200 (CD4 < 200)
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-12
Source: Table S5, Tab 1
Description: Differentially abundant bacterial taxa in subjects with CD4 < 200 compared to HIV-negative subjects.
Abundance in Group 1: decreased abundance in CD4 T cell counts < 200 (CD4 < 200)
Revision editor(s): KateRasheed
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-12-12
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CD4 T cell counts >200 (CD4 > 200)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV infected patients with less than 200 CD4 T cells/mL circulating in the blood.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-12
Source: Table S5, Tab 2
Description: Differentially abundant bacterial taxa in subjects with CD4 < 200 compared to subjects with CD4 > 200.
Abundance in Group 1: increased abundance in CD4 T cell counts < 200 (CD4 < 200)
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-12
Source: Table S5, Tab 2
Description: Differentially abundant bacterial taxa in subjects with CD4 < 200 compared to subjects with CD4 > 200.
Abundance in Group 1: decreased abundance in CD4 T cell counts < 200 (CD4 < 200)
Revision editor(s): InimfonD, KateRasheed
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