Alterations in the gut microbiota of patients with acquired immune deficiency 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
Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y, Nie Y
Journal
Journal of cellular and molecular medicine
Year
2018
Keywords:
acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route
Acquired immune deficiency syndrome (AIDS), caused by infection with human immunodeficiency virus (HIV), is associated with gastrointestinal disease, systemic immune activation and changes in the gut microbiota. Here, we aim to investigate the gut microbiota patterns of HIV-infected individuals and HIV-uninfected individuals in populations from South China. We enrolled 33 patients with HIV (14 participants treated with highly active antiretroviral therapy [HAART] for more than 3 months; the remaining 19 individuals had not received treatment) and 35 healthy controls (HC) for a cross-sectional comparison of gut microbiota using stool samples. Gut microbial communities were profiled by sequencing the bacterial 16S rRNA genes. Dysbiosis was more common among patients with AIDS compared with healthy individuals. Dysbiosis was characterized by decreased α-diversity, low mean counts of Bacteroidetes, Faecalibacterium, Prevotella, Bacteroides vulgatus, Dialister and Roseburia inulnivorans, and high mean counts of Proteobacteria, Enterococcus, Streptococcus, Lactobacillus, Lachnociostridium, Ruminococcus gnavus and Streptococcus vestibularis. Increased abundance of Bacilli was observed in homosexual patients. Proteobacteria were higher among heterosexual patients with HIV infections. Tenericutes were higher among patients with history of intravenous drug abuse. Restoration of gut microbiota diversity and a significant increase in abundance of Faecalibacterium, Blautia and Bacteroides were found in patients receiving HAART compared to those who did not receive. HIV infection-associated dysbiosis is characterized by decreased levels of α-diversity and Bacteroidetes, increased levels of Proteobacteria and the alterations of gut microbiota correlate with the route of HIV transmission. The imbalanced faecal microbiota of HIV infection is partially restored after therapy.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Subjects
- Location of subjects
- China
- 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
- HIV infection [X]Human immunodeficiency virus disease,[X]Human immunodeficiency virus disease (disorder),[X]Unspecified human immunodeficiency virus [HIV] disease,[X]Unspecified human immunodeficiency virus [HIV] disease (disorder),HIV - Human immunodeficiency virus infection,HIV INFECT,HIV Infection,HIV infection,HIV Infections,HIV infectious disease,HTLV III INFECT,HTLV III Infections,HTLV III LAV INFECT,HTLV III LAV Infections,HTLV WIII INFECTIONS,HTLV WIII LAV INFECTIONS,HTLV-III Infection,HTLV-III Infections,HTLV-III-LAV Infection,HTLV-III-LAV Infections,HUMAN IMMUNO VIRUS DIS,human immunodeficiency virus,Human immunodeficiency virus [HIV] disease,HUMAN IMMUNOdeficiency VIRUS [HIV] INFECTION,Human immunodeficiency virus caused disease or disorder,Human immunodeficiency virus disease,Human immunodeficiency virus disease (disorder),Human immunodeficiency virus disease or disorder,Human immunodeficiency virus infection,Human immunodeficiency virus infection (disorder),Human immunodeficiency virus infection, NOS,Human immunodeficiency virus infectious disease,human immunodeficiency virus infectious disease,Infection, HIV,Infection, HTLV-III,Infection, HTLV-III-LAV,Infections, HIV,Infections, HTLV-III,Infections, HTLV-III-LAV,LYMPHOTROPIC VIRUS TYPE III INFECTIONS HUMAN T,T LYMPHOTROPIC VIRUS TYPE III INFECT HUMAN,T Lymphotropic Virus Type III Infections, Human,T-Lymphotropic Virus Type III Infections, Human,Unspecified human immunodeficiency virus [HIV] disease (disorder),hIV infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV infected patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients infected with HIV
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
- 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
- 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).
- 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
- 3
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Source: Figure 5b
Description: Differentially abundant microbial taxa in HIV infected patients compared with healthy controls
Abundance in Group 1: increased abundance in HIV infected patients
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Source: Figure 5b
Description: Differentially abundant microbial taxa in HIV infected patients compared with healthy controls
Abundance in Group 1: decreased abundance in HIV infected patients
Revision editor(s): WikiWorks, ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV infected patients who are homosexual
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- homosexual patients infected with HIV
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Source: Figure 6b
Description: Differential microbial abundance between HIV+ patients who were infected through homosexual sex and healthy controls
Abundance in Group 1: increased abundance in HIV infected patients who are homosexual
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Enterococcaceae | ||
| Enterococcus | ||
| Thomasclavelia | ||
| Thomasclavelia ramosa | ||
| Lactobacillales |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Source: Figure 6b
Description: Differential microbial abundance between HIV+ patients who were infected through homosexual sex and healthy controls
Abundance in Group 1: decreased abundance in HIV infected patients who are homosexual
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Intravenous drug abuse HIV patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Intravenous drug abuse patients infected with HIV
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Source: Figure 6b
Description: Differential microbial abundance between HIV+ patients who were infected through intravenous drug use and healthy controls
Abundance in Group 1: increased abundance in Intravenous drug abuse HIV patients
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacterales | ||
| Enterobacteriaceae | ||
| Lachnospiraceae | ||
| Lactobacillaceae | ||
| Lactobacillus | ||
| Streptococcaceae | ||
| Streptococcus | ||
| Mediterraneibacter gnavus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- heterosexual subjects with HIV
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- homosexual subjects with HIV
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- homosexual patients infected with HIV
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Source: Figure 6d
Description: Relative abundance bacteria with significance between heterosexual and homosexual subjects
Abundance in Group 1: decreased abundance in homosexual subjects with HIV
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnoclostridium | ||
| Parabacteroides | ||
| Phascolarctobacterium | ||
| Prevotella |
Revision editor(s): WikiWorks, ChiomaBlessing
Experiment 5
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HAART-treated HIV+ patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV infected patients treated with highly active antiretroviral therapy (HAART)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Source: Figure 7c
Description: Differential microbial abundance between HIV+ patients treated with HAART and healthy controls
Abundance in Group 1: increased abundance in HAART-treated HIV+ patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis | ||
| Escherichia | ||
| Escherichia coli | ||
| Lachnoclostridium | ||
| Shigella | ||
| Streptococcaceae | ||
| Streptococcus | ||
| Mediterraneibacter gnavus | ||
| Streptococcus thermophilus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Source: Figure 7c
Description: Differential microbial abundance between HIV+ patients treated with HAART and healthy controls
Abundance in Group 1: decreased abundance in HAART-treated HIV+ patients
Revision editor(s): Claregrieve1, WikiWorks
Experiment 6
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HAART untreated
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV infected patients not treated with HAART
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3
Source: Figure 7c
Description: Differential microbial abundance between HIV+ patients who are HAART-treatment naive and healthy controls
Abundance in Group 1: increased abundance in HAART untreated
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Enterobacterales | ||
| Enterobacteriaceae | ||
| Enterococcaceae | ||
| Enterococcus | ||
| Gammaproteobacteria | ||
| Lactobacillaceae | ||
| Lactobacillales | ||
| Lactobacillus | ||
| Pseudomonadota |
Revision editor(s): Claregrieve1, WikiWorks
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