HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome
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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
Meng J, Tao J, Abu Y, Sussman DA, Girotra M, Franceschi D, Roy S
Journal
Microbiology spectrum
Year
2023
Keywords:
16S RNA, HIV, antiretroviral therapy, human microbiome, intestinal microbiome, oral microbiome
This study characterized compositional and functional shifts in the intestinal and oral microbiome in HIV-positive patients on antiretroviral therapy compared to HIV-negative individuals. Seventy-nine specimens were collected from 5 HIV-positive and 12 control subjects from five locations (colon brush, colon wash, terminal ileum [TI] brush, TI wash, and saliva) during colonoscopy and at patient visits. Microbiome composition was characterized using 16S rRNA sequencing, and microbiome function was predicted using bioinformatics tools (PICRUSt and BugBase). Our analysis indicated that the β-diversity of all intestinal samples (colon brush, colon wash, TI brush, and TI wash) from patients with HIV was significantly different from patients without HIV. Specifically, bacteria from genera Prevotella, Fusobacterium, and Megasphaera were more abundant in samples from HIV-positive patients. On the other hand, bacteria from genera Ruminococcus, Blautia, and Clostridium were more abundant in samples from HIV-negative patients. Additionally, HIV-positive patients had higher abundances of biofilm-forming and pathogenic bacteria. Furthermore, pathways related to translation and nucleotide metabolism were elevated in HIV-positive patients, whereas pathways related to lipid and carbohydrate metabolism were positively correlated with samples from HIV-negative patients. Our analyses further showed variations in microbiome composition in HIV-positive and negative patients by sampling site. Samples from colon wash, colon brush, and TI wash were significant between groups, while samples from TI brush and saliva were not significant. Taken together, here, we report altered intestinal microbiome composition and predicted function in patients with HIV compared to uninfected patients, though we found no changes in the oral microbiome. IMPORTANCE Over 37 million people worldwide are living with HIV. Although the availability of antiretroviral therapy has significantly reduced the number of AIDS-related deaths, individuals living with HIV are at increased risk for opportunistic infections. We now know that HIV interacts with the trillions of bacteria, fungi, and viruses in the human body termed the microbiome. Only a limited number of previous studies have compared variations in the oral and gastrointestinal microbiome with HIV infection. Here, we detail how the oral and gastrointestinal microbiome changes with HIV infection, having used 5 different sampling sites to gain a more comprehensive view of these changes by location. Our results show site-specific changes in the intestinal microbiome associated with HIV infection. Additionally, we show that while there were significant changes in the intestinal microbiome, there were no significant changes in the oral microbiome.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-28
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
- Ileum , Colon Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum,Hindgut,Large bowel,Colon,colon
- 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
- Intestinal samples of Healthy Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Intestinal samples of HIV Positive Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All intestinal samples (colon brush, colon wash, terminal ileum brush, and terminal ileum wash) of HIV-positive individuals on antiretroviral therapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 30 days
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- 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 2024-5-28
Source: Fig. 1C
Description: Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between gut samples from HIV-positive compared to HIV-negative patients.
Abundance in Group 1: increased abundance in Intestinal samples of HIV Positive Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Collinsella | ||
| Eubacterium | ||
| Fusobacterium | ||
| Megasphaera | ||
| Mitsuokella | ||
| Mogibacterium | ||
| Peptostreptococcus | ||
| Phascolarctobacterium | ||
| Prevotella | ||
| Succinivibrio | ||
| Methanobrevibacter |
Revision editor(s): Eve10111, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-5-28
Source: Fig. 1C
Description: Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between gut samples from HIV-positive compared to HIV-negative patients.
Abundance in Group 1: decreased abundance in Intestinal samples of HIV Positive Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Clostridium | ||
| Ruminococcus |
Revision editor(s): Eve10111, Scholastica
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-5-28
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Colon wash samples of Healthy Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Colon wash samples of HIV Positive Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon wash samples of HIV-positive individuals on antiretroviral therapy
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-28
Source: Fig. 3C
Description: Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between colon wash samples from HIV-positive compared to HIV-negative patients.
Abundance in Group 1: increased abundance in Colon wash samples of HIV Positive Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Succinivibrio | ||
| Aggregatibacter |
Revision editor(s): Scholastica
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-5-28
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Colon brush samples of Healthy Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Colon brush samples of HIV Positive Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon brush samples of HIV-positive individuals on antiretroviral therapy
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- 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 2024-5-28
Source: Fig. 4C
Description: Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between colon brush samples from HIV-positive compared to HIV-negative patients.
Abundance in Group 1: increased abundance in Colon brush samples of HIV Positive Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera | ||
| Slackia |
Revision editor(s): Scholastica
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2024-5-28
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Terminal ileum wash samples of Healthy Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Terminal ileum wash samples of HIV Positive Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Terminal ileum (TI) wash samples of HIV-positive individuals on antiretroviral therapy
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- 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 2024-5-28
Source: Fig. 5C
Description: Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between terminal ileum (TI) samples from HIV-positive compared to HIV-negative patients.
Abundance in Group 1: increased abundance in Terminal ileum wash samples of HIV Positive Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Mogibacterium | ||
| Mitsuokella | ||
| Aggregatibacter |
Revision editor(s): Scholastica
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