Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function
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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.
Authors
Byrne A, Diener C, Brown BP, Maust BS, Feng C, Alinde BL, Gibbons SM, Koch M, Gray CM, Jaspan HB, Nyangahu DD
Journal
Microbiome
Year
2024
Keywords:
Gut microbiota, Inflammation, Neonates exposed to HIV but uninfected
BACKGROUND: Infants exposed to HIV but uninfected have altered immune profiles which include heightened systemic inflammation. The mechanism(s) underlying this phenomenon is unknown. Here, we investigated differences in neonatal gut bacterial and viral microbiome and associations with inflammatory biomarkers in plasma. Further, we tested whether HIV exposure impacts antibody-microbiota binding in neonatal gut and whether antibodies in breast milk impact the growth of commensal bacteria. RESULTS: Neonates exposed to HIV but uninfected (nHEU) exhibited altered gut bacteriome and virome compared to unexposed neonates (nHU). In addition, HIV exposure differentially impacted IgA-microbiota binding in neonates. The relative abundance of Blautia spp. in the whole stool or IgA-bound microbiota was positively associated with plasma concentrations of C-reactive protein. Finally, IgA from the breast milk of mothers living with HIV displayed a significantly lower ability to inhibit the growth of Blautia coccoides which was associated with inflammation in nHEU. CONCLUSION: nHEU exhibits profound alterations in gut bacterial microbiota with a mild impact on the enteric DNA virome. Elevated inflammation in nHEU could be due to a lower capacity of breast milk IgA from mothers living with HIV to limit growth the of gut bacteria associated with inflammation. Video Abstract.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2025-2-14
Subjects
- Location of subjects
- South Africa
- 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
- neonates HIV unexposed (nHU)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- neonates exposed to HIV (nHEU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- neonates exposed to HIV during pregnancy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Beta Binomial Regression
- 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
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-2-14
Source: Figure 2C
Description: Differentially abundant taxa between nHEU and nHU determined by both DESeq2 and corncob.
Abundance in Group 1: increased abundance in neonates exposed to HIV (nHEU)
Revision editor(s): Fiddyhamma, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-14
Source: Figure 2C
Description: Differentially abundant taxa between nHEU and nHU determined by both DESeq2 and corncob.
Abundance in Group 1: decreased abundance in neonates exposed to HIV (nHEU)
Revision editor(s): Fiddyhamma, WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-14
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-2-14
Source: Figure 3D
Description: Differentially abundant gut viruses between nHEU and nHU by DESeq2 and corncob.
Abundance in Group 1: increased abundance in neonates exposed to HIV (nHEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Peduovirus | ||
| Biseptimavirus | ||
| Alegriavirus |
Revision editor(s): Fiddyhamma, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-14
Source: Figure 3D
Description: Differentially abundant gut viruses between nHEU and nHU by DESeq2 and corncob.
Abundance in Group 1: decreased abundance in neonates exposed to HIV (nHEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Peeveelvirus |
Revision editor(s): Fiddyhamma, WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2025-2-14
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Increased inflammatory response Increased inflammatory response,increased inflammatory response
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Immunoglobulin A (IgA) bound fraction neonates HIV unexposed (nHU)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Immunoglobulin A (IgA) bound fraction neonates exposed to HIV (nHEU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- IgA bound fraction neonates exposed to HIV during pregnancy
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-2-14
Source: Figure 4F
Description: Differentially abundant bacterial taxa in IgA bound fraction
Abundance in Group 1: increased abundance in Immunoglobulin A (IgA) bound fraction neonates exposed to HIV (nHEU)
Revision editor(s): Fiddyhamma, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-14
Source: Fig 4E
Description: Differentially abundant bacterial taxa in IgA bound fraction
Abundance in Group 1: decreased abundance in Immunoglobulin A (IgA) bound fraction neonates exposed to HIV (nHEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces faecalis |
Revision editor(s): Fiddyhamma, WikiWorks
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