Antenatal gut microbiome profiles and effect on pregnancy outcome in HIV infected and HIV uninfected women in a resource limited setting
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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
Chandiwana P, Munjoma PT, Mazhandu AJ, Li J, Baertschi I, Wyss J, Jordi SBU, Mazengera LR, Yilmaz B, Misselwitz B, Duri K
Journal
BMC microbiology
Year
2023
Keywords:
Birth weight, HIV infection, Microbiome, Microbiota, Pregnancy
BACKGROUND: Human immunodeficiency virus (HIV) severely damages the epithelial cells of the gut lining leading to an inflamed leaky gut, translocation of microbial products, and dysbiosis resulting in systemic immune activation. Also, microbiota composition and maternal gut function can be altered in pregnancy through changes in the immune system and intestinal physiology. The aim of this study was to investigate the gut microbiota in HIV-infected and HIV-uninfected pregnant women and to compare and identify the association between gut microbial composition and adverse birth outcomes. RESULTS: A total of 94 pregnant women (35 HIV-infected and 59 HIV-uninfected controls) were recruited in Harare from 4 polyclinics serving populations with relatively poor socioeconomic status. Women were of a median age of 28 years (interquartile range, IQR: 22.3-32.0) and 55% of women were 35 weeks gestational age at enrolment (median 35.0 weeks, IQR: 32.5-37.2). Microbiota profiling in these participants showed that species richness was significantly lower in the HIV-infected pregnant women compared to their HIV-uninfected peers and significant differences in β-diversity using Bray-Curtis dissimilarity were observed. In contrast, there was no significant difference in α-diversity between immune-compromised (CD4+ < 350 cells/µL) and immune-competent HIV-infected women (CD4+ ≥ 350 cells/µL) even after stratification by viral load suppression. HIV infection was significantly associated with a reduced abundance of Clostridium, Turicibacter, Ruminococcus, Parabacteroides, Bacteroides, Bifidobacterium, Treponema, Oscillospira, and Faecalibacterium and a higher abundance of Actinomyces, and Succinivibrio. Low infant birth weight (< 2500 g) was significantly associated with high abundances of the phylum Spirochaetes, the families Spirochaeteceae, Veillonellaceae, and the genus Treponema. CONCLUSION: The results reported here show that the species richness and taxonomy composition of the gut microbiota is altered in HIV-infected pregnant women, possibly reflecting intestinal dysbiosis. Some of these taxa were also associated with low infant birth weight.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-11
Subjects
- Location of subjects
- Zimbabwe
- 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
- Human immunodeficiency virus (HIV) - uninfected Pregnant women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Human immunodeficiency virus (HIV) - infected Pregnant women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Human immunodeficiency virus (HIV) - infected pregnant women who were recruited in Harare from 4 polyclinics serving populations with relatively poor socioeconomic status.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 59
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V5-V6
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- arcsine square-root
- Statistical test
- MaAsLin2
- 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
- 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
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-11
Source: Figure 3a
Description: Taxonomic differences between the gut microbiota of HIV-infected women and healthy controls.
Abundance in Group 1: increased abundance in Human immunodeficiency virus (HIV) - infected Pregnant women
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Micrococcaceae | ||
| Succinivibrio | ||
| Succinivibrionaceae |
Revision editor(s): Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-11
Source: Figure 3a
Description: Taxonomic differences between the gut microbiota of HIV-infected women and healthy controls.
Abundance in Group 1: decreased abundance in Human immunodeficiency virus (HIV) - infected Pregnant women
Revision editor(s): Tosin
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-11
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Birth weight birthweight,Birth weight,birth weight
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infants with High birthweight >2500g
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infants with Low birthweight <2500g
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infants weighing less than 2500g at birth.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 81
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-11
Source: Figure 4
Description: Microbiota abundance and birth outcome. Taxonomic differences between the gut microbiota of groups stratified by baby birth weight
Abundance in Group 1: increased abundance in Infants with Low birthweight <2500g
| NCBI | Quality Control | Links |
|---|---|---|
| Spirochaetaceae | ||
| Treponema | ||
| Veillonellaceae | ||
| Spirochaetota |
Revision editor(s): Tosin
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-12-11
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Viral load viral burden,viral titer,viral titre,Viral load,viral load
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Human immunodeficiency virus (HIV) virally suppressed pregnant women (Viral Load ≤ 1000 copies/ml)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Human immunodeficiency virus (HIV) virally un-suppressed pregnant women (Viral Load > 1000 copies/ml)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV Un-suppressed pregnant women with viral load greater than 1000 cps/ml.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-11
Source: Figure 3b
Description: Taxonomic differences between the gut microbiota of groups stratified by viral load.
Abundance in Group 1: increased abundance in Human immunodeficiency virus (HIV) virally un-suppressed pregnant women (Viral Load > 1000 copies/ml)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| unclassified Paraprevotella |
Revision editor(s): Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-11
Source: Figure 3b
Description: Taxonomic differences between the gut microbiota of groups stratified by viral load.
Abundance in Group 1: decreased abundance in Human immunodeficiency virus (HIV) virally un-suppressed pregnant women (Viral Load > 1000 copies/ml)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium |
Revision editor(s): Tosin
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