Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- South Africa
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- HIV mother to child transmission HIV MTCT,HIV mother to child transmission
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV-unexposed infants (HUU)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-exposed uninfected infants (HEU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- In utero-HIV exposed uninfected infants (HEU)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 78
- Group 1 sample size Number of subjects in the case (exposed) group
- 76
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Infants that did not pass the sequence quality control, those on antibiotics, and HEU infants on Bactrim after 6 weeks of birth.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2d
Description: Genera with significantly different relative abundances between HEU and HUU at 6-weeks.
Abundance in Group 1: increased abundance in HIV-exposed uninfected infants (HEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Barnesiella | ||
| Blautia | ||
| Eggerthella | ||
| Odoribacter | ||
| Sneathia | ||
| unclassified Bacillota | ||
| unclassified Oscillospiraceae |
Revision editor(s): BLESSING123
Signature 2
Source: Figure 2d
Description: Genera with significantly different relative abundances between HEU and HUU at 6-weeks.
Abundance in Group 1: decreased abundance in HIV-exposed uninfected infants (HEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Saccharibacteria genomosp. TM7-H1 | ||
| Catenibacterium | ||
| Enterobacter | ||
| Megamonas | ||
| unclassified Bacteroidota |
Revision editor(s): BLESSING123
Experiment 2
Subjects
- Group 0 sample size Number of subjects in the control (unexposed) group
- 74
- Group 1 sample size Number of subjects in the case (exposed) group
- 71
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Unexposed Infants who had been on antibiotics and HIV-exposed uninfected infants that had not been on Bactrim after 28 weeks of birth were excluded
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- antibiotic exposure
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2d
Description: Genera with significantly different relative abundances between HEU and HUU at 28-weeks.
Abundance in Group 1: increased abundance in HIV-exposed uninfected infants (HEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Epulopiscium sp. | ||
| Klebsiella | ||
| Lactococcus | ||
| Megamonas | ||
| Parasutterella | ||
| unclassified Eubacteriales |
Revision editor(s): BLESSING123
Signature 2
Source: Figure 2d
Description: Genera with significantly different relative abundances between HEU and HUU at 28-weeks.
Abundance in Group 1: decreased abundance in HIV-exposed uninfected infants (HEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Atopobium | ||
| Gardnerella | ||
| Gemella | ||
| Mobiluncus | ||
| Parvimonas | ||
| Sneathia |
Revision editor(s): BLESSING123
Signature 3
Source: Figure 2e
Description: Genera with significantly different relative abundances between HEU and HUU exclusively (Excl.) breastfed at 28 weeks of life
Abundance in Group 1: increased abundance in HIV-exposed uninfected infants (HEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Epulopiscium sp. |
Revision editor(s): BLESSING123
Signature 4
Source: Figure 2e
Description: Genera with significantly different relative abundances between HEU and HUU exclusively (Excl.) breastfed at 28 weeks of life
Abundance in Group 1: decreased abundance in HIV-exposed uninfected infants (HEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Sneathia |
Revision editor(s): BLESSING123
Signature 5
Source: Figure 2e
Description: Genera with significantly different relative abundances between HEU and HUU not exclusively (Excl.) breastfed at 28 weeks of life
Abundance in Group 1: increased abundance in HIV-exposed uninfected infants (HEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Epulopiscium sp. | ||
| Klebsiella sp. | ||
| Parasutterella sp. |
Revision editor(s): BLESSING123
Signature 6
Source: figure 2e
Description: Genera with significantly different relative abundances between HEU and HUU not exclusively (Excl.) breastfed at 28 weeks of life
Abundance in Group 1: decreased abundance in HIV-exposed uninfected infants (HEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Gardnerella | ||
| Mobiluncus | ||
| Alistipes | ||
| Catenibacterium | ||
| Dialister | ||
| Finegoldia | ||
| Gemella | ||
| Peptococcus | ||
| Peptostreptococcus | ||
| Solobacterium | ||
| Sneathia |
Revision editor(s): BLESSING123
Experiment 3
Subjects
- Group 0 sample size Number of subjects in the control (unexposed) group
- 70
- Group 1 sample size Number of subjects in the case (exposed) group
- 61
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Infants who had been on antibiotics and HIV-exposed uninfected infants that had not been on Bactrim after 62 weeks of birth were excluded
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2d
Description: Genera with significantly different relative abundances between HEU and HUU at the indicated time points (FDR P < 0.05). 62 weeks
Abundance in Group 1: decreased abundance in HIV-exposed uninfected infants (HEU)
| NCBI | Quality Control | Links |
|---|---|---|
| Proteus | ||
| unclassified Coriobacteriaceae |
Revision editor(s): BLESSING123
Experiment 4
Subjects
- 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 mothers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mothers infected with HIV
- Group 0 sample size Number of subjects in the control (unexposed) group
- 110
- Group 1 sample size Number of subjects in the case (exposed) group
- 119
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Mothers on antibiotics as at the time of delivery
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Signature 1
Source: Figure 3F
Description: Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). Delivery
Abundance in Group 1: increased abundance in HIV-infected mothers
Revision editor(s): BLESSING123
Signature 2
Source: Figure 3F
Description: Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). Delivery
Abundance in Group 1: decreased abundance in HIV-infected mothers
| NCBI | Quality Control | Links |
|---|---|---|
| Asteroleplasma | ||
| Elusimicrobium | ||
| Faecalibacterium | ||
| Haemophilus | ||
| unclassified Clostridiales Family XVII. |
Revision editor(s): BLESSING123
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-infected mothers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 65
- Group 1 sample size Number of subjects in the case (exposed) group
- 71
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3F
Description: Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). 62 weeks
Abundance in Group 1: increased abundance in HIV-infected mothers
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus | ||
| Anaerostipes | ||
| Blautia | ||
| Collinsella | ||
| Dorea | ||
| Faecalibacterium | ||
| Flavonifractor | ||
| Megamonas | ||
| Parabacteroides | ||
| Subdoligranulum | ||
| Thalassospira | ||
| unclassified Synergistaceae |
Revision editor(s): BLESSING123
Signature 2
Source: Figure 3F
Description: Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). 62 weeks
Abundance in Group 1: decreased abundance in HIV-infected mothers
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Elusimicrobium | ||
| Gemella | ||
| Prevotella | ||
| Staphylococcus | ||
| Veillonella | ||
| unclassified Corynebacteriaceae | ||
| unclassified Veillonellaceae |
Revision editor(s): BLESSING123
Experiment 6
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Milk Mammary gland milk,Milk
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-infected mothers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 88
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4F
Description: Genera with significantly different abundances in mothers with and without HIV (FDR P < 0.05).
Abundance in Group 1: decreased abundance in HIV-infected mothers
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Peptostreptococcaceae |
Revision editor(s): BLESSING123
Signature 2
Source: Figure 4F
Description: Genera with significantly different abundances in mothers with and without HIV (FDR P < 0.05).
Abundance in Group 1: increased abundance in HIV-infected mothers
Revision editor(s): BLESSING123
