Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life
-
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. 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 mother to child transmission HIV MTCT,HIV mother to child transmission,hIV mother to child transmission
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV-unexposed infants (HUU) at 6 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-exposed uninfected infants (HEU) at 6 weeks
- 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) at 6 weeks
- 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).
- raw counts
- Statistical test
- 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
- 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) at 6 weeks
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) at 6 weeks
NCBI | Quality Control | Links |
---|---|---|
Candidatus Saccharibacteria genomosp. TM7-H1 | ||
Catenibacterium | ||
Enterobacter | ||
Megamonas | ||
unclassified Bacteroidota |
Revision editor(s): BLESSING123
Experiment 2
Curated date: 2023/03/09
Curator: BLESSING123
Revision editor(s): BLESSING123, Mcarlson, Folakunmi, Victoria
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV-unexposed infants (HUU) at 28 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-exposed uninfected infants (HEU) at 28 weeks
- 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
- 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) at 28 weeks
NCBI | Quality Control | Links |
---|---|---|
Candidatus Epulonipiscium 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) at 28 weeks
NCBI | Quality Control | Links |
---|---|---|
Atopobium | ||
Gardnerella | ||
Gemella | ||
Mobiluncus | ||
Parvimonas | ||
Sneathia |
Revision editor(s): BLESSING123
Experiment 3
Curated date: 2023/03/09
Curator: BLESSING123
Revision editor(s): BLESSING123, Mcarlson, Folakunmi, Victoria
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV-unexposed infants (HUU) at 62 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-exposed uninfected infants (HEU) at 62 weeks
- 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) at 62 weeks
- 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) at 62 weeks
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 at delivery
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-infected mothers at delivery
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mothers infected with HIV at delivery time point
- 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
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). Delivery
Abundance in Group 1: increased abundance in HIV-infected mothers at delivery
Revision editor(s): BLESSING123, Folakunmi
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 at delivery
NCBI | Quality Control | Links |
---|---|---|
Asteroleplasma | ||
Elusimicrobium | ||
Faecalibacterium | ||
Haemophilus | ||
unclassified Clostridiales Family XVII. |
Revision editor(s): BLESSING123
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls at 62 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-infected mothers at 62 weeks
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mothers infected with HIV at 62 weeks time point
- 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 at 62 weeks
Revision editor(s): BLESSING123, Folakunmi
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 at 62 weeks
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,milk
- 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
- 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
Experiment 7
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Exclusively breastfed HIV-unexposed infants (HUU) at 28 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Exclusively breastfed In utero-HIV exposed uninfected infants (HEU) at 28 weeks
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 52
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
- 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 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 Exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks
NCBI | Quality Control | Links |
---|---|---|
Candidatus Epulonipiscium |
Revision editor(s): Folakunmi
Signature 2
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 Exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks
NCBI | Quality Control | Links |
---|---|---|
Sneathia |
Revision editor(s): Folakunmi
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Not exclusively breastfed HIV-unexposed infants (HUU) at 28 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Not exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not exclusively breastfed (formula feeding) In utero-HIV exposed uninfected infants (HEU) at 28 weeks
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2e
Description: Genera with significantly different relative abundances between HEU and HUU not exclusively (Excl.) breastfed at 28 weeks of lif
Abundance in Group 1: increased abundance in Not exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks
NCBI | Quality Control | Links |
---|---|---|
Candidatus Epulonipiscium | ||
unclassified_E01-9C-26unclassified_E01-9C-26 | ||
Klebsiella | ||
Pasteurella |
Revision editor(s): Folakunmi
Signature 2
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 Not exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks
NCBI | Quality Control | Links |
---|---|---|
Gardnerella | ||
Mobiluncus | ||
Alistipes | ||
Catenibacterium | ||
Dialister | ||
Finegoldia | ||
Gemella | ||
Peptococcus | ||
Peptostreptococcus | ||
Solobacterium | ||
Sneathia |
Revision editor(s): Folakunmi