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
- 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 uninfected controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-exposed uninfected
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants exposed to HIV from their birth mothers but uninfected
- 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 who had been on antibiotics or HIV-exposed uninfected infants that had been on Bactrim after 6 weeks of birth were excluded.
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- antibiotic exposure
Signature 1
Source: Figure 2d
Description: Increased abundance in HIV-exposed uninfected infants
Abundance in Group 1: increased abundance in HIV-exposed uninfected
NCBI | Links |
---|---|
Eggerthella | |
Barnesiella | |
Odoribacter | |
Blautia | |
Sneathia | |
unclassified Bacillota | |
unclassified Oscillospiraceae |
Revision editor(s): BLESSING123
Signature 2
Source: Figure 2d
Description: Decreased abundance in HIV-exposed uninfected infants
Abundance in Group 1: decreased abundance in HIV-exposed uninfected
NCBI | Links |
---|---|
Catenibacterium | |
Megamonas | |
Enterobacter ⚠ | |
Candidatus Saccharibacteria genomosp. TM7-H1 | |
unclassified Bacteroidota |
Revision editor(s): BLESSING123
Experiment 2
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 uninfected controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-exposed uninfected
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants exposed to HIV from their birth mothers but uninfected
- 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)
- Infants who had been on antibiotics or HIV-exposed uninfected infants that had not been on Bactrim after 28 weeks of birth were excluded
Lab analysis
- Sequencing type
- 16S
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
- 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
- increased
Signature 1
Source: Figure 2d
Description: Increased abundance in HIV-exposed uninfected infants
Abundance in Group 1: increased abundance in HIV-exposed uninfected
NCBI | Links |
---|---|
Candidatus Epulonipiscium | |
Klebsiella ⚠ | |
Lactococcus | |
Megamonas | |
Parasutterella | |
unclassified Eubacteriales |
Revision editor(s): BLESSING123
Signature 2
Source: Figure 2d
Description: Decreased abundance in HIV-exposed uninfected infants
Abundance in Group 1: decreased abundance in HIV-exposed uninfected
NCBI | Links |
---|---|
Atopobium | |
Gardnerella ⚠ | |
Gemella | |
Mobiluncus | |
Parvimonas | |
Sneathia |
Revision editor(s): BLESSING123
Experiment 3
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 uninfected controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-exposed uninfected
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants exposed to HIV from their birth mothers but uninfected
- 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 or HIV-exposed uninfected infants that had not been on Bactrim after 62 weeks of birth were excluded
Lab analysis
- Sequencing type
- 16S
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
- 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: Decreased abundance in HIV-exposed uninfected infants
Abundance in Group 1: decreased abundance in HIV-exposed uninfected
NCBI | Links |
---|---|
Proteus | |
unclassified Coriobacteriaceae |
Revision editor(s): BLESSING123
Experiment 4
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
- 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
- Sequencing type
- 16S
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- sex
Signature 1
Source: Figure 3F
Description:
Abundance in Group 1: increased abundance in HIV-infected mothers
Revision editor(s): BLESSING123
Signature 2
Source: Figure 3F
Description:
Abundance in Group 1: decreased abundance in HIV-infected mothers
NCBI | Links |
---|---|
Elusimicrobium ⚠ | |
Asteroleplasma | |
unclassified Clostridiales Family XVII. | |
Faecalibacterium | |
Haemophilus |
Revision editor(s): BLESSING123
Experiment 5
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
- 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
- 65
- Group 1 sample size Number of subjects in the case (exposed) group
- 71
Lab analysis
- Sequencing type
- 16S
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
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:
Abundance in Group 1: increased abundance in HIV-infected mothers
NCBI | Links |
---|---|
Collinsella | |
Parabacteroides | |
Acidaminococcus ⚠ | |
Anaerostipes | |
Blautia | |
Dorea | |
Faecalibacterium | |
Flavonifractor | |
Megamonas | |
Subdoligranulum | |
Thalassospira | |
unclassified Synergistaceae |
Revision editor(s): BLESSING123
Signature 2
Source: Figure 3F
Description:
Abundance in Group 1: decreased abundance in HIV-infected mothers
NCBI | Links |
---|---|
unclassified Corynebacteriaceae | |
Prevotella | |
Elusimicrobium ⚠ | |
Gemella | |
Staphylococcus | |
Veillonella | |
unclassified Veillonellaceae | |
Acinetobacter ⚠ |
Revision editor(s): BLESSING123
Experiment 6
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
- Milk Mammary gland milk,Milk
- 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
- 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
- Sequencing type
- 16S
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- sex
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:
Abundance in Group 1: decreased abundance in HIV-infected mothers
NCBI | Links |
---|---|
unclassified Peptostreptococcaceae |
Revision editor(s): BLESSING123
Signature 2
Source: Figure 4F
Description:
Abundance in Group 1: increased abundance in HIV-infected mothers
Revision editor(s): BLESSING123