Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants
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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. 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
- Non-exclusively breastfed (NEBF) infants at 6 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Exclusively breastfed (EBF) infants at 6 weeks.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- EBF infants defined as infants fed breast milk only (except for prescribed medicine) from birth to the study visit(6 weeks).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 55
- Group 1 sample size Number of subjects in the case (exposed) group
- 44
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Text: Gut Microbiota Is Altered by Feeding Modality- At 6 weeks, EBF infants had lower relative abundance of Streptococcus luteciae and supplementary Figure 2
Description: Specific taxa differentially abundant in (exclusively breastfed) EBF versus (non-exclusively breastfed) NEBF infants at 6 Weeks. This study represents the gut microbial composition changes observed in non-exclusively breastfed (NEBF) infants compared to exclusively breastfed (EBF) infants.
Abundance in Group 1: decreased abundance in Exclusively breastfed (EBF) infants at 6 weeks.
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus lutetiensis |
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-exclusively breastfed (NEBF) infants at 14 weeks.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Exclusively breastfed (EBF) infants at 14 weeks.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- EBF infants defined as infants fed breast milk only (except for prescribed medicine) from birth to the study visit(14 weeks).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 67
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Text: Gut Microbiota Is Altered by Feeding Modality- (At 14 weeks, EBF infants had higher relative abundance of Streptococcus lactarius, as well as Actinomyces and Atopobium) and Supplementary Figure 2.
Description: Specific taxa differentially abundant in (exclusively breastfed) EBF versus (non-exclusively breastfed) NEBF infants at 14 Weeks. This study represents the gut microbial composition changes observed in non-exclusively breastfed (NEBF) infants compared to exclusively breastfed (EBF) infants.
Abundance in Group 1: increased abundance in Exclusively breastfed (EBF) infants at 14 weeks.
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Atopobium | ||
| Streptococcus lactarius |
Revision editor(s): Tosin
Signature 2
Source: Text: Gut Microbiota Is Altered by Feeding Modality- At 14 weeks, EBF infants had lower relative abundance of two Bacteroides OTUs and supplementary Figure 2.
Description: Specific taxa differentially abundant in (exclusively breastfed) EBF versus (non-exclusively breastfed) NEBF infants at 14 Weeks. This study represents the gut microbial composition changes observed in non-exclusively breastfed (NEBF) infants compared to exclusively breastfed (EBF) infants.
Abundance in Group 1: decreased abundance in Exclusively breastfed (EBF) infants at 14 weeks.
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides |
Revision editor(s): Tosin
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cell activation Cell activation,cell activation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infants with Low HL-ADR (Human Leukocyte Antigen - DR isotype) expression on CD4 + T-cell
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infants with High HL-ADR (Human Leukocyte Antigen - DR isotype) expression on CD4 + T-cell
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants with high CD4+HLA-DR+ T-cell frequency
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age
Signature 1
Source: Figure 4B
Description: Gut microbial composition partially explains peripheral blood CD4+ T-cell activation. Significantly differentially abundant OTUs merged at the lowest taxonomic level in infants with high HLA-DR expression vs those with low HLA-DR expression, as computed by DeSeq2.
Abundance in Group 1: increased abundance in Infants with High HL-ADR (Human Leukocyte Antigen - DR isotype) expression on CD4 + T-cell
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila |
Revision editor(s): Tosin
Signature 2
Source: Figure 4B
Description: Gut microbial composition partially explains peripheral blood CD4+ T-cell activation. Significantly differentially abundant OTUs merged at the lowest taxonomic level in infants with high HLA-DR expression vs those with low HLA-DR expression, as computed by DeSeq2.
Abundance in Group 1: decreased abundance in Infants with High HL-ADR (Human Leukocyte Antigen - DR isotype) expression on CD4 + T-cell
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Bifidobacterium bifidum | ||
| Streptococcus lactarius | ||
| Gemellaceae | ||
| Staphylococcus | ||
| Pantoea agglomerans |
Revision editor(s): Tosin
