Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial
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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
- Burkina Faso
- 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
- Balanced reciprocal translocation Balanced reciprocal translocation,balanced reciprocal translocation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mother / Infant Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mother / Infant Intervention
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of taxa shared between mothers and infants across time points from third trimester, 1-2 months and 5–6 months postpartum.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 131
- Group 1 sample size Number of subjects in the case (exposed) group
- 122
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- log transformation
- Statistical test
- ANCOM-BC2
- 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
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Fig. 3C
Description: Relative abundance of taxa shared between mothers and infants across time points
Abundance in Group 1: increased abundance in Mother / Infant Intervention
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis | ||
| Escherichia coli | ||
| Bacteroides fragilis ABacteroides fragilis A | ||
| Prevotella sp.900544825Prevotella sp.900544825 |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 3C
Description: Relative abundance of taxa shared between mothers and infants across time points
Abundance in Group 1: decreased abundance in Mother / Infant Intervention
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella sp. | ||
| Veillonella parvula |
Revision editor(s): Joiejoie
Experiment 2
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of the top ten most abundant taxa species shared between mothers and infants across time points from third trimester, 1-2 months and 5–6 months postpartum.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Fig. 3D
Description: Relative abundance of the top ten most abundant species in both mother and infant samples.
Abundance in Group 1: increased abundance in Mother / Infant Intervention
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 3D
Description: Relative abundance of the top ten most abundant species in both mother and infant samples.
Abundance in Group 1: decreased abundance in Mother / Infant Intervention
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella sp.900548535Prevotella sp.900548535 | ||
| C941 sp.004557565C941 sp.004557565 | ||
| Prevotella sp. |
Revision editor(s): Joiejoie
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mother-Tri2 Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mother-Tri2 Intervention
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mothers whose stool microbiome samples were collected in the intervention group during the second trimester of pregnancy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Fig. 5A
Description: Differentially abundant taxa associated with the intervention at the second trimester (Tri2)
Abundance in Group 1: increased abundance in Mother-Tri2 Intervention
| NCBI | Quality Control | Links |
|---|---|---|
| CAG 103 sp. 000432375CAG 103 sp. 000432375 |
Revision editor(s): Joiejoie
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mother-Tri3 Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mother-Tri3 Intervention
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mothers whose stool microbiome samples were collected in the intervention group during the third trimester of pregnancy.
- 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
- 71
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Fig. 5A
Description: Differentially abundant taxa associated with the intervention at the third trimester (Tri3)
Abundance in Group 1: increased abundance in Mother-Tri3 Intervention
| NCBI | Quality Control | Links |
|---|---|---|
| UMGS882 sp.UMGS882 sp. | ||
| UBA1436 sp.UBA1436 sp. | ||
| Lachnospiraceae sp.Lachnospiraceae sp. |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 5A
Description: Differentially abundant taxa associated with the intervention at the third trimester (Tri3)
Abundance in Group 1: decreased abundance in Mother-Tri3 Intervention
| NCBI | Quality Control | Links |
|---|---|---|
| CAG 245 sp. 000434196CAG 245 sp. 000434196 |
Revision editor(s): Joiejoie
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mother-Pn12 Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mother-Pn12 Intervention
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mothers whose stool microbiome samples were collected in the intervention group at 1 to 2 months postpartum.
- 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
- 66
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Fig. 5A
Description: Differentially abundant taxa associated with the intervention at the postnatal 1–2 months (Pn12)
Abundance in Group 1: increased abundance in Mother-Pn12 Intervention
| NCBI | Quality Control | Links |
|---|---|---|
| CAG 452 sp. 000434035CAG 452 sp. 000434035 | ||
| Ruminococcus C sp. 000433635Ruminococcus C sp. 000433635 | ||
| CAG 533 sp.900551106CAG 533 sp.900551106 |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 5A
Description: Differentially abundant taxa associated with the intervention at the postnatal 1–2 months (Pn12)
Abundance in Group 1: decreased abundance in Mother-Pn12 Intervention
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter sp. | ||
| Agathobacter sp. 900546625Agathobacter sp. 900546625 |
Revision editor(s): Joiejoie
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mother-Pn56 Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mother-Pn56 Intervention
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mothers whose stool microbiome samples were collected in the intervention group at 5 to 6 months postpartum.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 75
- Group 1 sample size Number of subjects in the case (exposed) group
- 67
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Fig. 5A
Description: Differentially abundant taxa associated with the intervention at the postnatal 5–6 months (Pn56)
Abundance in Group 1: increased abundance in Mother-Pn56 Intervention
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella sp. | ||
| Zag 111 sp. 003258735Zag 111 sp. 003258735 |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 5A
Description: Differentially abundant taxa associated with the intervention at the postnatal 5–6 months (Pn56)
Abundance in Group 1: decreased abundance in Mother-Pn56 Intervention
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis | ||
| UMGS874 sp.UMGS874 sp. | ||
| UBA1232 sp. 900544815UBA1232 sp. 900544815 | ||
| Phascolarctobacterium A sp. 900551335Phascolarctobacterium A sp. 900551335 |
Revision editor(s): Joiejoie
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mother + Infant Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mother + Infant Intervention
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group received a specific treatment or dietary intervention during pregnancy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 381
- Group 1 sample size Number of subjects in the case (exposed) group
- 350
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Fig. 5C
Description: Relative abundance of the 16 taxa that were significantly different between the intervention and control groups across all time points combined.
Abundance in Group 1: increased abundance in Mother + Infant Intervention
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 5C
Description: Relative abundance of the 16 taxa that were significantly different between the intervention and control groups across all time points combined.
Abundance in Group 1: decreased abundance in Mother + Infant Intervention
Revision editor(s): Joiejoie
