Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations
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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
- Bangladesh
- 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
- Breastfeeding duration Breastfeeding duration,breastfeeding duration
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Exclusive Breast Feeding (EBF)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non_Exclusive Breast Feeding (Non-EBF)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants who was feed breast milk with either formula or solid.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 138
- Group 1 sample size Number of subjects in the case (exposed) group
- 178
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).
- relative abundances
- Statistical test
- Random Forest Analysis
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Table 11, Table 2, Table 3
Description: Gut bacterial taxa with differential relative abundances from 6 months to 2 years of age between infants with duration of exclusive breastfeeding >2 months vs. ≤2 months from birth.
Abundance in Group 1: increased abundance in Non_Exclusive Breast Feeding (Non-EBF)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Enterococcus |
Revision editor(s): Shulamite, Peace Sandy
Signature 2
Source: Table 11, Table 2, Table 3
Description: Gut bacterial taxa with differential relative abundances from 6 months to 2 years of age between infants with duration of exclusive breastfeeding >2 months vs. ≤2 months from birth.
Abundance in Group 1: decreased abundance in Non_Exclusive Breast Feeding (Non-EBF)
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Catenibacterium | ||
| Collinsella | ||
| Lactobacillus | ||
| Prevotella | ||
| Ruminococcus | ||
| unclassified Clostridiaceae | ||
| unclassified Coriobacteriaceae | ||
| unclassified Lachnospiraceae |
Revision editor(s): Shulamite, Rahila, Peace Sandy
Experiment 2
Subjects
- Location of subjects
- Canada
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Increasing Exclusive Breast Feeding (EBF)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Reduced exclusivity of beast feeding to none breastfeeding
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Introducing other foods or liquids while still breastfeeding
- Group 0 sample size Number of subjects in the control (unexposed) group
- 86
- Group 1 sample size Number of subjects in the case (exposed) group
- 48
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.005
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Table 3, Table 2
Description: Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, nonexclusive breastfeeding and non breastfeeding groups.
Abundance in Group 1: increased abundance in Reduced exclusivity of beast feeding to none breastfeeding
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bacillota | ||
| Bacteroidia | ||
| Blautia | ||
| Coprococcus | ||
| Eubacterium | ||
| Verrucomicrobiota | ||
| Bacteroides | ||
| Clostridium | ||
| Megasphaera | ||
| Veillonella | ||
| Eubacterium sp. |
Revision editor(s): Shulamite, Rahila, Peace Sandy
Signature 2
Source: Table 3, Table 2
Description: Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, nonexclusive breastfeeding and non breastfeeding groups.
Abundance in Group 1: decreased abundance in Reduced exclusivity of beast feeding to none breastfeeding
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Staphylococcus |
Revision editor(s): Shulamite, Peace Sandy
Experiment 3
Subjects
- Location of subjects
- Haiti
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Exclusively Breastfeeding (EBF), Vaginally Born and C-section Born
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants fed with breast milk plus solid or formula
- Group 0 sample size Number of subjects in the control (unexposed) group
- 37
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Signature 1
Source: Table 2, Table 3.
Description: Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.
Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.
Abundance in Group 1: increased abundance in Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bacillota | ||
| Blautia | ||
| Coprococcus | ||
| Eubacterium | ||
| Verrucomicrobiota |
Revision editor(s): Shulamite, Peace Sandy
Signature 2
Source: Table 2 and Table 3
Description: Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.
Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.
Abundance in Group 1: decreased abundance in Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Staphylococcus |
Revision editor(s): Peace Sandy
Signature 3
Source: Table 3 and Table 2
Description: Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.
Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.
Abundance in Group 1: decreased abundance in Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Staphylococcus |
Revision editor(s): Peace Sandy
Signature 4
Source: Table 2 and Table 3
Description: Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.
Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.
Abundance in Group 1: decreased abundance in Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Staphylococcus |
Revision editor(s): Peace Sandy
Experiment 4
Subjects
- Location of subjects
- South Africa
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Exclusive Breastfeeding (EBF)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-Exclusive Breastfeeding (Non-EBF)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants fed with breast milk plus solid or formula
- Group 0 sample size Number of subjects in the control (unexposed) group
- 86
- Group 1 sample size Number of subjects in the case (exposed) group
- 57
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Table 2, Table 3.
Description: Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.
Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.
Abundance in Group 1: increased abundance in Non-Exclusive Breastfeeding (Non-EBF)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Clostridium | ||
| Eubacterium | ||
| Megasphaera | ||
| Veillonella | ||
| Akkermansia | ||
| Bacillota | ||
| Blautia | ||
| Coprococcus | ||
| Verrucomicrobiota |
Revision editor(s): Shulamite, Rahila, Peace Sandy
Signature 2
Source: Table 2, Table 3.
Description: Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.
Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.
Abundance in Group 1: decreased abundance in Non-Exclusive Breastfeeding (Non-EBF)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Staphylococcus |
Revision editor(s): Peace Sandy
Experiment 5
Subjects
- Location of subjects
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Increasing Exclusive Breast Feeding (EBF)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Reduced exclusivity of beast feeding to none breastfeeding
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Exclusive breastfeeding to infants were reduced.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 150
- Group 1 sample size Number of subjects in the case (exposed) group
- 68
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.005
Signature 1
Source: Table 7
Description: Meta-analysis stratified by mode of delivery for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.
Abundance in Group 1: increased abundance in Reduced exclusivity of beast feeding to none breastfeeding
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus | ||
| Eubacterium | ||
| unclassified Lachnospiraceae | ||
| Bacteroides | ||
| Erysipelotrichaceae | ||
| unclassified Clostridiaceae | ||
| Aggregatibacter | ||
| Lactococcus | ||
| Blautia |
Revision editor(s): Shulamite
Signature 3
Source: Table 7
Description: Meta-analysis stratified by mode of delivery for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.
Abundance in Group 1: decreased abundance in Reduced exclusivity of beast feeding to none breastfeeding
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Phascolarctobacterium | ||
| Proteus | ||
| Pseudomonadota | ||
| Staphylococcus | ||
| unclassified Enterobacteriaceae |
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Exclusive BreastFeeding (EBF)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-Exclusive Breastfeeding (Non-EBF)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants fed with breast milk plus solid or formula.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 38
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- Not specified
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Signature 1
Source: Table 6
Description: Meta-analysis of six studies without data from VDAART trial study for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age (sensitivity analysis).
Abundance in Group 1: increased abundance in Non-Exclusive Breastfeeding (Non-EBF)
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus | ||
| Bacteroides | ||
| Clostridium | ||
| Coprococcus | ||
| Eubacterium | ||
| Megasphaera | ||
| Veillonella |
Revision editor(s): Shulamite
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Increasing Exclusive Breast Feeding (EBF)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Reduced exclusivity of beast feeding to none breastfeeding
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not specified
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Random Forest Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Richness Number of species
- increased
Signature 1
Source: Table 4
Description: Meta-analysis of six studies without data from North Carolina study for gut bacterial taxa with differential relative abundances between non-exclusivelybreastfed vs. exclusively breastfed infants ≤6 months of age (sensitivity analysis).
Abundance in Group 1: increased abundance in Reduced exclusivity of beast feeding to none breastfeeding
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Clostridium | ||
| Eubacterium | ||
| Lachnospiraceae | ||
| Megasphaera | ||
| unclassified Clostridiaceae | ||
| Eubacteriales | ||
| Bacteroidia |
