Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)
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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
- United States of America
- 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
- Milk Mammary gland milk,Milk,milk
- 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
- Medium Total Time Breastfeeding
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Total Time Breastfeeding
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breastfeeding pattern
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Any antibiotics consumed by or administered to the mother or infant in the past 30 days
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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).
- centered log-ratio
- Statistical test
- ANCOM
- 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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3A
Description: Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [A] total time breastfeeding group in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score
Abundance in Group 1: decreased abundance in Low Total Time Breastfeeding
| NCBI | Quality Control | Links |
|---|---|---|
| Agreia | ||
| Bifidobacterium | ||
| Pedobacter | ||
| Stenotrophomonas | ||
| Rugamonas |
Revision editor(s): Peace Sandy
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Total Time Breastfeeding
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3A
Description: Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [A] total time breastfeeding group in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score
Abundance in Group 1: decreased abundance in High Total Time Breastfeeding
| NCBI | Quality Control | Links |
|---|---|---|
| Agreia | ||
| Bifidobacterium | ||
| Pedobacter | ||
| Stenotrophomonas | ||
| Rugamonas |
Revision editor(s): Peace Sandy
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Medium Breastfeeding Bouts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Breastfeeding Bouts
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3B
Description: Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score
Abundance in Group 1: increased abundance in Low Breastfeeding Bouts
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Micrococcus |
Revision editor(s): Peace Sandy
Signature 2
Source: Figure 3B
Description: Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score
Abundance in Group 1: decreased abundance in Low Breastfeeding Bouts
| NCBI | Quality Control | Links |
|---|---|---|
| Pedobacter | ||
| Acidocella | ||
| Achromobacter |
Revision editor(s): Peace Sandy
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Breastfeeding Bouts
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3B
Description: Log-fold change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test. Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score
Abundance in Group 1: increased abundance in High Breastfeeding Bouts
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): Peace Sandy
Signature 2
Source: Figure 3B
Description: Log-fold change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test. Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score
Abundance in Group 1: decreased abundance in High Breastfeeding Bouts
| NCBI | Quality Control | Links |
|---|---|---|
| Micrococcus | ||
| Pedobacter | ||
| Acidocella | ||
| Achromobacter |
Revision editor(s): Peace Sandy
