Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes 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
- Luxembourg
- 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
- Cesarean section caesarean section,Cesarean section,cesarean section
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vaginal delivery at day 3
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- c-section
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- meconium samples were collected at day 1 after delivery
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.
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
- Mann-Whitney (Wilcoxon)
- 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
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 7 and Fig. S4
Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.
Abundance in Group 1: increased abundance in c-section
NCBI | Quality Control | Links |
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Staphylococcus | ||
Lactobacillus |
Revision editor(s): WikiWorks
Experiment 2
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Aiyshaaaa, ChiomaBlessing
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vaginal delivery at day 5
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- 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 6S
Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.
Abundance in Group 1: increased abundance in c-section
NCBI | Quality Control | Links |
---|---|---|
Bacillota |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 6S
Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.
Abundance in Group 1: decreased abundance in c-section
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vaginal delivery at day 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 6S and Fig. S4
Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.
Abundance in Group 1: decreased abundance in c-section
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota | ||
Bacteroides |
Revision editor(s): WikiWorks
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vaginal delivery at day 150
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- 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 6S
Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.
Abundance in Group 1: decreased abundance in c-section
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota | ||
Bacteroides |
Revision editor(s): WikiWorks
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vaginal delivery at day 365
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- 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 6S
Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.
Abundance in Group 1: decreased abundance in c-section
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota |
Revision editor(s): WikiWorks
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Premature birth Birth, Premature,Birth, Preterm,Births, Premature,Births, Preterm,Premature Births,Preterm Birth,Preterm Births,Premature birth,premature birth
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- full-term delivery >39 weeks at day 3
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- late preterm 34-36 weeks
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
Signature 1
Source: text pg11 and figure 7s
Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.
Abundance in Group 1: decreased abundance in late preterm 34-36 weeks
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota |
Revision editor(s): WikiWorks
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cesarean section caesarean section,Cesarean section,cesarean section
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vaginal delivery
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- overall time point infants samples of c-section
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Signature 1
Source: supplemantry file 9
Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.
Abundance in Group 1: increased abundance in overall time point infants samples of c-section
Signature 2
Source: supplemantry file 9
Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.
Abundance in Group 1: decreased abundance in overall time point infants samples of c-section
NCBI | Quality Control | Links |
---|---|---|
Parabacteroides | ||
Bacteroides | ||
Alistipes |
Revision editor(s): WikiWorks
Experiment 8
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Meconium Meconium,meconium
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- C-section
- 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
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 11 mothers (6 controls and 5 cases) used antibiotics 12 hours before and after delivery, 3 VD mothers were positive group B Streptococcus screening.
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased