Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode
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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
- Tunisia
- 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
- Delivery method DeliveryMethod,Delivery method,delivery method
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vaginally Delivered(VD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Elective Cesarean Section (ECS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants whose delivery mode (DM) was through elective cesarean section (ECS)
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Last trimester of pregnancy.
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- 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: Supplementary Figure 2 c.
Description: Differentially abundant taxa between elective cesarean section (ECS) versus vaginally delivered (VD) newborns detected by linear discriminant analysis effect size (LEfSe) analysis.
Abundance in Group 1: increased abundance in Elective Cesarean Section (ECS)
Revision editor(s): Ayibatari
Signature 2
Source: Supplementary Figure 2 c.
Description: Differentially abundant taxa between elective cesarean section (ECS) versus vaginally delivered (VD) newborns detected by linear discriminant analysis effect size (LEfSe) analysis.
Abundance in Group 1: decreased abundance in Elective Cesarean Section (ECS)
Revision editor(s): Ayibatari
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vaginally Delivered(VD) at Day 0
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Elective Cesarean Section (ECS) at Day 0
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4 A.
Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 0 (A). Relative abundance of ESKAPE members in ECS newborns at each collection time point.
Abundance in Group 1: increased abundance in Elective Cesarean Section (ECS) at Day 0
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter | ||
| Citrobacter freundii | ||
| Clostridia | ||
| Eubacteriales |
Revision editor(s): Ayibatari
Signature 2
Source: Figure 4 A.
Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 0 (A). Relative abundance of ESKAPE members in ECS newborns at each collection time point.
Abundance in Group 1: decreased abundance in Elective Cesarean Section (ECS) at Day 0
| NCBI | Quality Control | Links |
|---|---|---|
| Methylorubrum | ||
| Methylorubrum populi |
Revision editor(s): Ayibatari
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vaginally Delivered(VD) at Day 15
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Elective Cesarean Section (ECS) at Day 15
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4 B.
Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 15 (B). Relative abundance of ESKAPE members in ECS newborns at each collection time point.
Abundance in Group 1: increased abundance in Elective Cesarean Section (ECS) at Day 15
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Clostridium | ||
| Bifidobacterium dentium | ||
| Actinomyces oris | ||
| Actinomyces sp. oral taxon 897 | ||
| Bifidobacterium actinocoloniiforme |
Revision editor(s): Ayibatari
Signature 2
Source: Figure 4 B.
Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 15 (B). Relative abundance of ESKAPE members in ECS newborns at each collection time point.
Abundance in Group 1: decreased abundance in Elective Cesarean Section (ECS) at Day 15
Revision editor(s): Ayibatari
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vaginally Delivered(VD) at Day 30
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Elective Cesarean Section (ECS) at Day 30
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4 C.
Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 30 (C). Relative abundance of ESKAPE members in ECS newborns at each collection time point.
Abundance in Group 1: increased abundance in Elective Cesarean Section (ECS) at Day 30
Revision editor(s): Ayibatari
Signature 2
Source: Figure 4 C.
Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 30 (C). Relative abundance of ESKAPE members in ECS newborns at each collection time point.
Abundance in Group 1: decreased abundance in Elective Cesarean Section (ECS) at Day 30
Revision editor(s): Ayibatari
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Not specified
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- An experiment for group 1 (day 0) vs. group 0 (days 15 and 30)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tunisian newborns' at day 0 sampling time points.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Supplementary Table_3.
Description: Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 0 with Day 15 and Day 30 .
Abundance in Group 1: increased abundance in An experiment for group 1 (day 0) vs. group 0 (days 15 and 30)
| NCBI | Quality Control | Links |
|---|---|---|
| Comamonadaceae | ||
| Lysobacteraceae | ||
| Lysobacterales | ||
| Stenotrophomonas | ||
| Pseudomonadaceae | ||
| Pseudomonas | ||
| Methylorubrum |
Revision editor(s): Ayibatari
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- An experiment for group 1 (day 15) vs. group 0 (days 0 and 30)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tunisian newborns' at day 15 sampling time points.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 2
Source: Supplementary Table_3.
Description: Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 15 with Day 0 and Day 30 .
Abundance in Group 1: increased abundance in An experiment for group 1 (day 15) vs. group 0 (days 0 and 30)
Revision editor(s): Folakunmi
Experiment 7
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- An experiment for group 1 (day 30) vs. group 0 (days 0 and 15)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tunisian newborns' at day 30 sampling time points.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Supplementary Table_3.
Description: Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 30 with Day 0 and Day 15.
Abundance in Group 1: increased abundance in An experiment for group 1 (day 30) vs. group 0 (days 0 and 15)
Revision editor(s): Ayibatari
