Maternal smoking during pregnancy increases the risk of gut microbiome-associated childhood overweight and obesity
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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
Curated date: 2024/04/21
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Scholastica
Subjects
- Location of subjects
- Canada
- 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
- Smoking behaviour measurement Smoking behaviour measurement,smoking behaviour measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Early infants (3 months) with maternal history of 'NO' 'smoking
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Early infants (3 months) with maternal history of 'YES' 'smoking
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants (3 months old) whose mothers quit smoking during pregnancy, reduced the number of cigarettes, or had the same number of cigarettes (as before conception) during pregnancy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 1458
- Group 1 sample size Number of subjects in the case (exposed) group
- 134
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
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
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Curated date: 2024/04/21
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Scholastica
Source: Figure 2B, Supplementary Table S8
Description: Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed early infants (3 months old)
Abundance in Group 1: increased abundance in Early infants (3 months) with maternal history of 'YES' 'smoking
Revision editor(s): Omojokunoluwatomisin, Scholastica
Signature 2
Curated date: 2024/04/21
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Scholastica
Source: Figure 2B, Supplementary Table S8
Description: Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed early infants (3 months old)
Abundance in Group 1: decreased abundance in Early infants (3 months) with maternal history of 'YES' 'smoking
NCBI | Quality Control | Links |
---|---|---|
Blautia | ||
Haemophilus | ||
Micrococcaceae | ||
Micrococcales | ||
Oscillospiraceae | ||
Pasteurellaceae | ||
Pasteurellales | ||
Rothia |
Revision editor(s): Omojokunoluwatomisin, Scholastica
Experiment 2
Curated date: 2024/04/22
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Scholastica
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Late infants (12months) with maternal history of 'NO' 'smoking
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Late infants (12months) with maternal history of 'YES' 'smoking
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants (12 months old) whose mothers quit smoking during pregnancy, reduced the number of cigarettes, or had the same number of cigarettes (as before conception) during pregnancy.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Curated date: 2024/04/22
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Scholastica
Source: Figure 2B, Supplementary Table S8
Description: Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed late infants (12 months old)
Abundance in Group 1: increased abundance in Late infants (12months) with maternal history of 'YES' 'smoking
Revision editor(s): Omojokunoluwatomisin, Scholastica
Signature 2
Curated date: 2024/04/22
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Scholastica
Source: Figure 2B, Supplementary Table S8
Description: Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed late infants (12 months old)
Abundance in Group 1: decreased abundance in Late infants (12months) with maternal history of 'YES' 'smoking
NCBI | Quality Control | Links |
---|---|---|
Haemophilus | ||
Lachnospira | ||
Pasteurellaceae | ||
Pasteurellales | ||
Selenomonadales | ||
Veillonella | ||
Veillonellaceae |
Revision editor(s): Omojokunoluwatomisin, Scholastica