Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery
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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
- Feces , Saliva , Anterior naris , Posterior fornix of vagina , Epithelium of elbow 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,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva,Anterior nostril,Anterior naris,anterior naris,Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina,posterior fornix of vagina,Cubital region epithelial tissue,Cubital region epithelium,Elbow epithelial tissue,Elbow epithelium,Epithelial tissue of cubital region,Epithelial tissue of elbow,Epithelium of cubital region,Epithelium of elbow,epithelium of elbow
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Microbiome Microbiome,microbiome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Maternal samples taken at delivery.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Neonatal samples taken at delivery
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Neonatal samples taken at delivery
- Group 0 sample size Number of subjects in the control (unexposed) group
- 82
- Group 1 sample size Number of subjects in the case (exposed) group
- 82
Lab analysis
- Sequencing type
- 16S
- 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
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Signature 1
Source: Fig. S3.
Description: Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. (A) Maternal samples taken at delivery. (B) Neonatal samples taken at delivery.
Abundance in Group 1: increased abundance in Neonatal samples taken at delivery
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Propionibacterium | ||
| Sphingomonas | ||
| Gardnerella | ||
| Prevotella | ||
| Lactobacillus | ||
| Enterobacteriaceae |
Revision editor(s): Peace Sandy, WikiWorks
Signature 2
Source: Fig. S3
Description: Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. (A) Maternal samples taken at delivery. (B) Neonatal samples taken at delivery.
Abundance in Group 1: decreased abundance in Neonatal samples taken at delivery
Revision editor(s): Peace Sandy, WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Maternal samples taken at 6 weeks postpartum
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infant samples taken at 6 weeks postpartum
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infant samples taken at 6 weeks postpartum
- Group 0 sample size Number of subjects in the control (unexposed) group
- 60
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. S3
Description: Fig. S3. Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. (C) Maternal samples taken at 6 weeks postpartum (D) Infant samples taken at 6 weeks postpartum
Abundance in Group 1: increased abundance in Infant samples taken at 6 weeks postpartum
Revision editor(s): Peace Sandy, WikiWorks
Signature 2
Source: Fig. S3
Description: Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. . (C) Maternal samples taken at 6 weeks postpartum (D) Infant samples taken at 6 weeks postpartum.
Abundance in Group 1: decreased abundance in Infant samples taken at 6 weeks postpartum
Revision editor(s): Peace Sandy, WikiWorks
