Variations in early gut microbiome are associated with childhood eczema
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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
- China
- 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
- Eczema Eczema,eczema
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- child with eczema
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting
- Group 0 sample size Number of subjects in the control (unexposed) group
- 123
- Group 1 sample size Number of subjects in the case (exposed) group
- 49
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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).
- raw counts
- Statistical test
- T-Test
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3a
Description: Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years
Abundance in Group 1: increased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia | ||
| Erwinia |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 3a
Description: Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years
Abundance in Group 1: decreased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Enterobacter |
Revision editor(s): WikiWorks
Experiment 2
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3b
Description: Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years
Abundance in Group 1: increased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Eubacteriales | ||
| Veillonella parvula | ||
| Clostridium neonatale |
Signature 2
Source: Figure 3b
Description: Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years
Abundance in Group 1: decreased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Actinomycetes | ||
| Bifidobacterium | ||
| Bifidobacteriales | ||
| Bifidobacteriaceae | ||
| Bifidobacterium longum subsp. longum | ||
| Pseudomonadota |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- T-Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3c
Description: Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years
Abundance in Group 1: increased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Erwinia |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 3c
Description: Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years
Abundance in Group 1: decreased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Lachnospira |
Revision editor(s): WikiWorks
Experiment 4
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3d
Description: Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years
Abundance in Group 1: increased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella parvula | ||
| Bacteroides fragilis |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 3d
Description: Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years
Abundance in Group 1: decreased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium bifidum |
Revision editor(s): WikiWorks
Experiment 5
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children age 0.5-1 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- T-Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3e
Description: Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years
Abundance in Group 1: increased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Erwinia |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 3e
Description: Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years
Abundance in Group 1: decreased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Streptococcus | ||
| Campylobacter |
Revision editor(s): WikiWorks
Experiment 6
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3f
Description: Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years
Abundance in Group 1: decreased abundance in child with eczema
Revision editor(s): WikiWorks
Experiment 7
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children age 1-2 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- T-Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3g
Description: Significantly diverse bacterial communities between healthy and eczema groups in age group 1-2 years
Abundance in Group 1: decreased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Enterobacter | ||
| Klebsiella | ||
| Streptococcus | ||
| Veillonella |
Experiment 8
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3h
Description: Significantly diverse bacterial communities between healthy and eczema groups in age group 1-2 years
Abundance in Group 1: decreased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Revision editor(s): WikiWorks
Experiment 9
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children age 2-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- T-Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3i
Description: Significantly diverse bacterial communities between healthy and eczema groups in age group 2-3 years
Abundance in Group 1: decreased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Sutterella | ||
| Clostridium | ||
| Collinsella | ||
| Bilophila |
Revision editor(s): WikiWorks
Experiment 10
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3j
Description: Significantly diverse bacterial communities between healthy and eczema groups in age group 2-3 years
Abundance in Group 1: decreased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Actinomycetota | ||
| Actinomycetes | ||
| Bifidobacteriales | ||
| Bifidobacteriaceae | ||
| Bifidobacterium | ||
| Pseudomonadota |
Revision editor(s): WikiWorks
