Imbalance of Gut Streptococcus, Clostridium, and Akkermansia Determines the Natural Course of Atopic Dermatitis in Infant
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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
- South Korea
- 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
- Atopic eczema allergic,allergic dermatitis,allergic form of dermatitis,Atopic Dermatitides,Atopic Dermatitis,Atopic dermatitis,atopic dermatitis and related conditions,Atopic dermatitis and related conditions (disorder),atopic eczema,Atopic Neurodermatitides,Atopic Neurodermatitis,Atopic neurodermatitis,Besnier's prurigo,Dermatitides, Atopic,Dermatitis, Atopic,Disseminated Neurodermatitides,Disseminated Neurodermatitis,eczema,Eczema, Atopic,Eczema, Infantile,eczematous dermatitis,Infantile Eczema,Neurodermatitides, Atopic,Neurodermatitides, Disseminated,Neurodermatitis, Atopic,Neurodermatitis, Disseminated,OTHER ATOPIC DERMATITIS,Other atopic dermatitis and related conditions,Atopic 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
- infant with transient atopic dermatitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infant with transient atopic dermatitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 84
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- before sample collection
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2a, Text
Description: Phylum level relative abundance of gut microbiota in infants with transient atopic dermatitis (AD) and healthy controls
Abundance in Group 1: increased abundance in infant with transient atopic dermatitis
NCBI | Quality Control | Links |
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Actinomycetota |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 2b, Text
Description: Genus level relative abundance of gut microbiota in infants with transient atopic dermatitis (AD) and healthy controls
Abundance in Group 1: increased abundance in infant with transient atopic dermatitis
NCBI | Quality Control | Links |
---|---|---|
Bifidobacterium | ||
Akkermansia |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants with persistent atopic dermatitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infant with persistent atopic dermatitis
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2b, Text
Description: Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and healthy controls
Abundance in Group 1: increased abundance in infants with persistent atopic dermatitis
NCBI | Quality Control | Links |
---|---|---|
Streptococcus |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 2b, Text
Description: Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and healthy controls
Abundance in Group 1: decreased abundance in infants with persistent atopic dermatitis
NCBI | Quality Control | Links |
---|---|---|
Clostridium |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- transient atopic dermatitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2b, Text
Description: Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and transient atopic dermatitis
Abundance in Group 1: increased abundance in infants with persistent atopic dermatitis
NCBI | Quality Control | Links |
---|---|---|
Streptococcus |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 2b, Text
Description: Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and transient atopic dermatitis
Abundance in Group 1: decreased abundance in infants with persistent atopic dermatitis
NCBI | Quality Control | Links |
---|---|---|
Akkermansia |
Revision editor(s): WikiWorks
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 0 sample size Number of subjects in the control (unexposed) group
- 84
Lab analysis
Statistical Analysis
- 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
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Figure S1a
Description: LEfSe analysis of the infant gut microbiota in healthy controls and persistent AD subjects
Abundance in Group 1: increased abundance in infants with persistent atopic dermatitis
Revision editor(s): WikiWorks
Signature 2
Source: Supplemental Figure S1a
Description: LEfSe analysis of the infant gut microbiota in healthy controls and persistent AD subjects
Abundance in Group 1: decreased abundance in infants with persistent atopic dermatitis
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- transient atopic dermatitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Figure S1b
Description: LEfSe analysis of the infant gut microbiota in transient AD and persistent AD subjects
Abundance in Group 1: increased abundance in infants with persistent atopic dermatitis
Signature 2
Source: Supplemental Figure S1b
Description: LEfSe analysis of the infant gut microbiota in transient AD and persistent AD subjects
Abundance in Group 1: decreased abundance in infants with persistent atopic dermatitis
NCBI | Quality Control | Links |
---|---|---|
Akkermansia | ||
Enterobacter | ||
Kosakonia | ||
Raoultella | ||
Verrucomicrobiia | ||
Verrucomicrobiales | ||
Verrucomicrobiota | ||
Verrucomicrobium |
Experiment 6
Subjects
- 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
- infant with transient atopic dermatitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infant with transient atopic dermatitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 84
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Figure S1c
Description: LEfSe analysis of the infant gut microbiota in healthy controls and transient AD subjects
Abundance in Group 1: increased abundance in infant with transient atopic dermatitis
NCBI | Quality Control | Links |
---|---|---|
Actinomycetota | ||
Bifidobacteriaceae | ||
Bifidobacteriales | ||
Bifidobacterium |
Signature 2
Source: Supplemental Figure S1c
Description: LEfSe analysis of the infant gut microbiota in healthy controls and transient AD subjects
Abundance in Group 1: decreased abundance in infant with transient atopic dermatitis
NCBI | Quality Control | Links |
---|---|---|
Micrococcaceae | ||
Rothia | ||
Micrococcales |
Revision editor(s): WikiWorks