The skin microbiome is different in pediatric versus adult atopic dermatitis
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM, Li H
Journal
The Journal of allergy and clinical immunology
Year
2016
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
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
- Skin of body Entire integument,Entire skin,Integument,Integumental organ,Pelt,Skin,Skin organ,Skin of body,skin of body
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 2-12 years
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 18-62 years
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- adult age 18-62
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 45
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 week (oral antibiotics)
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
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Source: Figure 1b, Supplemental table E2, Figure 2b text
Description: Skin microorganisms differ with age in the healthy skin
Abundance in Group 1: increased abundance in 18-62 years
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium sp. | ||
| Cutibacterium acnes | ||
| Staphylococcus epidermidis | ||
| Propionibacterium | ||
| Corynebacterium | ||
| Staphylococcus | ||
| Lactobacillus | ||
| Finegoldia | ||
| Anaerococcus |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Source: Figure 1b, Supplemental table E2, Figure 2b text
Description: Skin microorganisms differ with age in the healthy skin
Abundance in Group 1: decreased abundance in 18-62 years
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus sp. | ||
| Rothia | ||
| Streptococcus | ||
| Granulicatella | ||
| Gemella | ||
| Haemophilus |
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Differences from previous experiment shown
Subjects
- 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
- non-lesional skin
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- lesional skin
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- atopic dermatitis lesional skin
- Group 0 sample size Number of subjects in the control (unexposed) group
- 59
- Group 1 sample size Number of subjects in the case (exposed) group
- 59
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Source: text
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among children
Abundance in Group 1: decreased abundance in lesional skin
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Propionibacterium |
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 2-12 years
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 13-62 years
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- teenager/adult age 13-62
- Group 1 sample size Number of subjects in the case (exposed) group
- 69
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Source: Supplemental Table E4
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with lesional skin
Abundance in Group 1: increased abundance in 13-62 years
| NCBI | Quality Control | Links |
|---|---|---|
| Propionibacterium | ||
| Corynebacterium | ||
| Lactobacillus |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Source: Supplemental Table E4
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with lesional skin
Abundance in Group 1: decreased abundance in 13-62 years
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Granulicatella | ||
| Gemella | ||
| Neisseria | ||
| Haemophilus | ||
| Rothia | ||
| Veillonella |
Experiment 4
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 18-62 years
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- adult age 18-62
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 45
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Source: Supplemental Table E3
Description: Taxonomic compositions of the healthy skin microbiome at the species level
Abundance in Group 1: increased abundance in 18-62 years
| NCBI | Quality Control | Links |
|---|---|---|
| Cutibacterium acnes | ||
| Staphylococcus epidermidis | ||
| Lactobacillus iners |
Revision editor(s): WikiWorks
Experiment 5
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Differences from previous experiment shown
Subjects
- 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
- non-lesional skin in young children
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- lesional skin in young children
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- atopic dermatitis lesional skin
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 69
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Source: Supplemental Table E5
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the species level among adults-teenagers
Abundance in Group 1: increased abundance in lesional skin in young children
Experiment 6
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-lesional skin
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- lesional skin
- Group 0 sample size Number of subjects in the control (unexposed) group
- 59
- Group 1 sample size Number of subjects in the case (exposed) group
- 59
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Source: Supplemental Table E5
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the species level among children
Abundance in Group 1: increased abundance in lesional skin
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus aureus |
Revision editor(s): WikiWorks
Experiment 7
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 2-12 years
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 18-62 years
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- teenager/adult age 13-62
- Group 1 sample size Number of subjects in the case (exposed) group
- 69
Lab analysis
Statistical Analysis
- 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
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Source: Supplemental Table E5
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with lesional skin
Abundance in Group 1: increased abundance in 18-62 years
| NCBI | Quality Control | Links |
|---|---|---|
| Cutibacterium acnes | ||
| Lactobacillus iners | ||
| Staphylococcus epidermidis |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-14
Source: Supplemental Table E5
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with lesional skin
Abundance in Group 1: decreased abundance in 18-62 years
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus cristatus | ||
| Rothia mucilaginosa |
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