The skin microbiome is different in pediatric versus adult atopic dermatitis
-
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 (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 1b, text
Description: Skin microorganisms differ with age in the healthy skin
Abundance in Group 1: increased abundance in 18-62 years
| NCBI | Links |
|---|---|
| Corynebacterium sp. | |
| Cutibacterium acnes | |
| Staphylococcus epidermidis |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 1b, text
Description: Skin microorganisms differ with age in the healthy skin
Abundance in Group 1: decreased abundance in 18-62 years
| NCBI | Links |
|---|---|
| Streptococcus sp. |
Revision editor(s): WikiWorks
Signature 3
Source: Supplemental Table E2, Figure 2b, text
Description: Taxonomic compositions of the healthy skin microbiome at the genus level
Abundance in Group 1: increased abundance in 18-62 years
| NCBI | Links |
|---|---|
| Propionibacterium ⚠ | |
| Corynebacterium | |
| Staphylococcus | |
| Lactobacillus | |
| Finegoldia | |
| Anaerococcus ⚠ |
Revision editor(s): WikiWorks
Signature 4
Source: Supplemental Table E2, Figure 2b, text
Description: Taxonomic compositions of the healthy skin microbiome at the genus level
Abundance in Group 1: decreased abundance in 18-62 years
| NCBI | Links |
|---|---|
| Rothia | |
| Streptococcus | |
| Granulicatella | |
| Gemella | |
| Haemophilus |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- 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
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplemental Table E4, Figure 2b
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among children
Abundance in Group 1: increased abundance in lesional skin
| NCBI | Links |
|---|---|
| Staphylococcus |
Revision editor(s): WikiWorks
Signature 2
Source: Supplemental Table E4, Figure 2b
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 | Links |
|---|---|
| Corynebacterium | |
| Actinomyces | |
| Streptococcus | |
| Gemella | |
| Veillonella | |
| Porphyromonas | |
| Fusobacterium |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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 0 sample size Number of subjects in the control (unexposed) group
- 59
- Group 1 sample size Number of subjects in the case (exposed) group
- 69
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
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 | Links |
|---|---|
| Propionibacterium ⚠ | |
| Corynebacterium | |
| Lactobacillus |
Revision editor(s): WikiWorks
Signature 2
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 | Links |
|---|---|
| Streptococcus | |
| Granulicatella | |
| Gemella | |
| Neisseria | |
| Haemophilus |
Revision editor(s): WikiWorks
Signature 3
Source: Supplemental Table E4
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with non-lesional skin
Abundance in Group 1: increased abundance in 13-62 years
| NCBI | Links |
|---|---|
| Propionibacterium ⚠ | |
| Corynebacterium | |
| Lactobacillus |
Revision editor(s): WikiWorks
Signature 4
Source: Supplemental Table E4
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with non-lesional skin
Abundance in Group 1: decreased abundance in 13-62 years
| NCBI | Links |
|---|---|
| Rothia | |
| Streptococcus | |
| Granulicatella | |
| Gemella | |
| Veillonella | |
| Neisseria | |
| Haemophilus |
Revision editor(s): WikiWorks
Experiment 4
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
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 | Links |
|---|---|
| Cutibacterium acnes | |
| Staphylococcus epidermidis | |
| Lactobacillus iners |
Revision editor(s): WikiWorks
Experiment 5
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- 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
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 69
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
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
| NCBI | Links |
|---|---|
| Staphylococcus aureus |
Revision editor(s): WikiWorks
Experiment 6
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- 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
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
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 | Links |
|---|---|
| Staphylococcus aureus |
Revision editor(s): WikiWorks
Experiment 7
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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 0 sample size Number of subjects in the control (unexposed) group
- 59
- Group 1 sample size Number of subjects in the case (exposed) group
- 69
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
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 | Links |
|---|---|
| Cutibacterium acnes | |
| Lactobacillus iners |
Revision editor(s): WikiWorks
Signature 2
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 | Links |
|---|---|
| Streptococcus cristatus |
Revision editor(s): WikiWorks
Signature 3
Source: Supplemental Table E5
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with non-lesional skin
Abundance in Group 1: increased abundance in 18-62 years
| NCBI | Links |
|---|---|
| Cutibacterium acnes | |
| Staphylococcus epidermidis | |
| Lactobacillus iners |
Revision editor(s): WikiWorks
Signature 4
Source: Supplemental Table E5
Description: Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with non-lesional skin
Abundance in Group 1: decreased abundance in 18-62 years
| NCBI | Links |
|---|---|
| Rothia mucilaginosa | |
| Streptococcus cristatus |
Revision editor(s): WikiWorks
