The skin microbiome is different in pediatric versus adult atopic dermatitis

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
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


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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