Microbe-host interplay in atopic dermatitis and psoriasis

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31619666

DOI Digital object identifier for electronic documents.

10.1038/s41467-019-12253-y

URI

Authors

Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B, Alenius H

Journal

Nature communications

Year

2019

Despite recent advances in understanding microbial diversity in skin homeostasis, the relevance of microbial dysbiosis in inflammatory disease is poorly understood. Here we perform a comparative analysis of skin microbial communities coupled to global patterns of cutaneous gene expression in patients with atopic dermatitis or psoriasis. The skin microbiota is analysed by 16S amplicon or whole genome sequencing and the skin transcriptome by microarrays, followed by integration of the data layers. We find that atopic dermatitis and psoriasis can be classified by distinct microbes, which differ from healthy volunteers microbiome composition. Atopic dermatitis is dominated by a single microbe (Staphylococcus aureus), and associated with a disease relevant host transcriptomic signature enriched for skin barrier function, tryptophan metabolism and immune activation. In contrast, psoriasis is characterized by co-occurring communities of microbes with weak associations with disease related gene expression. Our work provides a basis for biomarker discovery and targeted therapies in skin dysbiosis.

Experiment 1

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Curated date: 2021/01/10

Curator: WikiWorks

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Subjects

Location of subjects: Finland; Germany; United Kingdom

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: healthy control
Group 1 name Corresponds to the case (exposed) group for case-control studies: adult with atopic dermatitis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: adult with atopic dermatitis
Group 0 sample size Number of subjects in the control (unexposed) group: 115
Group 1 sample size Number of subjects in the case (exposed) group: 82
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 weeks

Lab analysis

Sequencing type: 16S

Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

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)?: Yes
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged
Richness Number of species: unchanged

Signature 1

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Curated date: 2021/01/10

Curator: Lucy Mellor

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Source: Figure 1c, Supplemental Figure 3b

Description: Differentially abundant OTUs among adults with atopic dermatitis (AD) and healthy controls

Abundance in Group 1: increased abundance in adult with atopic dermatitis

NCBI	Quality Control	Links
Staphylococcus aureus

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Signature 2

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Curated date: 2021/01/10

Curator: Lucy Mellor

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Source: Figure 1c, Supplemental Figure 3b

Description: Differentially abundant OTUs among adults with atopic dermatitis (AD) and healthy controls

Abundance in Group 1: decreased abundance in adult with atopic dermatitis

NCBI	Quality Control	Links
Burkholderia sp.
Finegoldia sp.
Staphylococcus sp.
Lactobacillus sp.
Pelomonas sp.
Cutibacterium acnes

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Experiment 2

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Curated date: 2021/01/10

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: psoriasis Other and unspecified pityriasis,OTHER PSORIASIS,Other psoriasis and similar disorders,Other psoriasis and similar disorders (disorder),Other psoriasis and similar disorders excluding psoriatic arthropathy,Palmoplantaris Pustulosis,PITYRIASIS NEC & NOS,PSORIAS RELATED DIS NEC,Psoriases,psoriasis,Psoriasis and similar disorders,Psoriasis and similar disorders (disorder),Psoriasis and similar disorders (navigational concept),Psoriasis and similar disorders NOS,Psoriasis and similar disorders NOS (disorder),Pustular Psoriasis of Palms and Soles,PUSTULAR PSORIASIS OF PALMS SOLES,Pustulosis of Palms and Soles,PUSTULOSIS OF PALMS SOLES,Pustulosis Palmaris et Plantaris

Group 1 name Corresponds to the case (exposed) group for case-control studies: adult with psoriasis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: adult with psoriasis
Group 1 sample size Number of subjects in the case (exposed) group: 119