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
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
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Subjects
- Location of subjects
- Finland
- Germany
- United Kingdom
- 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
- 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
- adult with atopic dermatitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- adult with moderate-to-severe chronic 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
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Source: Figure 1c
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 |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Source: Figure 1c
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. | ||
| Cutibacterium acnes | ||
| Finegoldia sp. | ||
| Lactobacillus sp. | ||
| Roseateles sp. | ||
| Staphylococcus sp. |
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
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,Psoriasis
- 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
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Source: Figure 1c
Description: Differentially abundant OTUs among adults with psoriasis (PSO) and healthy controls
Abundance in Group 1: increased abundance in adult with psoriasis
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerococcus sp. | ||
| Corynebacterium kroppenstedtii | ||
| Corynebacterium simulans | ||
| Finegoldia sp. | ||
| Neisseriaceae |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Source: Figure 1c
Description: Differentially abundant OTUs among adults with psoriasis (PSO) and healthy controls
Abundance in Group 1: decreased abundance in adult with psoriasis
| NCBI | Quality Control | Links |
|---|---|---|
| Burkholderia sp. | ||
| Lactobacillus sp. | ||
| Roseateles sp. |
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
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 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 moderate-to-severe chronic atopic dermatitis
- Group 1 sample size Number of subjects in the case (exposed) group
- 82
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- Kruskall-Wallis
- Spearman Correlation
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Confounders controlled for: "anatomical location" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.anatomical location, Confounders controlled for: "clinic center" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.clinic center
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Source: supplementary table 2
Description: Abundant OTUs that were significantly associated with disease and also significantly associated with a confounded effect.
Abundance in Group 1: increased abundance in adult with atopic dermatitis
| NCBI | Quality Control | Links |
|---|---|---|
| Finegoldia sp. | ||
| Bradyrhizobium sp. | ||
| Anaerococcus sp. | ||
| Variovorax paradoxus | ||
| Lactobacillus sp. | ||
| Staphylococcus aureus |
Revision editor(s): Folakunmi
Experiment 4
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- adults with psoriasis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- adult with moderate-to-severe chronic plaque-type psoriasis
- Group 1 sample size Number of subjects in the case (exposed) group
- 119
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- Mann-Whitney (Wilcoxon)
- Spearman Correlation
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Source: supplementary table 2
Description: Abundant OTUs that were significantly associated with disease and also significantly associated with a confounded effect.
Abundance in Group 1: increased abundance in adults with psoriasis
| NCBI | Quality Control | Links |
|---|---|---|
| Finegoldia sp. | ||
| Bradyrhizobium sp. | ||
| Corynebacterium sp. | ||
| Corynebacterium kroppenstedtii |
Revision editor(s): Folakunmi
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