Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare
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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
- Singapore
- 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 epithelium Skin epithelium,skin epithelium
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Eczema Eczema,eczema
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Atopic dermatitis case group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Atopic dermatitis case group with volunteers reporting past atopic dermatitis episodes
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
- Sequencing type
- WMS
- 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
- Illumina
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Curated date: 2023/03/30
Curator: Ufuoma Ejite
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Source: Supplementary Table 5
Description: Differential microbial abundance between controls and AD case group
Abundance in Group 1: decreased abundance in Atopic dermatitis case group
NCBI | Quality Control | Links |
---|---|---|
Gemella | ||
Haemophilus | ||
Streptococcus | ||
Veillonella |
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Signature 2
Curated date: 2023/03/30
Curator: Ufuoma Ejite
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Source: Supplementary Table 5
Description: Differential microbial abundance between controls and AD case group
Abundance in Group 1: increased abundance in Atopic dermatitis case group
NCBI | Quality Control | Links |
---|---|---|
Dermacoccus | ||
Methylobacterium | ||
Deinococcus |
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Females (controls)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Females (cases)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Atopic dermatitis (AD) case females
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
Signature 1
Curated date: 2023/03/30
Curator: Ufuoma Ejite
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Source: Supplementary Figure 6B
Description: Differential microbial abundance between female controls and female AD case group
Abundance in Group 1: decreased abundance in Females (cases)
NCBI | Quality Control | Links |
---|---|---|
Dermacoccus | ||
Methylobacterium |
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Males (control)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Males (case)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Atopic dermatitis (AD) case males
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Curated date: 2023/03/30
Curator: Ufuoma Ejite
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Source: Supplementary Figure 6B
Description: Differential microbial abundance between male controls and male AD case group
Abundance in Group 1: decreased abundance in Males (case)
NCBI | Quality Control | Links |
---|---|---|
Deinococcus | ||
Dermacoccus |
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Signature 2
Curated date: 2023/03/30
Curator: Ufuoma Ejite
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Source: Supplementary Figure 6B
Description: Differential microbial abundance between male controls and male AD case group
Abundance in Group 1: increased abundance in Males (case)
NCBI | Quality Control | Links |
---|---|---|
Streptococcus | ||
Gemella | ||
Veillonella | ||
Haemophilus |
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- AD cases with no reported cream usage
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- AD cases with no reported cream usage (no emollient creams or topical corticosteroids)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
Signature 1
Curated date: 2023/03/30
Curator: Ufuoma Ejite
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Source: Supplementary Figure 6C
Description: Differential microbial abundance between controls and AD case group with no cream usage
Abundance in Group 1: decreased abundance in AD cases with no reported cream usage
NCBI | Quality Control | Links |
---|---|---|
Dermacoccus | ||
Methylobacterium |
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Signature 2
Curated date: 2023/03/30
Curator: Ufuoma Ejite
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Source: Supplementary Figure 6C
Description: Differential microbial abundance between controls and AD case group with no cream usage
Abundance in Group 1: increased abundance in AD cases with no reported cream usage
NCBI | Quality Control | Links |
---|---|---|
Streptococcus | ||
Gemella | ||
Veillonella | ||
Haemophilus |
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks