Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Lwaldron on 2023-4-1
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
Reviewed Marked as Reviewed by Lwaldron on 2023-4-2
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: decreased abundance in Atopic dermatitis case group
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella | ||
| Haemophilus | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): Ufuoma Ejite, Lwaldron, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2023-4-2
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
