The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-10-16
Subjects
- Location of subjects
- Germany
- 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 epidermis Epidermis,Skin,Vertebrate epidermis,Skin epidermis,skin epidermis
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cutaneous T-cell lymphoma CTCL,cutaneous T cell lymphoma,cutaneous T-cell lymphoma,cutaneous T-cell non-Hodgkin lymphoma,cutaneous T-cell non-Hodgkin's lymphoma,PCTCL,primary cutaneous T-cell non-Hodgkin lymphoma,primary cutaneous T-cell non-Hodgkin's lymphoma,skin T-cell non-Hodgkin's lymphoma,T-cell non-Hodgkin's lymphoma of skin,T-cell non-Hodgkin's lymphoma of the skin,Cutaneous T-cell lymphoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control( ΔSA-neutral subgroup)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mycosis fungoides( ΔSA-positive)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with significant dysbiosis on MF lesions exhibiting S. aureus expansion. Antimicrobial peptides (AMPs) were probably less prevalent when the overgrowth occurred, and S. aureus was able to adapt to these peptides to become a more virulent strain on the lesions.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- PCR
- 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).
- raw counts
- Statistical test
- ANOVA
- 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
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-10-16
Source: fig 2b, d-g
Description: Differential abundance analysis of microbial species for N = 65 metagenomic samples.
Abundance in Group 1: increased abundance in Mycosis fungoides( ΔSA-positive)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus aureus |
Revision editor(s): Jayybb, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-10-16
Source: fig 2b, d-g
Description: Differential abundance analysis of microbial species for N = 65 metagenomic samples.
Abundance in Group 1: decreased abundance in Mycosis fungoides( ΔSA-positive)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus epidermidis | ||
| Staphylococcus hominis | ||
| Cutibacterium acnes |
Revision editor(s): Jayybb, Peace Sandy
