Salivary microbiota and inflammation-related proteins in patients with psoriasis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-6-1
Curated date: 2023/03/30
Curator: Ellajessica
Revision editor(s): Ellajessica, Aiyshaaaa, Peace Sandy
Subjects
- Location of subjects
- Denmark
- 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- 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 0 name Corresponds to the control (unexposed) group for case-control studies
- orally healthy individuals
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Psoriasis patient
- Group 0 sample size Number of subjects in the control (unexposed) group
- 52
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .0001
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-1
Source: Figure 2(b)
Description: Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between healthy controls and Psoriasis.
Abundance in Group 1: increased abundance in Psoriasis patient
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter sp. | ||
| Capnocytophaga sp. | ||
| Haemophilus parainfluenzae | ||
| Neisseria perflava | ||
| Peptoniphilus lacrimalis | ||
| Prevotella melaninogenica | ||
| Rothia mucilaginosa |
Revision editor(s): Ellajessica, Aiyshaaaa
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-1
Source: Figure 2(b)
Description: Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between healthy controls and Psoriasis.
Abundance in Group 1: decreased abundance in Psoriasis patient
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces sp. | ||
| Arachnia propionica | ||
| Capnocytophaga sp. | ||
| Lactobacillus gasseri | ||
| Neisseria macacae | ||
| Streptococcus mutans | ||
| Streptococcus sobrinus | ||
| Veillonella atypica | ||
| Veillonella sp. |
Revision editor(s): Ellajessica, Aiyshaaaa
