Abundance alteration of nondominant species in fecal-associated microbiome of patients with SAPHO syndrome/Experiment 1
Curated date: 2024/03/06
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Peace Sandy
Subjects
- Location of subjects
- China
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- SAPHO syndrome Acquired Hyperostosis Syndrome,acquired hyperostosis syndrome,PPHS,Pustulo-psoriatic hyperostotic Spondyloarthritis,SAPHO syndrome,synovitis acne pustulosis hyperostosis osteitis,synovitis, acne, Pustlosis, hyperostosis, and osteomyelitis,Synovitis, acne, pustulosis palmaris, hyperostosis, osteomyelitis syndrome,synovitis, acne, pustulosis palmaris, hyperostosis, osteomyelitis syndrome,synovitis, acne, pustulosis, hyperostosis, and osteitis syndrome,synovitis-acne-pustulosis-hyperostosis-osteitis syndrome,sAPHO syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SAPHO syndrome Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SAPHO (synovitis, acne, pustulosis, hyperostosis and osteosis) syndrome, The main features of SAPHO syndrome consist of cutaneous and osteoarticular manifestations, the latter more often affects the anterior chest wall and has a typical radiologic finding called the “bull’s head sign”
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Curated date: 2024/03/08
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Peace Sandy
Source: Figure 3
Description: Distingushing taxa identified in the HC and SAPHO groups using LEfSe analysis. (a) Cladogram and (b) LDA score bar chart constructed using the LEfSe method. HC, healthy control; SAPHO, SAPHO syndrome
Abundance in Group 1: increased abundance in SAPHO syndrome Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Gemella |
Revision editor(s): Omojokunoluwatomisin, Peace Sandy
Signature 2
Curated date: 2024/03/09
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Peace Sandy
Source: Figure 3
Description: Distingushing taxa identified in the HC and SAPHO groups using LEfSe analysis. (a) Cladogram and (b) LDA score bar chart constructed using the LEfSe method. HC, healthy control; SAPHO, SAPHO syndrome
Abundance in Group 1: decreased abundance in SAPHO syndrome Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Ruminiclostridium |
Revision editor(s): Omojokunoluwatomisin, Peace Sandy
