Investigation of systemic granulomatosis in cultured meagre, Argyrosomus regius, using clinical metagenomics/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Subjects
- Location of subjects
- Greece
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Argyrosomus regius
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Kidney Reniculate kidney,Kidney,kidney
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Granulomatosis with Polyangiitis ANCA-associated vasculitis,GPA,granulomatosis - Wegener's,granulomatosis with polyangiitis,Midline granulomatosis,necrotizing respiratory granulomatosis,pauci-immune glomerulonephritis associated with granulomatosis with polyangiitis,Wegener Granulomatosis,Wegener granulomatosis,Wegener's granulomatosis,Wegener's syndrome,Wg,Granulomatosis with Polyangiitis,granulomatosis with Polyangiitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy/Healthy with no visible granuloma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Kidneys with calcification
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Meagre fishes with tissue calcification in their kidneys
- 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
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Figure 6, Table 2
Description: The differential abundance of microbial taxa as identified by LefSe in two health groups (healthy and kidney with calcification)
Abundance in Group 1: increased abundance in Kidneys with calcification
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Actinomarina sp. | ||
| Flavobacteriaceae |
Revision editor(s): Barrakat
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Table 2, Figure 6
Description: The differential abundance of microbial taxa as identified by LefSe in two health groups (healthy and kidney with calcification)
Abundance in Group 1: decreased abundance in Kidneys with calcification
| NCBI | Quality Control | Links |
|---|---|---|
| Anoxybacillus | ||
| Dermacoccus | ||
| Micrococcus | ||
| Paracoccus |
Revision editor(s): Barrakat, Svetlana up
