Investigation of systemic granulomatosis in cultured meagre, Argyrosomus regius, using clinical metagenomics
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
In this study, we have applied amplicon metagenomics of the 16S rRNA gene in kidneys of fish exhibiting different health states, ranging from apparently healthy to kidneys with calcification. Comparison of the kidney microbiomes of the different fish groups showed that all fish had similar bacterial communities. Linear discriminant analysis effect size revealed only three OTUs significantly enriched in the sick individuals, with no known granuloma-causing species being present among them, reinforcing the hypothesis of a non-infectious cause of the disease in this fish species.
Experiment 1
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
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
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
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Systemic Granulomatosis (SG)-affected
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sick with Kidney calcification
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Meagre fishes with tissue calcifications in their kidneys
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6, Table 2
Description: The differential abundance of microbial taxa as identified by LefSe in two health groups: Systemic granulomatosis (SG)-affected and kidney with calcification.
Abundance in Group 1: increased abundance in Sick with Kidney calcification
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Actinomarina sp. | ||
| Flavobacteriaceae |
Revision editor(s): Barrakat
Signature 2
Source: Table 2 Fig 6
Description: The differential abundance of microbial taxa as identified by LefSe in two health groups: Systemic granulomatosis (SG)-affected and kidney with calcification.
Abundance in Group 1: decreased abundance in Sick with Kidney calcification
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Burkholderiaceae | ||
| Paracoccus | ||
| Pyrinomonas | ||
| Sphingobacteriales | ||
| unclassified Beijerinckiaceae |
Revision editor(s): Barrakat
Experiment 3
Subjects
- 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
- Sick
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Meagre fishes with SG-affected kidneys and 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
- 20
Lab analysis
Statistical Analysis
Signature 1
Source: Table 2, Supplementary Figure 2, Supplementary Figure 3
Description: The differential abundance of microbial taxa as identified by LefSe in two health groups (healthy and sick)
Abundance in Group 1: increased abundance in Sick
| NCBI | Quality Control | Links |
|---|---|---|
| Burkholderiaceae | ||
| Gallionellaceae | ||
| Rhodobacterales |
Revision editor(s): Barrakat, Svetlana up
Signature 2
Source: Table 2, Supplementary Figure 2, Supplementary Figure 3
Description: The differential abundance of microbial taxa as identified by LefSe in two health groups (healthy and sick)
Abundance in Group 1: decreased abundance in Sick
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Bacillus | ||
| Coraliomargarita | ||
| Meiothermus | ||
| Paracoccus | ||
| Streptococcus |
Revision editor(s): Barrakat, Svetlana up
