Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus
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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
Experiment 1
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Strongylocentrotus purpuratus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Body external integument structure Body external integument structure,body external integument structure
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Strongylocentrotus purpuratus purple sea urchin,purple urchin,Strongylocentrotus purpuratus (Stimpson, 1857),Strongylocentrotus purpuratus,strongylocentrotus purpuratus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy sea urchins
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diseased sea urchins
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Sea urchins with spotting disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Table S3
Description: Significantly differentially abundant taxa as identified by LEfSe for diseased versus healthy global surface microbiome samples
Abundance in Group 1: increased abundance in Diseased sea urchins
NCBI | Quality Control | Links |
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Lutibacter | ||
Pseudoteredinibacter | ||
Cyclobacteriaceae |
Revision editor(s): Ndruscilla, Scholastica
Signature 2
Source: Supplementary Table S3
Description: Significantly differentially abundant taxa as identified by LEfSe for diseased versus healthy global surface microbiome samples
Abundance in Group 1: decreased abundance in Diseased sea urchins
NCBI | Quality Control | Links |
---|---|---|
Enterobacterales | ||
Candidatus Gastranaerophilales |
Revision editor(s): Ndruscilla, Scholastica
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Microbiome measurement Microbiome measurement,microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lesion surface samples (LS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lesion body wall samples (LBW)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Lesion body wall samples from sea urchins with spotting disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Table S6
Description: Significantly differentially abundant taxa as identified by LEFSe for the lesion surface (LS) versus lesion body wall (LBW) microbiome samples
Abundance in Group 1: increased abundance in Lesion body wall samples (LBW)
NCBI | Quality Control | Links |
---|---|---|
Candidatus Photodesmus |
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Table S6
Description: Significantly differentially abundant taxa as identified by LEFSe for the lesion surface (LS) versus lesion body wall (LBW) microbiome samples
Abundance in Group 1: decreased abundance in Lesion body wall samples (LBW)
NCBI | Quality Control | Links |
---|---|---|
Cellvibrionaceae | ||
HOC36HOC36 | ||
Gammaproteobacteria | ||
Roseobacter |
Revision editor(s): Scholastica
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Coelomic fluid , Body wall Coelomic fluid,coelomic fluid,Trunk wall,Wall fo trunk,Wall of trunk,Body wall,body wall
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy coelomic fluid (HCF)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diseased coelomic fluid (DCF) and lesion body wall (LBW)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diseased coelomic fluid (DCF) and lesion body wall (LBW) samples from sea urchins with spotting disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table S9
Description: Significantly differentially abundance taxa as identified by LEfSe in the tissue microbiome samples
Abundance in Group 1: decreased abundance in Diseased coelomic fluid (DCF) and lesion body wall (LBW)
NCBI | Quality Control | Links |
---|---|---|
Microbacterium | ||
BD2-3BD2-3 | ||
Bacteroidia | ||
vadinHA49vadinHA49 | ||
Brevibacterium |
Revision editor(s): Scholastica
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy coelomic fluid (HCF) and diseased coelomic fluid (DCF)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lesion body wall (LBW)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Lesion body wall (LBW) samples from sea urchins with spotting disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table S9
Description: Significantly differentially abundance taxa as identified by LEfSe in the tissue microbiome samples
Abundance in Group 1: increased abundance in Lesion body wall (LBW)
NCBI | Quality Control | Links |
---|---|---|
Cyclobacteriaceae | ||
Candidatus Photodesmus | ||
Cryomorphaceae | ||
Vibrio | ||
Pseudoteredinibacter | ||
Lutibacter |
Revision editor(s): Scholastica
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy coelomic fluid (HCF) and lesion body wall (LBW)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diseased coelomic fluid (DCF)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diseased coelomic fluid (DCF) samples from sea urchins with spotting disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table S9
Description: Significantly differentially abundance taxa as identified by LEfSe in the tissue microbiome samples
Abundance in Group 1: increased abundance in Diseased coelomic fluid (DCF)
NCBI | Quality Control | Links |
---|---|---|
Pseudoalteromonas | ||
Pseudophaeobacter |
Revision editor(s): Scholastica