Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium
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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
- Cellular bone tissue Cellular bone tissue,cellular bone tissue
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Bacterial disease Bacteria caused disease or disorder,Bacteria disease or disorder,Bacteria infectious disease,bacterial disease,bacterial disorder,bacterial infection,bacterial infectious disease,infection, bacterial,infections, bacterial,Bacterial disease
- 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
- Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 6 & Supplementary Data file 2, Table S7.
Description: Taxa with significantly different abundances in the microbiomes on sea urchins
Abundance in Group 1: increased abundance in Diseased sea urchins
Revision editor(s): Omojokunoluwatomisin
Signature 2
Source: Figure 6 & Supplementary Data file 2, Table S7.
Description: Taxa with significantly different abundances in the microbiomes on sea urchins among the groups.
Abundance in Group 1: decreased abundance in Diseased sea urchins
Revision editor(s): Omojokunoluwatomisin
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Recovered sea urchins
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist.
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 6 & Supplementary Data file 2, Table S7.
Description: Taxa with significantly different abundances in the microbiomes on sea urchins among the groups.
Abundance in Group 1: increased abundance in Recovered sea urchins
Revision editor(s): Omojokunoluwatomisin
Signature 2
Source: Figure 6 & Supplementary Data file 2, Table S7.
Description: Taxa with significantly different abundances in the microbiomes on sea urchins among the groups.
Abundance in Group 1: decreased abundance in Recovered sea urchins
Revision editor(s): Omojokunoluwatomisin
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Recovered 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
- Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 6 & Supplementary Data file 2, Table S7.
Description: Taxa with significantly different abundances in the microbiomes on sea urchins among the groups.
Abundance in Group 1: increased abundance in Diseased sea urchins
Revision editor(s): Omojokunoluwatomisin
Signature 2
Source: Figure 6 & Supplementary Data file 2, Table S7.
Description: Taxa with significantly different abundances in the microbiomes on sea urchins in each groups
Abundance in Group 1: decreased abundance in Diseased sea urchins
Revision editor(s): Omojokunoluwatomisin
Experiment 4
Curated date: 2024/04/16
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Carita Ndibe
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Anatomical surface Anatomical surface,anatomical surface
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Sea water from healthy sea urchins aquarium
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sea water from diseased sea urchins aquarium
- Group 0 sample size Number of subjects in the control (unexposed) group
- 2
- Group 1 sample size Number of subjects in the case (exposed) group
- 2
Lab analysis
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina, Non-quantitative PCR
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Supplementary Data File 2,Table S6
Description: Relative abundance of the most abundant genera in the seawater samples.
Abundance in Group 1: increased abundance in Sea water from diseased sea urchins aquarium
| NCBI | Quality Control | Links |
|---|---|---|
| Colwellia | ||
| Erwiniaceae | ||
| Gammaproteobacteria | ||
| Leucothrix | ||
| Lutibacter | ||
| Spongiibacteraceae | ||
| rhodobacteraceaerhodobacteraceae | ||
| ruegeriaruegeria | ||
| NS10 marine groupNS10 marine group |
Revision editor(s): Carita Ndibe
Signature 2
Source: Supplementary Data File 2, Table S6
Description: Relative abundance of the most abundant genera in the seawater samples
Abundance in Group 1: decreased abundance in Sea water from diseased sea urchins aquarium
Revision editor(s): Carita Ndibe
Experiment 5
Curated date: 2024/04/16
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Carita Ndibe
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sea water from recovered sea urchins aquarium
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist.
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Supplementary Data File 2, Table S6
Description: Relative abundance of the most abundant genera in the seawater samples
Abundance in Group 1: increased abundance in Sea water from recovered sea urchins aquarium
| NCBI | Quality Control | Links |
|---|---|---|
| Psychromonas | ||
| rhodobacteracearhodobacteracea | ||
| Gammaproteobacteria | ||
| Spongiibacteraceae | ||
| NCBI:txid97050NCBI:txid97050 | ||
| Alteromonadaceae | ||
| Alphaproteobacteria |
Revision editor(s): Carita Ndibe
Signature 2
Source: Supplementary Data File 2, Table S6
Description: Relative abundance of the most abundant genera in the seawater samples
Abundance in Group 1: decreased abundance in Sea water from recovered sea urchins aquarium
Revision editor(s): Carita Ndibe
Experiment 6
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Cellular bone tissue Cellular bone tissue,cellular bone tissue
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Recovered 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
- Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.
- 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
- PCR
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
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
Signature 1
Source: Supplementary Data file 3, figure 6A & TableS4-5.
Description: Taxa have different abundances in microbiomes from samples collected from diseased sea urchins compared to recovered sea urchins
Abundance in Group 1: increased abundance in Diseased sea urchins
Revision editor(s): Omojokunoluwatomisin
Signature 2
Source: Supplementary Data file 3, figure 6A & TableS4-5.
Description: Taxa have different abundances in microbiomes from samples collected from diseased sea urchins compared to recovered sea urchins
Abundance in Group 1: decreased abundance in Diseased sea urchins
Revision editor(s): Omojokunoluwatomisin
Experiment 7
Curated date: 2024/04/17
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Carita Ndibe
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Anatomical surface Anatomical surface,anatomical surface
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Sea water from recovered sea urchins aquarium
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sea water diseased sea urchins aquarium
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The sample collected from the water in the aquarium where the sea urchins with Bald sea urchin disease (BSUD) were cultured.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 2
- Group 1 sample size Number of subjects in the case (exposed) group
- 2
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, Non-quantitative PCR
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Supplementary Data File 2, Table S6
Description: Relative abundance of the most abundant genera in the seawater samples
Abundance in Group 1: increased abundance in Sea water diseased sea urchins aquarium
| NCBI | Quality Control | Links |
|---|---|---|
| Vibrio | ||
| Colwellia | ||
| RhodobacteraceaeRhodobacteraceae | ||
| Leucothrix | ||
| NCBI:txid97050NCBI:txid97050 | ||
| Erwiniaceae | ||
| Lutibacter | ||
| NS10 marine groupNS10 marine group |
Revision editor(s): Carita Ndibe
Signature 2
Source: Supplementary Data File 2, Table S6
Description: Relative abundance of the most abundant genera in the seawater samples
Abundance in Group 1: decreased abundance in Sea water diseased sea urchins aquarium
Revision editor(s): Carita Ndibe
Experiment 8
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Cellular bone tissue Cellular bone tissue,cellular bone tissue
- 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
- Recovered sea urchins
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist.
- 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
- PCR
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
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
Signature 1
Source: Supplementary Data file 3, figure 6B & TableS4-5.
Description: Taxa have different abundances in microbiomes from samples collected from recovered sea urchins compared to healthy sea urchins
Abundance in Group 1: increased abundance in Recovered sea urchins
Revision editor(s): Omojokunoluwatomisin
Signature 2
Source: Supplementary Data file 3, figure 6B & TableS4-5.
Description: Taxa have different abundances in microbiomes from samples collected from recovered sea urchins compared to healthy sea urchins
Abundance in Group 1: decreased abundance in Recovered sea urchins
Revision editor(s): Omojokunoluwatomisin
