Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Shaw CG, Pavloudi C, Crow RS, Saw JH, Smith LC
Journal
BMC microbiology
Year
2024
Keywords:
16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic
BACKGROUND: Spotting disease infects a variety of sea urchin species across many different marine locations. The disease is characterized by discrete lesions on the body surface composed of discolored necrotic tissue that cause the loss of all surface appendages within the lesioned area. A similar, but separate disease of sea urchins called bald sea urchin disease (BSUD) has overlapping symptoms with spotting disease, resulting in confusions in distinguishing the two diseases. Previous studies have focus on identifying the underlying causative agent of spotting disease, which has resulted in the identification of a wide array of pathogenic bacteria that vary based on location and sea urchin species. Our aim was to investigate the spotting disease infection by characterizing the microbiomes of the animal surface and various tissues. RESULTS: We collected samples of the global body surface, the lesion surface, lesioned and non-lesioned body wall, and coelomic fluid, in addition to samples from healthy sea urchins. 16S rRNA gene was amplified and sequenced from the genomic DNA. Results show that the lesions are composed mainly of Cyclobacteriaceae, Cryomorphaceae, and a few other taxa, and that the microbial composition of lesions is the same for all infected sea urchins. Spotting disease also alters the microbial composition of the non-lesioned body wall and coelomic fluid of infected sea urchins. In our closed aquarium systems, sea urchins contracted spotting disease and BSUD separately and therefore direct comparisons could be made between the microbiomes from diseased and healthy sea urchins. CONCLUSION: Results show that spotting disease and BSUD are separate diseases with distinct symptoms and distinct microbial compositions.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
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
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
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: increased abundance in Diseased sea urchins
| NCBI | Quality Control | Links |
|---|---|---|
| Lutibacter | ||
| Pseudoteredinibacter | ||
| Cyclobacteriaceae |
Revision editor(s): Ndruscilla, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
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
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
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: increased abundance in Lesion body wall samples (LBW)
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Photodesmus |
Revision editor(s): Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
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 | ||
| Pseudophaeobacter | ||
| HOC36HOC36 | ||
| Gammaproteobacteria | ||
| Roseobacter |
Revision editor(s): Scholastica
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
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
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
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
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
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
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