Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus

From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
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

Curated date: 2024/03/20

Curator: Ndruscilla

Revision editor(s): Ndruscilla, Scholastica

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

Curated date: 2024/03/20

Curator: Ndruscilla

Revision editor(s): Ndruscilla, Scholastica

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 ControlLinks
Lutibacter
Pseudoteredinibacter
Cyclobacteriaceae

Revision editor(s): Ndruscilla, Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-8-2

Curated date: 2024/03/20

Curator: Ndruscilla

Revision editor(s): Ndruscilla, Scholastica

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 ControlLinks
Enterobacterales
Candidatus Gastranaerophilales

Revision editor(s): Ndruscilla, Scholastica

Experiment 2


Reviewed Marked as Reviewed by Svetlana up on 2024-8-2

Curated date: 2024/08/01

Curator: Scholastica

Revision editor(s): Scholastica

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

Curated date: 2024/08/01

Curator: Scholastica

Revision editor(s): Scholastica

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 ControlLinks
Candidatus Photodesmus

Revision editor(s): Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-8-2

Curated date: 2024/08/01

Curator: Scholastica

Revision editor(s): Scholastica

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 ControlLinks
Cellvibrionaceae
HOC36HOC36
Gammaproteobacteria
Roseobacter

Revision editor(s): Scholastica

Experiment 3


Reviewed Marked as Reviewed by Svetlana up on 2024-8-2

Curated date: 2024/08/01

Curator: Scholastica

Revision editor(s): Scholastica

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

Curated date: 2024/08/01

Curator: Scholastica

Revision editor(s): Scholastica

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 ControlLinks
Microbacterium
BD2-3BD2-3
Bacteroidia
vadinHA49vadinHA49
Brevibacterium

Revision editor(s): Scholastica

Experiment 4


Reviewed Marked as Reviewed by Svetlana up on 2024-8-2

Curated date: 2024/08/01

Curator: Scholastica

Revision editor(s): Scholastica

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

Curated date: 2024/08/01

Curator: Scholastica

Revision editor(s): Scholastica

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 ControlLinks
Cyclobacteriaceae
Candidatus Photodesmus
Cryomorphaceae
Vibrio
Pseudoteredinibacter
Lutibacter

Revision editor(s): Scholastica

Experiment 5


Reviewed Marked as Reviewed by Svetlana up on 2024-8-2

Curated date: 2024/08/01

Curator: Scholastica

Revision editor(s): Scholastica

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

Curated date: 2024/08/01

Curator: Scholastica

Revision editor(s): Scholastica

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 ControlLinks
Pseudoalteromonas
Pseudophaeobacter

Revision editor(s): Scholastica