Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Shaw CG, Pavloudi C, Barela Hudgell MA, Crow RS, Saw JH, Pyron RA, Smith LC
Journal
Pathogens and disease
Year
2023
Keywords:
16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome
Bald sea urchin disease (BSUD) is most likely a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages. The disease has a variety of additional symptoms, which may be the result of the many bacteria that are associated with BSUD. Previous studies have investigated causative agents of BSUD, however, there are few reports on the surface microbiome associated with the infection. Here, we report changes to the surface microbiome on purple sea urchins in a closed marine aquarium that contracted and then recovered from BSUD in addition to the microbiome of healthy sea urchins in a separate aquarium. 16S rRNA gene sequencing shows that microhabitats of different aquaria are characterized by different microbial compositions, and that diseased, recovered, and healthy sea urchins have distinct microbial compositions, which indicates that there is a correlation between microbial shifts and recovery from disease.

Experiment 1


Needs review

Curated date: 2024/04/12

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

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

Needs review

Curated date: 2024/04/15

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

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

NCBI Quality ControlLinks
Amoebophilaceae
Amylibacter
Arcobacteraceae
Aureispira
Colwellia
Cryomorphaceae
Donghicola
Flavobacteriaceae
Fusibacter
Granulosicoccus
Halieaceae
Halocynthiibacter
Haloferula
Leucothrix
Luteibaculum
Lutimonas
Paracoccaceae
Planctomicrobium
Poseidonibacter
Pseudoteredinibacter
Reichenbachiella
Rhodopirellula
Rickettsiaceae
Rickettsiales
Roseimarinus
Roseobacter
Saccharospirillaceae
Saprospiraceae
Spongiibacteraceae
Gammaproteobacteria EC3Gammaproteobacteria EC3
Planctomycetota vadinHA49Planctomycetota vadinHA49
Anaerolineae SBR1031 A4bAnaerolineae SBR1031 A4b
Spongiibacteraceae BD1-7 cladeSpongiibacteraceae BD1-7 clade
Verrucomicrobiales DEV007Verrucomicrobiales DEV007
Bdellovibrionaceae OM27 cladeBdellovibrionaceae OM27 clade
Chitinophagales 37-13Chitinophagales 37-13

Revision editor(s): Omojokunoluwatomisin

Signature 2

Needs review

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

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

NCBI Quality ControlLinks
Agarivorans
Bacteroidia
Candidatus Entotheonella
Candidatus Riegeria
Chitinophagales
Christensenellaceae
Clostridia
Desulfobulbus
Desulfotalea
Devosia
Draconibacterium
Flagellimonas
Flavobacteriaceae
Halioglobus
Hyphococcus
Hyphomonadaceae
Jannaschia
Lachnospiraceae
Marinifilaceae
Pseudahrensia
Psychroflexus
Rhodopirellula
Roseimarinus
Rubidimonas
Shewanella
Terasakiellaceae
Ulvibacter
Phycisphaerales AKAU3564 sediment groupPhycisphaerales AKAU3564 sediment group
ChloroplastChloroplast
Bacteroidetes BD2-2Bacteroidetes BD2-2
Bdellovibrionaceae OM27 cladeBdellovibrionaceae OM27 clade
Clostridia vadinBB60 groupClostridia vadinBB60 group
Kiritimatiellaceae MSBL3Kiritimatiellaceae MSBL3
Roseobacter clade Marinomonas lineageRoseobacter clade Marinomonas lineage
Planctomycetota OM190Planctomycetota OM190
Lentisphaeria P.palmC41Lentisphaeria P.palmC41

Revision editor(s): Omojokunoluwatomisin

Experiment 2


Needs review

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

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

NCBI Quality ControlLinks
Aestuariicella
Aliikangiella
Bacteriovoracaceae
Chitinophagales
Christensenellaceae
Clostridia
Coxiella
Desulfobacteraceae
Desulforhopalus
Desulfovibrio
Gammaproteobacteria
Hyphomonadaceae
Lachnospiraceae
Oceanicoccus
Oscillospiraceae
Rickettsiales
Roseibacillus
Rubritalea
Spongiibacteraceae
Thalassotalea
Vibrio
Kiritimatiellae WCHB1-41Kiritimatiellae WCHB1-41
Kiritimatiellaceae R76-B128Kiritimatiellaceae R76-B128
Gracilibacteria JGI 0000069-P22Gracilibacteria JGI 0000069-P22
MicavibrionaceaeMicavibrionaceae
Spirochaetota MVP-15Spirochaetota MVP-15
Phycisphaerales AKAU3564 sediment groupPhycisphaerales AKAU3564 sediment group
Absconditabacteriales (SR1)Absconditabacteriales (SR1)
Rickettsiales SM2D12Rickettsiales SM2D12
Bacteroidales vadinHA21Bacteroidales vadinHA21
RubinisphaeraceaeRubinisphaeraceae
Bdellovibrionaceae OM27 cladeBdellovibrionaceae OM27 clade
Acidobacteriae PAUC26fAcidobacteriae PAUC26f

Revision editor(s): Omojokunoluwatomisin

Signature 2

Needs review

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

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

NCBI Quality ControlLinks
Bacteroidia
Candidatus Entotheonella
Desulfotalea
Devosia
Draconibacterium
Flavobacteriaceae
Halocynthiibacter
Haloferula
Hyphococcus
Hyphomonadaceae
Jannaschia
Kiritimatiellaceae
Luteibaculum
Marinifilaceae
Pseudahrensia
Pseudobdellovibrionaceae
Roseobacter
Rubidimonas
Saprospiraceae
Shewanella
Terasakiellaceae
Ulvibacter
Phycisphaerales AKAU3564Phycisphaerales AKAU3564
chloroplastchloroplast
Bacteroidetes BD2-2Bacteroidetes BD2-2
Clostridia vadinBB60Clostridia vadinBB60
Gammaproteobacteria EC3Gammaproteobacteria EC3

Revision editor(s): Omojokunoluwatomisin

Experiment 3


Needs review

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/17

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

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

NCBI Quality ControlLinks
Amoebophilaceae
Amylibacter
Arcobacteraceae
Aureispira
Colwellia
Cryomorphaceae
Donghicola
Flavobacteriaceae
Fusibacter
Granulosicoccus
Halieaceae
Halocynthiibacter
Haloferula
Leucothrix
Luteibaculum
Lutimonas
Paracoccaceae
Planctomicrobium
Poseidonibacter
Pseudoteredinibacter
Reichenbachiella
Rhodopirellula
Rickettsiaceae
Rickettsiales
Roseimarinus
Roseobacter
Saccharospirillaceae
Saprospiraceae
Spongiibacteraceae
Gammaproteobacteria EC3Gammaproteobacteria EC3
Planctomycetota vadinHA49Planctomycetota vadinHA49
Anaerolineae SBR1031 A4bAnaerolineae SBR1031 A4b
Spongiibacteraceae BD1-7 cladeSpongiibacteraceae BD1-7 clade
Verrucomicrobiales DEV007Verrucomicrobiales DEV007
Bdellovibrionaceae OM27 cladeBdellovibrionaceae OM27 clade
Chitinophagales 37-13Chitinophagales 37-13

Revision editor(s): Omojokunoluwatomisin

Signature 2

Needs review

Curated date: 2024/04/17

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

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

NCBI Quality ControlLinks
Aestuariicella
Aliikangiella
Bacteriovoracaceae
Chitinophagales
Clostridia
Coxiella
Desulfobacteraceae
Desulfovibrio
Gammaproteobacteria
Hyphomonadaceae
Lachnospiraceae
Oceanicoccus
Rickettsiales
Roseibacillus
Rubritalea
Spongiibacteraceae
Thalassotalea
Vibrio
Kiritimatiellae WCHB1-41Kiritimatiellae WCHB1-41
Kiritimatiellaceae R76-B128Kiritimatiellaceae R76-B128
Gracilibacteria JGI 0000069-P22Gracilibacteria JGI 0000069-P22
MicavibrionaceaeMicavibrionaceae
Spirochaetota MVP-15Spirochaetota MVP-15
Phycisphaerales AKAU3564Phycisphaerales AKAU3564
Absconditabacteriales (SR1)Absconditabacteriales (SR1)
Rickettsiales SM2D12Rickettsiales SM2D12
Bacteroidales vadinHA21Bacteroidales vadinHA21
RubinisphaeraceaeRubinisphaeraceae
Bdellovibrionaceae OM27 cladeBdellovibrionaceae OM27 clade
Acidobacteriae PAUC26fAcidobacteriae PAUC26f
Christensenellaceae
Oscillospiraceae

Revision editor(s): Omojokunoluwatomisin

Experiment 4


Needs review

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, Carita Ndibe

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/22

Curator: Carita Ndibe

Revision editor(s): Carita Ndibe

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 ControlLinks
Colwellia
Erwiniaceae
Gammaproteobacteria
Leucothrix
Lutibacter
Spongiibacteraceae
rhodobacteraceaerhodobacteraceae
ruegeriaruegeria
NS10 marine groupNS10 marine group

Revision editor(s): Carita Ndibe

Signature 2

Needs review

Curated date: 2024/04/22

Curator: Carita Ndibe

Revision editor(s): Carita Ndibe

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

NCBI Quality ControlLinks
Alphaproteobacteria
Alteromonadaceae
Bacteroidia
Desulfotalea
Marinifilaceae
Pseudahrensia
Pseudoalteromonas
Psychromonas
Roseimarinus
Vibrio
Bacteroidetes BD2-2Bacteroidetes BD2-2
vadinHA21vadinHA21
NCBI:txid72275NCBI:txid72275

Revision editor(s): Carita Ndibe

Experiment 5


Needs review

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, Carita Ndibe

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/22

Curator: Carita Ndibe

Revision editor(s): Carita Ndibe

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 ControlLinks
Psychromonas
rhodobacteracearhodobacteracea
Gammaproteobacteria
Spongiibacteraceae
NCBI:txid97050NCBI:txid97050
Alteromonadaceae
Alphaproteobacteria

Revision editor(s): Carita Ndibe

Signature 2

Needs review

Curated date: 2024/04/23

Curator: Carita Ndibe

Revision editor(s): Carita Ndibe

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

NCBI Quality ControlLinks
Vibrio
Colwellia
Leucothrix
Marinifilaceae
Desulfotalea
Bacteroidia
Pseudoalteromonas
Roseimarinus
Bacteroidetes BD2-2Bacteroidetes BD2-2
Lutibacter
Pseudahrensia
vadinHA21vadinHA21
NS10 marine groupNS10 marine group

Revision editor(s): Carita Ndibe

Experiment 6


Needs review

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/17

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

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

NCBI Quality ControlLinks
Cognaticolwellia aestuarii
Colwellia
Colwellia psychrerythraea
Erwinia
Erwinia rhapontici
Leucothrix
Leucothrix mucor
Lutibacter
Lutibacter agarilyticus
Psychromonas arctica
Vibrio
genus unknown sp18586genus unknown sp18586
colwellia meonggei sp56501colwellia meonggei sp56501
Fluviicola sp16216Fluviicola sp16216
Leucothrix mucor sp64100Leucothrix mucor sp64100
Blastopirellula sp41404-sp41424Blastopirellula sp41404-sp41424
Arcobacter sp55236Arcobacter sp55236
unclassified Oceanospirillaceae
unknown Saprospiraceaeunknown Saprospiraceae
Fluviicola
Octadecabacter
Arcobacter
Blastopirellula
Polaribacter
unknown family Bdellovibrionaceaeunknown family Bdellovibrionaceae
unknown family Saprospiraceaeunknown family Saprospiraceae

Revision editor(s): Omojokunoluwatomisin

Signature 2

Needs review

Curated date: 2024/04/17

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

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

NCBI Quality ControlLinks
Cobetia
Desulfotalea
Sulfurimonas
Alteromonas
Psychromonas
Psychromonas kaikoae
Desulfotalea sp52097Desulfotalea sp52097
sulfurimonas sp.55735sulfurimonas sp.55735
Alteromonas sp. unknownAlteromonas sp. unknown
Psychromonas profunda
Francisella persica tularensisFrancisella persica tularensis
Rubritalea sp69317-sp69326Rubritalea sp69317-sp69326
unclassified Cellvibrionaceae
Cobetia litoralis marinaCobetia litoralis marina
Kordiimonas sp43012Kordiimonas sp43012
Vibrio panuliri
Arenicella xantha
unknown Nannocystaceaeunknown Nannocystaceae
Roseibacillus ponti
Nitrosarchaeum koreense
Phycisphaera sp40965Phycisphaera sp40965
Rhodopirellula sp41964-sp42046Rhodopirellula sp41964-sp42046
Altererythrobacter sp47504Altererythrobacter sp47504
Coxiella sp60512Coxiella sp60512
Coxiella sp60417-sp60493-sp60525Coxiella sp60417-sp60493-sp60525
Thiohalophilus sp60165Thiohalophilus sp60165
Roseibium aquae
Rubritalea
Francisella
Kordiimonas
Altererythrobacter
Coxiella
Arenicella
Nitrosarchaeum
Roseibacillus
Winogradskyella
Roseibium

Revision editor(s): Omojokunoluwatomisin

Experiment 7


Needs review

Curated date: 2024/04/17

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, Carita Ndibe

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/23

Curator: Carita Ndibe

Revision editor(s): Carita Ndibe

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 ControlLinks
Vibrio
Colwellia
RhodobacteraceaeRhodobacteraceae
Leucothrix
NCBI:txid97050NCBI:txid97050
Erwiniaceae
Lutibacter
NS10 marine groupNS10 marine group

Revision editor(s): Carita Ndibe

Signature 2

Needs review

Curated date: 2024/04/23

Curator: Carita Ndibe

Revision editor(s): Carita Ndibe

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

NCBI Quality ControlLinks
Alphaproteobacteria
Alteromonadaceae
Bacteroidia
Desulfotalea
Gammaproteobacteria
Marinifilaceae
Pseudahrensia
Pseudoalteromonas
Psychromonas
Roseimarinus
Spongiibacteraceae
Bacteroidetes BD2-2Bacteroidetes BD2-2
vadinHA21vadinHA21

Revision editor(s): Carita Ndibe

Experiment 8


Needs review

Curated date: 2024/04/17

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/17

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

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

NCBI Quality ControlLinks
Alteromonas
Cobetia
Desulfotalea
Psychromonas
Psychromonas kaikoae
Psychromonas profunda
Sulfurimonas
Alteromonas sp.unknownAlteromonas sp.unknown
sulfurimonas sp55735sulfurimonas sp55735
Desulfotalea sp52097Desulfotalea sp52097
Genus unknown sp57249Genus unknown sp57249
Francisella persica tularensisFrancisella persica tularensis
Rubritalea sp69317-sp69326Rubritalea sp69317-sp69326
unknown family Cellvibrionaceaeunknown family Cellvibrionaceae
Cobetia litoralis marinaCobetia litoralis marina
Kordiimonas sp43012Kordiimonas sp43012
Vibrio panuliri
Arenicella xantha
unknown family Nannocystaceaeunknown family Nannocystaceae
Roseibacillus ponti
Nitrosoarchaeum koreensisNitrosoarchaeum koreensis
Phycisphaera sp40965Phycisphaera sp40965
Rhodopirellula sp41964-sp42046Rhodopirellula sp41964-sp42046
Altererythrobacter sp47504Altererythrobacter sp47504
Coxiella sp60512Coxiella sp60512
Coxiella sp60417-sp60493-sp60525Coxiella sp60417-sp60493-sp60525
Thiohalophilus sp60165Thiohalophilus sp60165
Roseibium aquae
Rubritalea
Francisella
Kordiimonas
Altererythrobacter
Coxiella
Arenicella
Desulfovibrio
NitrosoarchaeumNitrosoarchaeum
Roseibacillus
Winogradskyella
ThiohalophilusThiohalophilus
Roseibium

Revision editor(s): Omojokunoluwatomisin

Signature 2

Needs review

Curated date: 2024/04/17

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin

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

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Colwellia
Neiella
Parvularcula
Pseudoalteromonas
Psychromonas heitensis
Vibrio
Desulfotalea sp52096Desulfotalea sp52096
Genus unknown sp60188Genus unknown sp60188
parvularcula sp43129parvularcula sp43129
Nieiella sp56428Nieiella sp56428
Pseudoalteromonas sp. UnknownPseudoalteromonas sp. Unknown
Psychromonas heitensis kaikoaePsychromonas heitensis kaikoae
Prolixibacter sp.
Oceaniovalibus sp44845Oceaniovalibus sp44845
Desulfopila Desulfotalea sp52047-sp52096Desulfopila Desulfotalea sp52047-sp52096
Sulfurimonas sp55715-sp55735Sulfurimonas sp55715-sp55735
Loktanella cinnabarina hongkongensisLoktanella cinnabarina hongkongensis
Oceanispirochaeta litoralis
Litoribacillus sp61538-sp61539Litoribacillus sp61538-sp61539
Marinobacter salarius
Vibrio litoralis
Marinobacter salarius similisMarinobacter salarius similis
Halomonas denitrificans saccharevitansHalomonas denitrificans saccharevitans
Halomonas sp.
Saccharicrinis sp12936Saccharicrinis sp12936
Vibrio atypicus panuliriVibrio atypicus panuliri
Draconibacterium sp14871Draconibacterium sp14871
Halomonas alkaliantarctica boliviensisHalomonas alkaliantarctica boliviensis
Nitrospira sp39765Nitrospira sp39765
Shewanella olleyana
Planctomyces
Marinosulfonomonas methylotropha
Mycolicibacterium hippocampi
Psychromonas
Shewanella
Prolixibacter
Desulfopila DesulfotaleaDesulfopila Desulfotalea
Oceaniovalibus
Marinobacter
Loktanella
Spirochaeta
Litoribacillus
Marinosulfonomonas
Saccharicrinis
Sulfitobacter
Draconibacterium
Nitrosospira
Gilvibacter
Mycobacterium
Psychroflexus
unknown family Sandaracinaceaeunknown family Sandaracinaceae

Revision editor(s): Omojokunoluwatomisin