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

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Reviewed Marked as Reviewed by Svetlana up on 2025-1-22

Curated date: 2024/04/12

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, KateRasheed

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: Anatomical surface Anatomical surface,anatomical surface

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: Diseased + Recovered sea urchins

Group 1 name Corresponds to the case (exposed) group for case-control studies: Healthy sea urchins

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Healthy sea urchins refers to sea urchins in aquarium A and B that are healthy.

Group 0 sample size Number of subjects in the control (unexposed) group: 8

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: 3

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-22

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, KateRasheed

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 Healthy sea urchins

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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
Bacteroidetes BD2-2Bacteroidetes BD2-2
Clostridia vadinBB60 groupClostridia vadinBB60 group
Kiritimatiellaceae MSBL3Kiritimatiellaceae MSBL3
Roseobacter clade Marinomonas lineageRoseobacter clade Marinomonas lineage
Planctomycetota OM190Planctomycetota OM190
Lentisphaeria P.palmC41Lentisphaeria P.palmC41
OM27 clade
Cyanobacteriota

Revision editor(s): Omojokunoluwatomisin, KateRasheed

Experiment 2

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Reviewed Marked as Reviewed by Svetlana up on 2025-1-22

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy + Diseased 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.

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-22

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, KateRasheed

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 Control	Links
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
Rickettsiales SM2D12Rickettsiales SM2D12
Bacteroidales vadinHA21Bacteroidales vadinHA21
RubinisphaeraceaeRubinisphaeraceae
Bdellovibrionaceae OM27 cladeBdellovibrionaceae OM27 clade
Acidobacteriae PAUC26fAcidobacteriae PAUC26f
Candidatus Absconditibacteriota

Revision editor(s): Omojokunoluwatomisin, KateRasheed

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-1-22

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Recovered + 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.

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-22

Curated date: 2024/04/17

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, KateRasheed

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 Control	Links
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
Chitinophagales 37-13Chitinophagales 37-13
Candidatus Berkiella
OM27 clade

Revision editor(s): Omojokunoluwatomisin, KateRasheed

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-1-22

Curated date: 2025/01/21

Curator: KateRasheed

Revision editor(s): KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Recovered + Diseased sea urchins - ZymoResearch pipeline

Group 1 name Corresponds to the case (exposed) group for case-control studies: Healthy sea urchins - ZymoResearch pipeline

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Healthy sea urchins refers to healthy sea urchins in aquarium A and B

Lab analysis

Statistical Analysis

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: 2

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-22

Curated date: 2025/01/22

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Supplementary Data file 3, TableS4-5.

Description: Taxa have different abundances in microbiomes from samples collected from healthy sea urchins compared to recovered and diseased sea urchins

Abundance in Group 1: increased abundance in Healthy sea urchins - ZymoResearch pipeline

NCBI	Quality Control	Links
Halomonas sp.
Marinobacter salarius
Marinosulfonomonas methylotropha
Mycolicibacterium hippocampi
Neiella sp.
Oceanispirochaeta litoralis
Planctomyces sp.
Prolixibacter sp.
Shewanella olleyana
Vibrio litoralis
Psychromonas heitensis kaikoaePsychromonas heitensis kaikoae
Desulfopila Desulfotalea sp52047-sp52096Desulfopila Desulfotalea sp52047-sp52096
Oceaniovalibus sp44845Oceaniovalibus sp44845
Sulfurimonas sp55715-sp55735Sulfurimonas sp55715-sp55735
Loktanella cinnabarina hongkongensisLoktanella cinnabarina hongkongensis
Litoribacillus sp61538-sp61539Litoribacillus sp61538-sp61539
Marinobacter salarius similisMarinobacter salarius similis
Halomonas denitrificans saccharevitansHalomonas denitrificans saccharevitans
Saccharicrinis sp12936Saccharicrinis sp12936
Vibrio atypicus panuliriVibrio atypicus panuliri
Draconibacterium sp14871Draconibacterium sp14871
Halomonas alkaliantarctica boliviensisHalomonas alkaliantarctica boliviensis
Nitrospira sp39765Nitrospira sp39765
Psychromonas
Shewanella
Prolixibacter
Desulfopila DesulfotaleaDesulfopila Desulfotalea
unclassified Sandaracinaceae
Oceaniovalibus
Marinobacter
Loktanella
Neiella
Spirochaeta
Litoribacillus
Marinosulfonomonas
Pseudoalteromonas
Saccharicrinis
Sulfitobacter
Draconibacterium
Gilvibacter
Psychroflexus
Mycobacterium
Nitrospira
Planctomyces

Revision editor(s): KateRasheed

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-1-22

Curated date: 2024/04/16

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Recovered + Healthy sea urchins - ZymoResearch pipeline

Group 1 name Corresponds to the case (exposed) group for case-control studies: Diseased sea urchins - ZymoResearch pipeline

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-22

Curated date: 2024/04/17

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, KateRasheed

Source: Supplementary Data file 3, TableS4-5.

Description: Taxa have different abundances in microbiomes from samples collected from diseased sea urchins compared to recovered and healthy sea urchins

Abundance in Group 1: increased abundance in Diseased sea urchins - ZymoResearch pipeline

NCBI	Quality Control	Links
Arcobacter
Blastopirellula
Colwellia
Erwinia
Erwinia rhapontici
Fluviicola
Leucothrix
Lutibacter
Lutibacter agarilyticus
Octadecabacter
Polaribacter
unclassified Oceanospirillaceae
Leucothrix mucor sp64100Leucothrix mucor sp64100
Blastopirellula sp41404-sp41424Blastopirellula sp41404-sp41424
Arcobacter sp55236Arcobacter sp55236
Fluviicola sp.
Colwellia meonggei sp56501Colwellia meonggei sp56501
Colwellia meonggei sp56501-sp56505Colwellia meonggei sp56501-sp56505
unclassified Pseudobdellovibrionaceae
unclassified Saprospiraceae

Revision editor(s): Omojokunoluwatomisin, KateRasheed

Experiment 8

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-1-22

Curated date: 2024/04/17

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy + Diseased sea urchins - ZymoResearch pipeline

Group 1 name Corresponds to the case (exposed) group for case-control studies: Recovered sea urchins - ZymoResearch pipeline

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

Signature 1