Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-8-2
Curated date: 2024/03/20
Curator: Ndruscilla
Revision editor(s): WikiWorks, Scholastica, Aleru Divine, Ndruscilla
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
- Animal disease animal disease,diseases, animal,non-human animal disease,Animal 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
- 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, WikiWorks
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, WikiWorks
