Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium/Experiment 5
From BugSigDB
Needs review
Curated date: 2024/04/16
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Carita Ndibe
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
- Sea water from healthy sea urchins aquarium
- 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.
- 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
- 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
- decreased
Signature 1
Needs review
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 Control | Links |
|---|---|---|
| Psychromonas | ||
| rhodobacteracearhodobacteracea | ||
| Gammaproteobacteria | ||
| Spongiibacteraceae | ||
| NCBI:txid97050NCBI:txid97050 | ||
| Alteromonadaceae | ||
| Alphaproteobacteria |
Revision editor(s): Carita Ndibe
Signature 2
Needs review
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
Revision editor(s): Carita Ndibe
