Genomic investigations of acute munitions exposures on the health and skin microbiome composition of leopard frog (Rana pipiens) tadpoles/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-13
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Rana pipiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Tadpole Tadpole stage,Tadpole,tadpole
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Environmental exposure measurement Environmental exposure measurement,environmental exposure measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tadpoles exposed to 3560 mg/L Nitroguanidine (NQ)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tadpoles were exposed to the concentration of 3560 mg/L of Nitroguanidine (NQ) for 96 hours.
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-13
Source: Figure 6
Description: LEfSe-identified significant taxa in the NQ exposed group compared to the control group
Abundance in Group 1: increased abundance in Tadpoles exposed to 3560 mg/L Nitroguanidine (NQ)
| NCBI | Quality Control | Links |
|---|---|---|
| Aeromonadaceae | ||
| Aeromonadales | ||
| Comamonadaceae | ||
| Gammaproteobacteria | ||
| Pseudomonadaceae | ||
| Shewanellaceae |
Revision editor(s): Victoria, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-13
Source: Figure 6
Description: LEfSe-identified significant taxa in the NQ exposed group compared to the control group
Abundance in Group 1: decreased abundance in Tadpoles exposed to 3560 mg/L Nitroguanidine (NQ)
Revision editor(s): Victoria, ChiomaBlessing
