Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-4-3
Subjects
- Location of subjects
- Australia
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Phascolarctos cinereus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Marsupium Marsupial pouch,Pouch,Marsupium,marsupium
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Neonatal death Neonatal lethal,Neonatal death,neonatal death
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Successful breeders
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Unsuccessful breeders
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Captive Koalas who lost their pouch young during lactation.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
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).
- raw counts
- Statistical test
- DESeq2
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-4-3
Source: supplementary Table 11
Description: Differentially abundant genera in the pouch microbiota of successful vs. unsuccessful breeding koalas during early lactation.
Abundance in Group 1: increased abundance in Unsuccessful breeders
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium faecium | ||
| Pseudomonas | ||
| Escherichia/Shigella sp. | ||
| Klebsiella | ||
| Pluralibacter | ||
| Lonepinella |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-4-3
Source: supplementary Table 11
Description: Differentially abundant genera in the pouch microbiota of successful vs. unsuccessful breeding koalas during early lactation.
Abundance in Group 1: decreased abundance in Unsuccessful breeders
| NCBI | Quality Control | Links |
|---|---|---|
| Muribaculum | ||
| Phascolarctobacterium faecium |
