Signatures within the esophageal microbiome are associated with host genetics, age, and disease/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- Australia
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Esophagus Gullet,Oesophagus,Esophagus,esophagus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Microbiome measurement Microbiome measurement,microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cluster 1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cluster 2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The esophageal microbiome was found to cluster into functionally distinct community types (esotypes)
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Additional file 1, page 6
Description: The esophageal microbiome clusters into different community types
Abundance in Group 1: increased abundance in Cluster 2
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillales | ||
| Porphyromonas | ||
| Prevotella | ||
| Streptococcaceae | ||
| Streptococcus | ||
| unclassified Bacillales |
Revision editor(s): Fiddyhamma
Signature 2
Needs review
Source: Additional file 1, page 6
Description: Description: The esophageal microbiome clusters into different community types
Abundance in Group 1: decreased abundance in Cluster 2
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella |
Revision editor(s): Fiddyhamma
