Signatures within the esophageal microbiome are associated with host genetics, age, and disease/Experiment 3
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
- Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cluster 2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cluster 3
- 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) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Additional file 1, page 6
Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.
Abundance in Group 1: increased abundance in Cluster 3
Revision editor(s): Fiddyhamma, Victoria
Signature 2
Needs review
Source: Additional file 1, page 6
Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.
Abundance in Group 1: decreased abundance in Cluster 3
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillales | ||
| Porphyromonas | ||
| Prevotella | ||
| Streptococcaceae | ||
| Streptococcus | ||
| unclassified Bacillales |
Revision editor(s): Fiddyhamma, Victoria
