Signatures within the esophageal microbiome are associated with host genetics, age, and disease/Experiment 18
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
- Gastroesophageal reflux disease acid reflux,Esophageal Reflux,Gastresophageal reflux,Gastro Esophageal Reflux,Gastro oesophageal Reflux,Gastro-Esophageal Reflux,gastro-esophageal reflux,Gastro-oesophageal Reflux,Gastroesophageal Reflux,gastroesophageal reflux,GASTROESOPHAGEAL REFLUX DIS,gastroesophageal reflux disease,gastroesophageal reflux, pediatric,ger,GERD,GERD - gastro-esophageal reflux disease,Reflux, Gastro-Esophageal,Reflux, Gastro-oesophageal,Reflux, Gastroesophageal,Gastroesophageal reflux disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal (Cluster 1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GERD(Gastroesophageal reflux disease) (Cluster 1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with Gastroesophageal reflux disease.
- 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
Signature 1
Needs review
Source: Additional file 3, page 6
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 1)
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Flavobacteriaceae | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): Fiddyhamma
Signature 2
Needs review
Source: Additional file 3, page 6
Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis
Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 1)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Enterobacteriaceae | ||
| Enterobacterales |
Revision editor(s): Fiddyhamma
