Signatures within the esophageal microbiome are associated with host genetics, age, and disease/Experiment 7
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 (Normal esophagus)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GERD (Gastroesophageal reflux disease)
- 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.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 59
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
- 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
Signature 1
Needs review
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: increased abundance in GERD (Gastroesophageal reflux disease)
| NCBI | Quality Control | Links |
|---|---|---|
| Acetoanaerobium | ||
| Filifactor | ||
| unclassified Flavobacteriaceae | ||
| Campylobacter |
Revision editor(s): Fiddyhamma, Victoria
Signature 2
Needs review
Source: Additional file 3, page 4
Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).
Abundance in Group 1: decreased abundance in GERD (Gastroesophageal reflux disease)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Enterobacteriaceae | ||
| Enterobacterales | ||
| Escherichia/Shigella sp. |
Revision editor(s): Victoria, Fiddyhamma
