Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Subjects
- Location of subjects
- United States of America
- 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
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Esophageal cancer Aerodigestive tract cancer, susceptibility to,Ca lower third oesophagus,Ca middle third oesophagus,cancer of esophagus,Escc, susceptibility to,esophageal cancer,esophageal squamous cell carcinoma, susceptibility to,esophagus cancer,gastric cardia adenocarcinoma, susceptibility to,malignant esophageal neoplasm,malignant esophageal tumor,malignant esophagus neoplasm,malignant esophagus tumor,malignant neoplasm of distal third of esophagus,malignant neoplasm of esophagus,malignant neoplasm of lower third of oesophagus,malignant neoplasm of middle third of oesophagus,malignant neoplasm of proximal third of esophagus,malignant neoplasm of the esophagus,malignant neoplasm of upper third esophagus,malignant tumor of abdominal esophagus,malignant tumor of distal third of esophagus,malignant tumor of esophagus,malignant tumor of proximal third of esophagus,malignant tumor of the esophagus,malignant tumor of the middle third of the esophagus,Esophageal cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Esophageal Squamous cell carcinoma (ESCC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- diagnosed with easophageal cancer anytime after oral wash sample collection
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Logistic Regression
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex, race
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- smoking behavior, body mass index, alcohol drinking
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 Fatima Zohra on 2021/02/09
Source: Figure 1, Text
Description: Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value
Abundance in Group 1: increased abundance in Esophageal Squamous cell carcinoma (ESCC)
| NCBI | Quality Control | Links |
|---|---|---|
| Hoylesella nanceiensis | ||
| Bergeyella | ||
| Neisseria weaveri | ||
| Treponema vincentii |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: Figure 1, Text
Description: Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value
Abundance in Group 1: decreased abundance in Esophageal Squamous cell carcinoma (ESCC)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Prevotella | ||
| Aggregatibacter aphrophilus |
Revision editor(s): WikiWorks
