Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers/Experiment 2

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Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

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 ControlLinks
Hoylesella nanceiensis
Bergeyella
Neisseria weaveri
Treponema vincentii

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

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 ControlLinks
Lachnospiraceae
Prevotella
Aggregatibacter aphrophilus

Revision editor(s): WikiWorks