Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers/Experiment 3

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/25

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

Subjects

Location of subjects
China
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
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
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 cancer patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients with esophageal cancer
Group 0 sample size Number of subjects in the control (unexposed) group
24
Group 1 sample size Number of subjects in the case (exposed) group
12
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V2
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Ion Torrent

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
3
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Chao1 Abundance-based estimator of species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/25

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure S3, Figure 5

Description: Bacterial species corresponding to the differentially abundant OTUs between esophageal cancer patients and control subjects

Abundance in Group 1: increased abundance in esophageal cancer patients

NCBI Quality ControlLinks
Aggregatibacter segnis
Corynebacterium
Leptotrichia hofstadii
Leptotrichia sp.
Megasphaera micronuciformis
Porphyromonas gingivalis
Streptococcus sp.

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/25

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure S3, Figure 5

Description: Bacterial species corresponding to the differentially abundant OTUs between esophageal cancer patients and control subjects

Abundance in Group 1: decreased abundance in esophageal cancer patients

NCBI Quality ControlLinks
Actinomyces
Prevotella melaninogenica
Rothia dentocariosa
Streptococcus
Neisseria
Streptococcus australis

Revision editor(s): Claregrieve1, WikiWorks