Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Subjects
- Location of subjects
- Japan
- 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
- Digestive system cancer cancer of digestive system,digestive system cancer,gastrointestinal system cancer,gastrointestinal tract cancer,GI tumor,malignant digestive system neoplasm,malignant gastrointestinal neoplasm,malignant gastrointestinal system neoplasm,malignant neoplasm of digestive system,Digestive system 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
- digestive tract cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with digestive tract cancers (tongue/pharynx, esophagus, stomach and/or large intestine)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 118
- Group 1 sample size Number of subjects in the case (exposed) group
- 59
- 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
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Figure 3, Figure S1
Description: Bacterial species corresponding to the differentially abundant OTUs between digestive tract cancer patients and control subjects
Abundance in Group 1: increased abundance in digestive tract cancer patients
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Figure 3, Figure S1
Description: Bacterial species corresponding to the differentially abundant OTUs between digestive tract cancer patients and control subjects
Abundance in Group 1: decreased abundance in digestive tract cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces graevenitzii | ||
| Porphyromonas | ||
| Porphyromonas pasteri | ||
| Porphyromonas sp. | ||
| Prevotella | ||
| Prevotella melaninogenica | ||
| Rothia | ||
| Rothia dentocariosa | ||
| Solobacterium moorei |
Revision editor(s): Claregrieve1, WikiWorks
