Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2021/07/16
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
- Squamous cell carcinoma carcinoma, squamous cell, malignant,epidermoid carcinoma,epidermoid cell cancer,malignant epidermoid cell neoplasm,malignant epidermoid cell tumor,malignant squamous cell neoplasm,malignant squamous cell tumor,squamous carcinoma,squamous cell cancer,squamous cell carcinoma,squamous cell carcinoma (morphologic abnormality),squamous cell carcinoma NOS (morphologic abnormality),squamous cell epithelioma,Squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- noncancer individuals
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Oral Squamous Cell Cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All diagnoses of oral squamous cell carcinoma were confirmed by biopsy and pathological findings.The control group was defined as individuals without any diagnosed mucosal diseases and other cancers and these individuals were over the age of 40.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 80
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 28 days
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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).
- raw counts
- Statistical test
- T-Test
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Fig 1,3 and Text
Description: Oral microbiota in japanese oral cancer patients vs. noncancer individuals: a case-control study
Abundance in Group 1: increased abundance in Oral Squamous Cell Cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Peptostreptococcus | ||
| Fusobacterium | ||
| Alloprevotella | ||
| Capnocytophaga |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Fig 1,3 and Text
Description: Oral microbiota in japanese oral cancer patients vs. noncancer individuals: a case-control study
Abundance in Group 1: decreased abundance in Oral Squamous Cell Cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia | ||
| Haemophilus |
Revision editor(s): WikiWorks
