Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma/Experiment 1
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 squamous cell carcinoma ESCC,esophageal epidermoid carcinoma,esophageal scc,esophageal squamous cell cancer,esophageal squamous cell carcinoma,esophagus scc,esophagus squamous cell carcinoma,scc of esophagus,scc of the esophagus,squamous cell car. - esophagus,squamous cell carcinoma of esophagus,squamous cell carcinoma of the esophagus,Esophageal squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- NC_oral - No carcinoma.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- EIESC_oral - Early-stage intramucosal esophageal squamous carcinoma.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Saliva was collected from patients diagnosed with early-stage intramucosal esophageal squamous carcinoma (EIESC).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients who have used antibiotics 4 weeks before admission.
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).
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig. 5A
Description: LEfSe analysis. Plot of LDA Effect Size. The length of the bar column represents the LDA score. The figure shows the oral microbial taxa with significant differences between the EIESC (orange) and Control (green) (LDA score>2)
Abundance in Group 1: increased abundance in EIESC_oral - Early-stage intramucosal esophageal squamous carcinoma.
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriales | ||
| Fusobacteriia | ||
| Fusobacteriota | ||
| Leptotrichia | ||
| Leptotrichiaceae | ||
| Parvimonas | ||
| Porphyromonadaceae | ||
| Porphyromonas | ||
| Pyramidobacter |
Revision editor(s): Victoria
Signature 2
Source: Fig. 5A
Description: LEfSe analysis. Plot of LDA Effect Size. The length of the bar column represents the LDA score. The figure shows the oral microbial taxa with significant differences between the EIESC (orange) and Control (green) (LDA score > 2).
Abundance in Group 1: decreased abundance in EIESC_oral - Early-stage intramucosal esophageal squamous carcinoma.
Revision editor(s): Victoria
