A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
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
- Gastric pit Foveola gastrica,Foveolae gastricae,Gastric foveola,Gastric pit,gastric pit
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer,Gastric cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-tumor tissues of gastric cancer patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- tumor tissues of gastric cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Gastric microbiome in tumor tissue samples from GC patients undergoing surgical treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 78
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
- 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
- V3-V5
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
Source: Supplementary figure 3A
Description: Differential bacteria between the tumor and non-tumor tissues of gastric cancer patients by LEfSe analysis (LDA scores >3.0)
Abundance in Group 1: decreased abundance in tumor tissues of gastric cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Nitriliruptoria | ||
| Mesorhizobium | ||
| Bradyrhizobium | ||
| Xanthobacteraceae | ||
| Moraxellaceae | ||
| Rhizobiaceae | ||
| Pseudomonadales | ||
| Hyphomicrobiales |
Revision editor(s): Chikamso
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
Source: Supplementary figure 3A
Description: Differential bacteria between the tumor and non-tumor tissues of gastric cancer patients by LEfSe analysis (LDA >3.0)
Abundance in Group 1: increased abundance in tumor tissues of gastric cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Fusobacteriaceae | ||
| Fusobacteriales | ||
| Fusobacteriia | ||
| Fusobacterium | ||
| Lactobacillales | ||
| Neisseriaceae | ||
| Fusobacteriota | ||
| subgroup 6subgroup 6 |
Revision editor(s): Chikamso
