Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-15
Subjects
- Location of subjects
- South Korea
- 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
- Mucosa of stomach Magenschleimhaut,Gastric mucosa,Gastric mucous membrane,Mucosa of organ of stomach,Mucosa of organ of ventriculus,Mucosa of ventriculus,Mucous membrane of stomach,Mucous membrane of ventriculus,Organ mucosa of stomach,Organ mucosa of ventriculus,Stomach mucosa,Stomach mucosa of organ,Stomach mucous membrane,Stomach organ mucosa,Tunica mucosa (gaster),Tunica mucosa gastricae,Tunica mucosa gastris,Ventriculus mucosa,Ventriculus mucosa of organ,Ventriculus mucous membrane,Ventriculus organ mucosa,Mucosa of stomach,mucosa of stomach
- 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
- chronic gastritis and intestinal metaplasia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- gastric cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- noncardia gastric cancer patients whose diagnosis were confirmed by histopathology
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- 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
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-15
Source: Supplemental Fig S1, S2
Description: Relative bacterial abundance of gastric mucosa at the class and family level in Helicobacter-dominant patients with chronic gastritis, intestinal metplasia and gastric cancer
Abundance in Group 1: increased abundance in gastric cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Streptococcaceae |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-15
Source: Supplemental Fig S1, S2
Description: Relative bacterial abundance of gastric mucosa at the class and family level in Helicobacter-dominant patients with chronic gastritis, intestinal metplasia and gastric cancer
Abundance in Group 1: decreased abundance in gastric cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacteraceae |
