Alterations in Gastric Microbial Communities Are Associated with Risk of Gastric Cancer in a Korean Population: A Case-Control Study/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/8
Curated date: 2022/06/29
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Victoria
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- gastric cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with histologically confirmed early gastric cancer (invasive carcinoma confined to the mucosa, regardless of lymph node metastasis status) within the preceding 3 months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 288
- Group 1 sample size Number of subjects in the case (exposed) group
- 268
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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/8
Source: Figure 2
Description: Differential microbial abundance between gastric cancer patients and healthy controls
Abundance in Group 1: increased abundance in gastric cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter jejuni | ||
| Streptococcus |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/8
Source: Figure 2
Description: Differential microbial abundance between gastric cancer patients and healthy controls
Abundance in Group 1: decreased abundance in gastric cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella taiwanensis | ||
| Prevotella intermedia | ||
| Prevotella melaninogenica | ||
| Prevotella nigrescens | ||
| Streptococcus vestibularis | ||
| Streptococcaceae | ||
| Streptococcus | ||
| Streptococcus sp. |
Revision editor(s): Claregrieve1, Merit
