Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1
Subjects
- Location of subjects
- Portugal
- 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
- Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,stomach
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gastric carcinoma Ca fundus - stomach,cancer of fundus of stomach,cancer of stomach,cancer of the stomach,carcinoma of stomach,carcinoma of the stomach,fundus of stomach cancer,gastric (stomach) cancer,gastric cancer,gastric cancer, NOS,gastric carcinoma,gastric fundus cancer,malignant fundus of stomach neoplasm,malignant neoplasm of fundus of stomach,malignant tumor of fundus of stomach,stomach cancer,stomach carcinoma,Gastric carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- chronic gastritis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- gastric carcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric carcinoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 81
- Group 1 sample size Number of subjects in the case (exposed) group
- 54
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V5-V6
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
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
- 4
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1
Source: Figure 3, Figure S4
Description: Differential microbial abundance between chronic gastritis and gastric carcinoma patients by LefSe
Abundance in Group 1: increased abundance in gastric carcinoma
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1
Source: Figure 3, Figure S4
Description: Differential microbial abundance between chronic gastritis and gastric carcinoma patients by LefSe
Abundance in Group 1: decreased abundance in gastric carcinoma
Revision editor(s): Claregrieve1, WikiWorks
