The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics/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
- Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,stomach
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gastric adenocarcinoma adenocarcinoma - stomach,adenocarcinoma of stomach,adenocarcinoma of the stomach,gastric (stomach) adenocarcinoma,gastric adenocarcinoma,STAD,stomach adenocarcinoma,Gastric adenocarcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Superficial gastritis (SG)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Gastric adenocarcinoma (GC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SG patients with mild to moderate epigastric discomfort. The disgnosis of malignancy was based on patological analysis of tissue biopsies
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Use of antibiotics within 6 months
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figure 2A and Figure 2B
Description: Taxonomic changes in GC microbiome. (A) Cladogram of the gastric microbial taxa associated with GC and SG. GC-enriched taxa are colored in red and SG-enriched taxa are in green. (B) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant taxonomic features between GC and SG groups. Significance obtained by LDA effect size (LEfSe) at p < 0.05 (Kruksal–Wallis test) and LDAscore>2.
Abundance in Group 1: increased abundance in Gastric adenocarcinoma (GC)
Revision editor(s): WikiWorks, Peace Sandy
Signature 2
Source: Figure 2A and Figure 2B
Description: Taxonomic changes in GC microbiome. (A) Cladogram of the gastric microbial taxa associated with GC and SG. GC-enriched taxa are colored in red and SG-enriched taxa are in green. (B) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant taxonomic features between GC and SG groups. Significance obtained by LDA effect size (LEfSe) at p < 0.05 (Kruksal–Wallis test) and LDAscore>2.
Abundance in Group 1: decreased abundance in Gastric adenocarcinoma (GC)
Revision editor(s): WikiWorks, Peace Sandy, MyleeeA
