Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China/Experiment 11
From BugSigDB
Needs review
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
- Cardia of stomach Antrum cardiacum,Cardiac antrum,Cardiac orifice,Cardiac region,Cardial orifice,Cardial part of stomach,Gastric cardia,Pars cardiaca (gaster),Pars cardiaca gastricae,Stomach cardiac region,Cardia of stomach,cardia of stomach
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Upper digestive tract disease disease of upper digestive tract,disease or disorder of upper digestive tract,disorder of upper digestive tract,disorder of upper gastrointestinal tract,upper digestive tract disease or disorder,upper gastrointestinal tract disease,Upper digestive tract disease,upper digestive tract disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Gastric juice samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cardia biopsy samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- One month before sample collection.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Figure 2B
Description: LEfSe results for characteristic genera in different GI sites.
Abundance in Group 1: increased abundance in Cardia biopsy samples
NCBI | Quality Control | Links |
---|---|---|
Weissella |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 2B
Description: LEfSe results for characteristic genera in different GI sites.
Abundance in Group 1: decreased abundance in Cardia biopsy samples
NCBI | Quality Control | Links |
---|---|---|
Pseudomonas |
Revision editor(s): Aleru Divine