Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China/Experiment 7
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
- Helicobacter pylori Campylobacter pylori,Campylobacter pylori subsp. pylori,Campylobacter pyloridis,Helicobacter nemestrinae,Helicobacter pylori,helicobacter pylori
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- H. pylori-negative cardia group (NC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- H. pylori-positive cardia group (PC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Biopsy samples from the cardia of patients with H. pylori infection.
- 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
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- One month
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)?
- No
- 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
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Table 2
Description: Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens
Abundance in Group 1: increased abundance in H. pylori-positive cardia group (PC)
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter | ||
| Pseudomonadota |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Table 2
Description: Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens
Abundance in Group 1: decreased abundance in H. pylori-positive cardia group (PC)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Alloprevotella | ||
| Bacteroidota | ||
| Prevotella | ||
| Pseudomonas | ||
| Selenomonas |
Revision editor(s): Aleru Divine
