Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China/Experiment 11

From BugSigDB


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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
Gastric juice Stomach secretion,Succus gastricus,Gastric juice,gastric juice
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 (N) group
Group 1 name Corresponds to the case (exposed) group for case-control studies
H. pylori-positive (P) group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Gastric juice samples from 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
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table S4

Description: LEfSe results showing the microbial composition in gastric juice

Abundance in Group 1: increased abundance in H. pylori-positive (P) group

NCBI Quality ControlLinks
Rothia

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Table S4

Description: LEfSe results showing the microbial composition in gastric juice

Abundance in Group 1: decreased abundance in H. pylori-positive (P) group

NCBI Quality ControlLinks
Pseudomonas
Acinetobacter

Revision editor(s): Aleru Divine