Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China/Experiment 1

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Curated date: 2024/03/12

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

Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

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

Esophagus samples

Group 1 name Corresponds to the case (exposed) group for case-control studies

Saliva samples

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Saliva 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

increased

Richness Number of species

increased

Signature 1

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Curated date: 2024/03/12

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Source: Figure 2B

Description: LEfSe results for characteristic genera in different GI sites.

Abundance in Group 1: increased abundance in Saliva samples

NCBI	Quality Control	Links
Neisseria
Prevotella

Revision editor(s): Aleru Divine

Signature 2

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Curated date: 2024/03/14

Curator: Aleru Divine

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Source: Figure 2B

Description: LEfSe results for characteristic genera in different GI sites.

Abundance in Group 1: decreased abundance in Saliva samples

NCBI	Quality Control	Links
Streptococcus
Haemophilus

Revision editor(s): Aleru Divine