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

From BugSigDB
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Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C, Wei W
Journal
Microbiology spectrum
Year
2022
Keywords:
Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota
The objective of this study was to describe and compare the dynamic microbiota characteristics in the gastrointestinal (GI) tract in Chinese participants via high-throughput sequencing techniques. The study collected saliva, esophageal swab, cardia biopsy, noncardia biopsy, gastric juice, and fecal specimens from 40 participants who underwent upper GI tract cancer screening in Linzhou (Henan, China) in August 2019. The V4 region of 16S rRNA genes was amplified and sequenced using the Illumina MiniSeq platform. The observed amplicon sequence variants (ASVs) gradually decreased from saliva to esophageal swab, cardia biopsy, noncardia biopsy, and gastric juice specimens and then increased from gastric juice to fecal specimens (P < 0.05). Each GI site had its own microbial characteristics that overlapped those of adjacent sites. Characteristic genera for each site were as follows: Neisseria and Prevotella in saliva, Streptococcus and Haemophilus in the esophagus, Helicobacter in the noncardia, Pseudomonas in gastric juice, Faecalibacterium, Roseburia, and Blautia in feces, and Weissella in the cardia. Helicobacter pylori-positive participants had decreased observed ASVs (cardia, P < 0.01; noncardia, P < 0.001) and Shannon index values (cardia, P < 0.001; noncardia, P < 0.001) compared with H. pylori-negative participants both in cardia and noncardia specimens. H. pylori infection played a more important role in the microbial composition of noncardia than of cardia specimens. In gastric juice, the gastric pH and H. pylori infection had similar additive effects on the microbial diversity and composition. These results show that each GI site has its own microbial characteristics that overlap those of adjacent sites and that differences and commonalities between and within microbial compositions coexist, providing essential foundations for the continuing exploration of disease-associated microbiota. IMPORTANCE Upper gastrointestinal (UGI) tract cancer is one of the most common cancers worldwide, while limited attention has been paid to the UGI microbiota. Microbial biomarkers, such as Fusobacteria nucleatum and Helicobacter pylori, bring new ideas for early detection of UGI tract cancer, which may be a highly feasible method to reduce its disease burden. This study revealed that each gastrointestinal site had its own microbial characteristics that overlapped those of adjacent sites. There were significant differences between the microbial compositions of the UGI sites and feces. Helicobacter pylori played a more significant role in the microbial composition of the noncardia stomach than in that of the cardia. Gastric pH and Helicobacter pylori had similar additive effects on the microbial diversity of gastric juice. These findings played a key role in delineating the microbiology spectrum of the gastrointestinal tract and provided baseline information for future microbial exploration covering etiology, primary screening, treatment, outcome, and health care products.

Experiment 1


Needs review

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

Needs review

Curated date: 2024/03/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: increased abundance in Saliva samples

NCBI Quality ControlLinks
Neisseria
Prevotella

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/14

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Saliva samples

NCBI Quality ControlLinks
Streptococcus
Haemophilus

Revision editor(s): Aleru Divine

Experiment 2


Needs review

Curated date: 2024/03/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Cardia biopsy samples

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2024/03/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: increased abundance in Saliva samples

NCBI Quality ControlLinks
Neisseria
Prevotella

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/14

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Saliva samples

NCBI Quality ControlLinks
Weissella

Revision editor(s): Aleru Divine

Experiment 3


Needs review

Curated date: 2024/03/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Non-cardia biopsy samples

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2024/03/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: increased abundance in Saliva samples

NCBI Quality ControlLinks
Neisseria
Prevotella

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/14

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Saliva samples

NCBI Quality ControlLinks
Helicobacter

Revision editor(s): Aleru Divine

Experiment 4


Needs review

Curated date: 2024/03/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Gastric juice sample

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2024/03/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: increased abundance in Saliva samples

NCBI Quality ControlLinks
Neisseria
Prevotella

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/14

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Saliva samples

NCBI Quality ControlLinks
Pseudomonas

Revision editor(s): Aleru Divine

Experiment 5


Needs review

Curated date: 2024/03/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Fecal samples

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2024/03/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: increased abundance in Saliva samples

NCBI Quality ControlLinks
Neisseria
Prevotella

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/14

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Saliva samples

NCBI Quality ControlLinks
Faecalibacterium
Roseburia
Blautia

Revision editor(s): Aleru Divine

Experiment 6


Needs review

Curated date: 2024/03/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Esophagus Gullet,Oesophagus,Esophagus,esophagus
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Cardia biopsy samples
Group 1 name Corresponds to the case (exposed) group for case-control studies
Esophageal swab samples
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Esophageal swab samples from 40 participants undergoing upper gastrointestinal endoscopy.

Lab analysis

Statistical Analysis

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: 2024/03/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: increased abundance in Esophageal swab samples

NCBI Quality ControlLinks
Streptococcus
Haemophilus

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/14

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Esophageal swab samples

NCBI Quality ControlLinks
Weissella

Revision editor(s): Aleru Divine

Experiment 7


Needs review

Curated date: 2024/03/14

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Non-cardia biopsy samples

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2024/03/14

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: increased abundance in Esophageal swab samples

NCBI Quality ControlLinks
Streptococcus
Haemophilus

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Esophageal swab samples

NCBI Quality ControlLinks
Helicobacter

Revision editor(s): Aleru Divine

Experiment 8


Needs review

Curated date: 2024/03/14

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Gastric juice samples

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: increased abundance in Esophageal swab samples

NCBI Quality ControlLinks
Streptococcus
Haemophilus

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Esophageal swab samples

NCBI Quality ControlLinks
Pseudomonas

Revision editor(s): Aleru Divine

Experiment 9


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Fecal samples

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: increased abundance in Esophageal swab samples

NCBI Quality ControlLinks
Streptococcus
Haemophilus

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Esophageal swab samples

NCBI Quality ControlLinks
Faecalibacterium
Roseburia
Blautia

Revision editor(s): Aleru Divine

Experiment 10


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Non-cardia biopsy 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.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Weissella

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Helicobacter

Revision editor(s): Aleru Divine

Experiment 11


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Gastric juice samples

Lab analysis

Statistical Analysis

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: Figure 2B

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

Abundance in Group 1: increased abundance in Cardia biopsy samples

NCBI Quality ControlLinks
Weissella

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Pseudomonas

Revision editor(s): Aleru Divine

Experiment 12


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Fecal samples

Lab analysis

Statistical Analysis

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: Figure 2B

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

Abundance in Group 1: increased abundance in Cardia biopsy samples

NCBI Quality ControlLinks
Weissella

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Faecalibacterium
Roseburia
Blautia

Revision editor(s): Aleru Divine

Experiment 13


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Body of stomach Corpus gastricum,Corpus gastricum (ventriculare),Corpus ventriculare,Corpus ventriculi,Gastric body,Gastric corpus,Stomach body,Body of stomach,body of stomach
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
Non-cardia biopsy samples
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Non-cardia biopsy samples from 40 participants undergoing upper gastrointestinal endoscopy.

Lab analysis

Statistical Analysis

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: Figure 2B

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

Abundance in Group 1: increased abundance in Non-cardia biopsy samples

NCBI Quality ControlLinks
Helicobacter

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Non-cardia biopsy samples

NCBI Quality ControlLinks
Pseudomonas

Revision editor(s): Aleru Divine

Experiment 14


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Fecal samples

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: increased abundance in Non-cardia biopsy samples

NCBI Quality ControlLinks
Helicobacter

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Non-cardia biopsy samples

NCBI Quality ControlLinks
Faecalibacterium
Roseburia
Blautia

Revision editor(s): Aleru Divine

Experiment 15


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

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
Group 1 name Corresponds to the case (exposed) group for case-control studies
Gastric juice samples
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Gastric juice samples from 40 participants undergoing upper gastrointestinal endoscopy.

Lab analysis

Statistical Analysis

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: Figure 2B

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

Abundance in Group 1: increased abundance in Gastric juice samples

NCBI Quality ControlLinks
Pseudomonas

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2B

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

Abundance in Group 1: decreased abundance in Gastric juice samples

NCBI Quality ControlLinks
Faecalibacterium
Roseburia
Blautia

Revision editor(s): Aleru Divine

Experiment 16


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
H. pylori negative group
Group 1 name Corresponds to the case (exposed) group for case-control studies
H. pylori positive group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants who tested positive for H. pylori infection (cardia samples)
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

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Richness Number of species
decreased

Experiment 17


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Body of stomach Corpus gastricum,Corpus gastricum (ventriculare),Corpus ventriculare,Corpus ventriculi,Gastric body,Gastric corpus,Stomach body,Body of stomach,body of stomach
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants who tested positive for H. pylori infection (non-cardia samples)

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Richness Number of species
decreased

Experiment 18


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
H (higher pH) group
Group 1 name Corresponds to the case (exposed) group for case-control studies
HP (higher pH and H. pylori positive) group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants with higher pH and H. pylori positive.
Group 0 sample size Number of subjects in the control (unexposed) group
12
Group 1 sample size Number of subjects in the case (exposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 19


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
HN (higher pH and H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 20


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
P (H. pylori positive) group
Group 0 sample size Number of subjects in the control (unexposed) group
20

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 21


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
LP (Lower pH and H. pylori positive) group
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 22


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
L (Lower pH ) group
Group 0 sample size Number of subjects in the control (unexposed) group
28

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Experiment 23


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
N (H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
20

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Experiment 24


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
LN (Lower pH and H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Experiment 25


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
HN (higher pH and H. pylori negative) group
Group 1 name Corresponds to the case (exposed) group for case-control studies
H (higher pH ) group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants with higher pH (pH of gastric juice of >2).
Group 1 sample size Number of subjects in the case (exposed) group
12

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 26


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
P (H. pylori positive) group
Group 0 sample size Number of subjects in the control (unexposed) group
20

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 27


Needs review

Curated date: 2024/03/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
LP (Lower pH and H. pylori positive) group
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 28


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
L (Lower pH ) group
Group 0 sample size Number of subjects in the control (unexposed) group
28

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Experiment 29


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
N (H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
20

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Experiment 30


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
LN (Lower pH and H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Experiment 31


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
P (H. pylori positive) group
Group 1 name Corresponds to the case (exposed) group for case-control studies
HN (Higher pH and H. pylori negative ) group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants with Higher pH and are H. pylori negative.
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
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 32


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
LP (Lower pH and H. pylori positive) group
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 33


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
L (Lower pH) group
Group 0 sample size Number of subjects in the control (unexposed) group
28

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 34


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
N (H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
20

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 35


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
LN (Lower pH and H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 36


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
LP (Lower pH and H. pylori positive) group
Group 1 name Corresponds to the case (exposed) group for case-control studies
P (H. pylori positive) group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants that tested positive for the H. pylori infection.
Group 1 sample size Number of subjects in the case (exposed) group
20

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 37


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
L (Lower pH) group
Group 0 sample size Number of subjects in the control (unexposed) group
28

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 38


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
N (H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
20

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 39


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
LN (Lower pH and H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 40


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
L (Lower pH) group
Group 1 name Corresponds to the case (exposed) group for case-control studies
LP (Lower pH and H. pylori positive) group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants with lower pH and tested positive for the H. pylori infection.
Group 0 sample size Number of subjects in the control (unexposed) group
28
Group 1 sample size Number of subjects in the case (exposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 41


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
N (H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
20

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 42


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
LN (Lower pH and H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 43


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
N (H. pylori negative) group
Group 1 name Corresponds to the case (exposed) group for case-control studies
L (Lower pH) group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants with lower pH (pH of gastric juice of <2).
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
28

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 44


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
LN (Lower pH and H. pylori negative) group
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Experiment 45


Needs review

Curated date: 2024/03/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
N (H. pylori negative) group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants that tested negative for the H. pylori infection.
Group 1 sample size Number of subjects in the case (exposed) group
20

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged