Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
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
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
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
Needs review
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
Experiment 2
Needs review
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
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
Needs review
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 |
|---|---|---|
| Weissella |
Revision editor(s): Aleru Divine
Experiment 3
Needs review
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
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
Needs review
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 |
|---|---|---|
| Helicobacter |
Revision editor(s): Aleru Divine
Experiment 4
Needs review
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
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
Needs review
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 |
|---|---|---|
| Pseudomonas |
Revision editor(s): Aleru Divine
Experiment 5
Needs review
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
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
Needs review
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 |
|---|---|---|
| Faecalibacterium | ||
| Roseburia | ||
| Blautia |
Revision editor(s): Aleru Divine
Experiment 6
Needs review
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
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 Control | Links |
|---|---|---|
| Streptococcus | ||
| Haemophilus |
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 Esophageal swab samples
| NCBI | Quality Control | Links |
|---|---|---|
| Weissella |
Revision editor(s): Aleru Divine
Experiment 7
Needs review
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
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 Control | Links |
|---|---|---|
| Streptococcus | ||
| Haemophilus |
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 Esophageal swab samples
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter |
Revision editor(s): Aleru Divine
Experiment 8
Needs review
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
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 Control | Links |
|---|---|---|
| Streptococcus | ||
| Haemophilus |
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 Esophageal swab samples
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas |
Revision editor(s): Aleru Divine
Experiment 9
Needs review
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
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 Control | Links |
|---|---|---|
| Streptococcus | ||
| Haemophilus |
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 Esophageal swab samples
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Roseburia | ||
| Blautia |
Revision editor(s): Aleru Divine
Experiment 10
Needs review
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
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 |
|---|---|---|
| Helicobacter |
Revision editor(s): Aleru Divine
Experiment 11
Needs review
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
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
Experiment 12
Needs review
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
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 |
|---|---|---|
| Faecalibacterium | ||
| Roseburia | ||
| Blautia |
Revision editor(s): Aleru Divine
Experiment 13
Needs review
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
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 Control | Links |
|---|---|---|
| Helicobacter |
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 Non-cardia biopsy samples
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas |
Revision editor(s): Aleru Divine
Experiment 14
Needs review
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
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 Control | Links |
|---|---|---|
| Helicobacter |
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 Non-cardia biopsy samples
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Roseburia | ||
| Blautia |
Revision editor(s): Aleru Divine
Experiment 15
Needs review
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
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 Control | Links |
|---|---|---|
| Pseudomonas |
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 Gastric juice samples
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Roseburia | ||
| Blautia |
Revision editor(s): Aleru Divine
Experiment 16
Needs review
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Contents
- 1 Experiment 1
- 2 Experiment 2
- 3 Experiment 3
- 4 Experiment 4
- 5 Experiment 5
- 6 Experiment 6
- 7 Experiment 7
- 8 Experiment 8
- 9 Experiment 9
- 10 Experiment 10
- 11 Experiment 11
- 12 Experiment 12
- 13 Experiment 13
- 14 Experiment 14
- 15 Experiment 15
- 16 Experiment 16
- 17 Experiment 17
- 18 Experiment 18
- 19 Experiment 19
- 20 Experiment 20
- 21 Experiment 21
- 22 Experiment 22
- 23 Experiment 23
- 24 Experiment 24
- 25 Experiment 25
- 26 Experiment 26
- 27 Experiment 27
- 28 Experiment 28
- 29 Experiment 29
- 30 Experiment 30
- 31 Experiment 31
- 32 Experiment 32
- 33 Experiment 33
- 34 Experiment 34
- 35 Experiment 35
- 36 Experiment 36
- 37 Experiment 37
- 38 Experiment 38
- 39 Experiment 39
- 40 Experiment 40
- 41 Experiment 41
- 42 Experiment 42
- 43 Experiment 43
- 44 Experiment 44
- 45 Experiment 45
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