Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China
From BugSigDB
Jump to:navigation, search
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 , Esophagus , Gastric juice , Stomach , Feces Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva,Gullet,Oesophagus,Esophagus,esophagus,Stomach secretion,Succus gastricus,Gastric juice,gastric juice,Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,stomach,Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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
- Esophageal swab, cardia biopsy, noncardia biopsy, gastric juice, and fecal 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 participants undergoing upper gastrointestinal endoscopy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 200
- 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
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
Signature 1
Needs review
Source: Figure 2B
Description: LEfSe results showing differentially abundant 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
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Saliva, cardia biopsy, noncardia biopsy, gastric juice, and fecal 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 participants undergoing upper gastrointestinal endoscopy.
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Figure 2B
Description: LEfSe results showing differentially abundant 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
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Saliva, esophageal swab, noncardia biopsy, gastric juice, and fecal 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 participants undergoing upper gastrointestinal endoscopy.
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Figure 2B
Description: LEfSe results showing differentially abundant 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
Experiment 4
Needs review
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva , Esophagus , Stomach , Gastric juice , Feces Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva,Gullet,Oesophagus,Esophagus,esophagus,Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,stomach,Stomach secretion,Succus gastricus,Gastric juice,gastric juice,Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Saliva, esophageal swab, cardia biopsy, gastric juice, and fecal samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Noncardia biopsy samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Noncardia biopsy samples from participants undergoing upper gastrointestinal endoscopy.
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Figure 2B
Description: LEfSe results showing differentially abundant genera in different GI sites.
Abundance in Group 1: increased abundance in Noncardia biopsy samples
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter |
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
- Saliva, esophageal swab, cardia biopsy, noncardia biopsy, and fecal samples
- 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 participants undergoing upper gastrointestinal endoscopy.
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Figure 2B
Description: LEfSe results showing differentially abundant 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
Experiment 6
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Saliva, esophageal swab, cardia biopsy, noncardia biopsy, and gastric juice samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Fecal samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal samples from participants undergoing upper gastrointestinal endoscopy.
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Figure 2B
Description: LEfSe results showing differentially abundant genera in different GI sites.
Abundance in Group 1: increased abundance in Fecal samples
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Roseburia | ||
| Blautia |
Revision editor(s): Aleru Divine
Experiment 7
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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Helicobacter pylori Campylobacter pylori,Campylobacter pylori subsp. pylori,Campylobacter pyloridis,Helicobacter nemestrinae,Helicobacter pylori,helicobacter pylori
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- H. pylori-negative cardia group (NC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- H. pylori-positive cardia group (PC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Biopsy samples from the cardia of patients with H. pylori infection.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
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
Signature 1
Needs review
Source: Table 2
Description: Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens
Abundance in Group 1: increased abundance in H. pylori-positive cardia group (PC)
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter | ||
| Pseudomonadota |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Table 2
Description: Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens
Abundance in Group 1: decreased abundance in H. pylori-positive cardia group (PC)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Alloprevotella | ||
| Bacteroidota | ||
| Prevotella | ||
| Pseudomonas | ||
| Selenomonas |
Revision editor(s): Aleru Divine
Experiment 8
Needs review
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,stomach
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- H. pylori-negative noncardia group (NN)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- H. pylori-positive noncardia group (PN)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Biopsy samples from the noncardia of patients with H. pylori infection.
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
Signature 1
Needs review
Source: Table 2
Description: Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens
Abundance in Group 1: increased abundance in H. pylori-positive noncardia group (PN)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Helicobacter |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Table 2
Description: Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens
Abundance in Group 1: decreased abundance in H. pylori-positive noncardia group (PN)
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
- H. pylori-positive noncardia group (PN)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- H. pylori-positive cardia group (PC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Biopsy samples from the cardia of patients with H. pylori infection.
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Table 2
Description: Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens
Abundance in Group 1: increased abundance in H. pylori-positive cardia group (PC)
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Table 2
Description: Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens
Abundance in Group 1: decreased abundance in H. pylori-positive cardia group (PC)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Helicobacter |
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
- Gastric juice Stomach secretion,Succus gastricus,Gastric juice,gastric juice
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lower-pH (L) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Higher-pH (H) 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 a gastric pH level higher than 2.
- 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
- 12
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: Table S4
Description: LEfSe results showing the microbial composition in gastric juice
Abundance in Group 1: increased abundance in Higher-pH (H) group
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Streptococcus | ||
| Neisseria | ||
| Veillonella | ||
| Haemophilus | ||
| Rothia |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Table S4
Description: LEfSe results showing the microbial composition in gastric juice
Abundance in Group 1: decreased abundance in Higher-pH (H) group
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas | ||
| Acinetobacter | ||
| Herbaspirillum | ||
| Amycolatopsis |
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
- 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
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: 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 Control | Links |
|---|---|---|
| Rothia |
Revision editor(s): Aleru Divine
Signature 2
Needs review
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 Control | Links |
|---|---|---|
| Pseudomonas | ||
| Acinetobacter |
Revision editor(s): Aleru Divine
Retrieved from "https://bugsigdb.org/w/index.php?title=Study_953&oldid=140706"
