Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer
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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.
URI Uniform resource identifier for web resources.
Authors
Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L, Ling Z
Journal
EBioMedicine
Year
2019
BACKGROUND: As part of the tumor microenvironment, the gastric microbiota play vital roles in tumor initiation, progression and metastasis, but stomach microhabitats are not always uniform. We aimed to characterize differences of gastric microbiota in stomach microhabitats associated with gastric cancer (GC) development. METHODS: A cohort of 276 GC patients without preoperative chemotherapy was enrolled retrospectively, and 230 normal, 247 peritumoral and 229 tumoral tissues were obtained for gastric microbiota analysis targeting the 16S rRNA gene by MiSeq sequencing. The microbial diversity and composition, bacterial co-occurrence correlations and predictive functional profiles were compared across different microhabitats. FINDINGS: GC-specific stomach microhabitats, not GC stages or types, determine the composition and diversity of the gastric microbiota. Most notably, bacterial richness was decreased in peritumoral and tumoral microhabitats, and the correlation network of abundant gastric bacteria was simplified in tumoral microhabitat. Helicobacter pylori (HP), Prevotella copri and Bacteroides uniformis were significantly decreased, whereas Prevotella melaninogenica, Streptococcus anginosus and Propionibacterium acnes were increased in tumoral microhabitat. Higher HP colonisation influenced the overall structure of the gastric microbiota in normal and peritumoral microhabitats. PiCRUSt analysis revealed that genes associated with nucleotide transport and metabolism and amino acid transport and metabolism were significantly enriched in tumoral microbiota, while gastric acid secretion was significantly higher in HP positive group of the tumoral microbiota. INTERPRETATION: Our present study provided new insights into the roles of gastric microbiota in different stomach microhabitats in gastric carcinogenesis, especially the pathogenesis of HP. FUND: National Natural Science Foundation of China.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal tissues
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- peritumoral tissues
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 230
- Group 1 sample size Number of subjects in the case (exposed) group
- 247
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 2a, 2c, 2f
Description: Comparison of the relative abundance of dominant bacterial taxa at different levels
Abundance in Group 1: increased abundance in peritumoral tissues
Revision editor(s): WikiWorks743
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 2a, 2c, 2f
Description: Comparison of the relative abundance of dominant bacterial taxa at different levels
Abundance in Group 1: decreased abundance in peritumoral tissues
Revision editor(s): WikiWorks743
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- peritumoral tissues
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- tumoral tissues
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 247
- Group 1 sample size Number of subjects in the case (exposed) group
- 229
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 2a, 2c, 2f
Description: Comparison of the relative abundance of dominant bacterial taxa at different levels
Abundance in Group 1: increased abundance in tumoral tissues
Revision editor(s): WikiWorks743
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 2a, 2c, 2f
Description: Comparison of the relative abundance of dominant bacterial taxa at different levels
Abundance in Group 1: decreased abundance in tumoral tissues
Revision editor(s): WikiWorks743
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal tissues
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- tumoral tissues
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 230
- Group 1 sample size Number of subjects in the case (exposed) group
- 229
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 2a, 2c, 2f
Description: Comparison of the relative abundance of dominant bacterial taxa at different levels
Abundance in Group 1: increased abundance in tumoral tissues
Revision editor(s): WikiWorks743
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 2a, 2c, 2f
Description: Comparison of the relative abundance of dominant bacterial taxa at different levels
Abundance in Group 1: decreased abundance in tumoral tissues
| NCBI | Links |
|---|---|
| Pseudomonadota | |
| Helicobacteraceae | |
| Azotobacter group | |
| Bacteroidaceae | |
| Helicobacter | |
| Sphingomonas ⚠ | |
| Pseudomonas ⚠ | |
| Bacteroides | |
| Helicobacter pylori | |
| Prevotella copri | |
| Bacteroides uniformis |
Revision editor(s): WikiWorks743
Experiment 4
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- early stage normal
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- early stage tumor
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 112
- Group 1 sample size Number of subjects in the case (exposed) group
- 116
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 4k, 4l, 4m, 4n
Description: Early-stage gastric microbiota between normal and tumor samples
Abundance in Group 1: increased abundance in early stage tumor
| NCBI | Links |
|---|---|
| Cutibacterium acnes | |
| Streptococcus anginosus |
Revision editor(s): WikiWorks743, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 4k, 4l, 4m, 4n
Description: Early-stage gastric microbiota between normal and tumor samples
Abundance in Group 1: decreased abundance in early stage tumor
| NCBI | Links |
|---|---|
| Prevotella copri | |
| Sphingomonas yabuuchiae ⚠ |
Revision editor(s): WikiWorks743, Claregrieve1
Experiment 5
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- early stage normal
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- early stage peritumor
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 112
- Group 1 sample size Number of subjects in the case (exposed) group
- 118
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 4k, 4l, 4m, 4n
Description: Early-stage gastric microbiota in normal and peritumor samples
Abundance in Group 1: decreased abundance in early stage peritumor
| NCBI | Links |
|---|---|
| Sphingomonas yabuuchiae ⚠ |
Revision editor(s): WikiWorks743, Claregrieve1
Experiment 6
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- late stage normal
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- late stage tumor
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 118
- Group 1 sample size Number of subjects in the case (exposed) group
- 113
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 4k, 4l, 4m, 4n
Description: Late-stage gastric microbiota in normal and tumor samples
Abundance in Group 1: increased abundance in late stage tumor
| NCBI | Links |
|---|---|
| Cutibacterium acnes | |
| Streptococcus anginosus |
Revision editor(s): WikiWorks743, Claregrieve1
Experiment 8
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- late stage normal
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- late stage peritumor
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 118
- Group 1 sample size Number of subjects in the case (exposed) group
- 129
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 4k, 4l, 4m, 4n
Description: late-stage gastric microbiota in normal vs peritumor samples
Abundance in Group 1: decreased abundance in late stage peritumor
| NCBI | Links |
|---|---|
| Prevotella copri |
Revision editor(s): WikiWorks743, Claregrieve1
Experiment 9
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal HP-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- normal HP+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- normal samples that are H. Pylori positive
- Group 0 sample size Number of subjects in the control (unexposed) group
- 64
- Group 1 sample size Number of subjects in the case (exposed) group
- 166
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 5l, Supp FigS9
Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat
Abundance in Group 1: increased abundance in normal HP+
Revision editor(s): WikiWorks743
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure 5, Supp FigS9
Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat
Abundance in Group 1: decreased abundance in normal HP+
Revision editor(s): WikiWorks743, Claregrieve1
Experiment 10
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- peritumor HP-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- peritumor HP+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- peritumor samples that are H. Pylori positive
- Group 0 sample size Number of subjects in the control (unexposed) group
- 65
- Group 1 sample size Number of subjects in the case (exposed) group
- 182
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure S10
Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in peritumor microhabitat
Abundance in Group 1: increased abundance in peritumor HP+
| NCBI | Links |
|---|---|
| Bacillaceae | |
| Bacillales | |
| Bacillus ⚠ | |
| Campylobacterales | |
| Campylobacterota | |
| Gemella | |
| Helicobacter | |
| Helicobacteraceae | |
| Pseudomonadota | |
| Streptococcaceae | |
| Streptococcus | |
| Bacillales Family X. Incertae Sedis |
Revision editor(s): WikiWorks743, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure S10
Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in peritumor microhabitat
Abundance in Group 1: decreased abundance in peritumor HP+
Revision editor(s): WikiWorks743
Experiment 11
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- tumor HP-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- tumor HP+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- tumor samples that are H. Pylori positive
- Group 0 sample size Number of subjects in the control (unexposed) group
- 77
- Group 1 sample size Number of subjects in the case (exposed) group
- 152
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure S11
Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in tumor microhabitat
Abundance in Group 1: increased abundance in tumor HP+
Revision editor(s): WikiWorks743
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Source: Figure S11
Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in tumor microhabitat
Abundance in Group 1: decreased abundance in tumor HP+
Revision editor(s): WikiWorks743
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