Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues
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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
Authors
Chen XH, Wang A, Chu AN, Gong YH, Yuan Y
Journal
Frontiers in microbiology
Year
2019
Keywords:
16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk
The link between microbiota and gastric cancer (GC) has attracted widespread attention. However, the phylogenetic profiles of niche-specific microbiota in the tumor microenvironment is still unclear. Here, mucosa-associated microorganisms from 62 pairs of matched GC tissues and adjacent non-cancerous tissues were characterized by 16S rRNA gene sequencing. Functional profiles of the microbiota were predicted using PICRUSt, and a co-occurrence network was constructed to analyze interactions among gastric microbiota. Results demonstrated that mucosa-associated microbiota from cancerous and non-cancerous tissues established micro-ecological systems that differed in composition, structure, interaction networks, and functions. Microbial richness and diversity were increased in cancerous tissues, with the co-occurrence network exhibiting greater complexity compared with that in non-cancerous tissue. The bacterial taxa enriched in the cancer samples were predominantly represented by oral bacteria (such as Peptostreptococcus, Streptococcus, and Fusobacterium), while lactic acid-producing bacteria (such as Lactococcus lactis and Lactobacillus brevis) were more abundant in adjacent non-tumor tissues. Colonization by Helicobacter pylori, which is a GC risk factor, also impacted the structure of the microbiota. Enhanced bacterial purine metabolism, carbohydrate metabolism and denitrification functions were predicted in the cancer associated microbial communities, which was consistent with the increased energy metabolism and concentration of nitrogen-containing compounds in the tumor microenvironment. Furthermore, the microbial co-occurrence networks in cancerous and non-cancerous tissues of GC patients were described for the first time. And differential taxa and functions between the two groups were identified. Changes in the abundance of certain bacterial taxa, especially oral microbiota, may play a role in the maintenance of the local microenvironment, which is associated with the development or progression of GC.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
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
- Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,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,Gastric cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- adjacent normal tissue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancer tissue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer patients who underwent subtotal gastrectomy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 62
- Group 1 sample size Number of subjects in the case (exposed) group
- 62
- 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
- V4-V5
- 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
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
Source: Figure 3
Description: Differential bacteria between non-cancerous tissues and cancerous tissues in Gastric Cancer Patients by LEfSe analysis
Abundance in Group 1: increased abundance in cancer tissue
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
Source: Figure3
Description: Differential bacteria between non-cancerous tissues and cancerous tissues in Gastric Cancer Patients by LEfSe analysis
Abundance in Group 1: decreased abundance in cancer tissue
Revision editor(s): WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- H-pylori sequencing negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- H-pylori sequencing positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- H-pylori sequencing positive non-cancerous samples while studying the correlation between non-cancerous tissue microbiota and gastric cancer risk factors
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
Source: supplementary figure 2
Description: Differential bacteria between H.pylori-sequencing positive and H.pylori-sequencing negative non-cancer samples by LEfSe analysis
Abundance in Group 1: increased abundance in H-pylori sequencing positive
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
Source: supplementary figure 2
Description: Differential bacteria between H.pylori-sequencing positive and H.pylori-sequencing negative non-cancer samples by LEfSe analysis
Abundance in Group 1: decreased abundance in H-pylori sequencing positive
| NCBI | Quality Control | Links |
|---|---|---|
| DSSF69DSSF69 | ||
| Prevotella intermedia | ||
| Prevotellaceae | ||
| Pseudomonas aeruginosa | ||
| Pseudomonadota | ||
| Gammaproteobacteria | ||
| Pseudomonas | ||
| Pseudomonadaceae | ||
| Pseudomonadales |
Revision editor(s): Folakunmi
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- adjacent normal tissue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancer tissue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer patients who underwent subtotal gastrectomy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 62
- Group 1 sample size Number of subjects in the case (exposed) group
- 62
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
Source: supplementary table S5
Description: Significantly differential bacteria identified among the top 20 abundant genera of the cancer and non-cancer groups
Abundance in Group 1: increased abundance in cancer tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Bacillus | ||
| Bacteroides | ||
| Sphingomonas | ||
| Peptostreptococcus | ||
| Streptococcus | ||
| Fusobacterium | ||
| Prevotella sp. |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
Source: supplementary table S5
Description: Significantly differential bacteria identified among the top 20 abundant genera of the cancer and non-cancer groups
Abundance in Group 1: decreased abundance in cancer tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter | ||
| Lactobacillus |
Revision editor(s): Folakunmi
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