A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients
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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
Wu ZF, Zou K, Wu GN, Jin ZJ, Xiang CJ, Xu S, Wang YH, Wu XY, Chen C, Xu Z, Li WS, Yao XQ, Zhang JF, Liu FK
Journal
Digestive diseases and sciences
Year
2021
Keywords:
Carcinogenesis, Gastric cancer, Microbiota, Stomach
BACKGROUND: How gastric cancer (GC) incidence is associated with changes in the gastric microbiome has not been firmly established. The present study therefore aims to investigate the microbial communities present within the gastric mucosa of patients with superficial gastritis (SG) or GC. METHODS: Paired tumor and paracancerous samples of the gastric mucosa were collected from 18 patients being surgically treated for GC and from 32 patients with SG being treated via gastroscopy. The gastric microbiome in these samples was then profiled via 16S rRNA sequencing, with a linear discriminant analysis effect size (LEfSe) approach used to identify and compare different bacteria, and with PICRUSt used for predictive functional analyses. RESULTS: GC patients exhibited a distinct gastric microbiota profile from that observed in SG patients. These changes were evident in both tumor and paracancerous tissues from GC patients. Specifically, we found that 6 bacterial genera were specifically enriched in GC tissue samples relative to SG samples, while 18 genera were depleted in these same samples. Based on the differential abundance of these bacteria, we were able to calculate microbial dysbiosis index (MDI) values, which were significantly higher in GC patients than in SG patients. In addition, MDI values were negatively correlated with gastric Shannon index and were positively correlated with relative Helicobacter spp. abundance. Importantly, these MDI values were readily able to discriminate between GC and SG patient samples. Functional analysis suggested that GC patients were more likely to harbor a nitrosating microbial community. CONCLUSIONS: GC patients exhibited a gastric microbiome profile distinct from that observed in SG patients, with these differences being evident in both tumor and paracancerous tissues. Differences in the relative abundance of Helicobacter spp. may be the primary driver of gastric dysbiosis in GC patients.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
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
- Gastric pit Foveola gastrica,Foveolae gastricae,Gastric foveola,Gastric pit,gastric pit
- 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
- Superficial gastritis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Gastric cancer (GC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Gastric microbiome in paired tumor and paracancerous tissue samples from GC patients undergoing surgical treatment
- 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
- 96
- 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-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)?
- No
- 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
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-9
Source: Figure 2B
Description: Cladogram representation of the gastric microbiota taxa associated with superficial gastritis (group 0) an gastric cancer (group1)
Abundance in Group 1: increased abundance in Gastric cancer (GC)
Revision editor(s): Chikamso, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-9
Source: Figure 2B
Description: Cladogram representation of the gastric microbiota taxa associated with superficial gastritis (group 0) and gastric cancer (group 1).
Abundance in Group 1: decreased abundance in Gastric cancer (GC)
Revision editor(s): Chikamso, ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-tumor tissues of gastric cancer patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- tumor tissues of gastric cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Gastric microbiome in tumor tissue samples from GC patients undergoing surgical treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 78
- 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
- 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 ChiomaBlessing on 2024-1-5
Source: Supplementary figure 3A
Description: Differential bacteria between the tumor and non-tumor tissues of gastric cancer patients by LEfSe analysis (LDA scores >3.0)
Abundance in Group 1: decreased abundance in tumor tissues of gastric cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Nitriliruptoria | ||
| Mesorhizobium | ||
| Bradyrhizobium | ||
| Xanthobacteraceae | ||
| Moraxellaceae | ||
| Rhizobiaceae | ||
| Pseudomonadales | ||
| Hyphomicrobiales |
Revision editor(s): Chikamso
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
Source: Supplementary figure 3A
Description: Differential bacteria between the tumor and non-tumor tissues of gastric cancer patients by LEfSe analysis (LDA >3.0)
Abundance in Group 1: increased abundance in tumor tissues of gastric cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Fusobacteriaceae | ||
| Fusobacteriales | ||
| Fusobacteriia | ||
| Fusobacterium | ||
| Lactobacillales | ||
| Neisseriaceae | ||
| Fusobacteriota | ||
| subgroup 6subgroup 6 |
Revision editor(s): Chikamso
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