Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota
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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
Komori E, Kato-Kogoe N, Imai Y, Sakaguchi S, Taniguchi K, Omori M, Ohmichi M, Nakamura S, Nakano T, Lee SW, Ueno T
Journal
Scientific reports
Year
2023
Gastric cancer is one of the leading causes of death worldwide, and resections are performed to cure the disease. We have previously reported the changes in the gastric microbiota after gastric cancer resection, which may be associated with the oral microbiota; however, the changes in the oral microbiota remain uncharacterized. This study aimed to characterize the changes in the salivary microbiota caused by gastric cancer resection and to evaluate their association with the gastric fluid microbiota. Saliva and gastric fluid samples were collected from 63 patients who underwent gastrectomy before and after surgery, and a 16S rRNA metagenomic analysis was performed to compare the microbiota composition. The number of bacterial species in the salivary microbiota decreased, and the bacterial composition changed after the resection of gastric cancer. In addition, we identified several bacterial genera that varied significantly in the salivary microbiota, some of which also showed similar changes in the gastric fluid microbiota. These findings indicate that changes in the gastric environment affect the oral microbiota, emphasizing the close association between the oral and gastric fluid microbiota. Our study signifies the importance of focusing on the oral microbiota in the perioperative period of gastrectomy in patients with gastric cancer.
Experiment 1
Reviewed Marked as Reviewed by Chloe on 2023-11-6
Subjects
- Location of subjects
- Japan
- 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
- 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
- Gastric cancer patients (Pre-gastrectomy)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Gastric cancer patients (Post-gastrectomy)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with primary gastric cancer who underwent distal gastrectomy and B1 or RY reconstruction
- Group 0 sample size Number of subjects in the control (unexposed) group
- 63
- Group 1 sample size Number of subjects in the case (exposed) group
- 63
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients who were on antibiotics three months preceding the sample collection were excluded from the study
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Chloe on 2023-11-6
Source: Figure 3a
Description: The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the saliva sample identified by linear discriminant analysis effect size (LEfSe).
Abundance in Group 1: increased abundance in Gastric cancer patients (Post-gastrectomy)
| NCBI | Quality Control | Links |
|---|---|---|
| Howardella | ||
| Lactobacillus | ||
| uncultured bacterium |
Revision editor(s): Aleru002
Signature 2
Reviewed Marked as Reviewed by Chloe on 2023-11-6
Source: Figure 3a
Description: The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the saliva sample identified by linear discriminant analysis effect size (LEfSe).
Abundance in Group 1: decreased abundance in Gastric cancer patients (Post-gastrectomy)
Revision editor(s): Aleru002
Experiment 2
Reviewed Marked as Reviewed by Chloe on 2023-11-6
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
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
Reviewed Marked as Reviewed by Chloe on 2023-11-6
Source: Figure 3b
Description: The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the gastric fluid sample identified by linear discriminant analysis effect size (LEfSe).
Abundance in Group 1: increased abundance in Gastric cancer patients (Post-gastrectomy)
| NCBI | Quality Control | Links |
|---|---|---|
| Bergeyella | ||
| Bifidobacterium | ||
| Klebsiella | ||
| Lactobacillus | ||
| Peptoclostridium |
Revision editor(s): Aleru002
Signature 2
Reviewed Marked as Reviewed by Chloe on 2023-11-6
Source: Figure 3b
Description: The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the gastric fluid sample identified by linear discriminant analysis effect size (LEfSe).
Abundance in Group 1: decreased abundance in Gastric cancer patients (Post-gastrectomy)
Revision editor(s): Aleru002
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