Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers
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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
Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T, Yamashita Y
Journal
Frontiers in microbiology
Year
2019
Keywords:
colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer
The salivary microbiota is constantly swallowed and delivered to the digestive tract. These bacteria may be associated with gastrointestinal diseases. This case-control study examined the salivary microbiota in patients with digestive tract cancer (DTC) and evaluated their differential distribution based on the cancer sites. We collected saliva samples from 59 patients with cancer in any part of the digestive tract (tongue/pharynx, esophagus, stomach, and large intestine) and from 118 age- and sex-matched control subjects. There was no significant difference in periodontal status between DTC patients and control subjects (P = 0.72). We examined the bacterial diversity and composition in saliva by 16S ribosomal RNA gene sequencing. Salivary bacterial diversity in DTC patients was significantly higher than that in control subjects [number of operational taxonomic units (OTUs), P = 0.02; Shannon index, P < 0.01; Chao1, P = 0.04]. Eleven differentially abundant OTUs in DTC patients were identified using the linear discriminant analysis effect size (LEfSe) method. Based on the cancer sites, the diversity of salivary bacteria was especially higher in tongue/pharyngeal or esophageal cancer patients than in control subjects. Among the 11 differentially abundant OTUs in DTC patients, an OTU corresponding to Porphyromonas gingivalis was more abundant in the saliva of all groups of DTC patients compared to that in control subjects, and an OTU corresponding to Corynebacterium species was more abundant in all groups other than gastric cancer patients (P < 0.01). In addition, the relative abundances of OTUs corresponding to Fusobacterium nucleatum, Streptococcus parasanguinis II, and Neisseria species were significantly higher in tongue/pharyngeal cancer patients compared to their abundances in control subjects (P < 0.01). The relative abundance of an OTU corresponding to the Neisseria species was also significantly higher in gastric cancer patients and that of an OTU corresponding to Actinomyces odontolyticus was significantly higher in colorectal cancer patients (P < 0.01). These results suggest that the salivary microbiota might be associated with various digestive tract cancers.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
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
- Digestive system cancer cancer of digestive system,digestive system cancer,gastrointestinal system cancer,gastrointestinal tract cancer,GI tumor,malignant digestive system neoplasm,malignant gastrointestinal neoplasm,malignant gastrointestinal system neoplasm,malignant neoplasm of digestive system,Digestive system cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- digestive tract cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with digestive tract cancers (tongue/pharynx, esophagus, stomach and/or large intestine)
- 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
- 59
- 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
- V1-V2
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Figure 3, Figure S1
Description: Bacterial species corresponding to the differentially abundant OTUs between digestive tract cancer patients and control subjects
Abundance in Group 1: increased abundance in digestive tract cancer patients
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Figure 3, Figure S1
Description: Bacterial species corresponding to the differentially abundant OTUs between digestive tract cancer patients and control subjects
Abundance in Group 1: decreased abundance in digestive tract cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces graevenitzii | ||
| Porphyromonas | ||
| Porphyromonas pasteri | ||
| Porphyromonas sp. | ||
| Prevotella | ||
| Prevotella melaninogenica | ||
| Rothia | ||
| Rothia dentocariosa | ||
| Solobacterium moorei |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Differences from previous experiment shown
Subjects
- Location of subjects
- China
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Tongue neoplasm Cancer of the Tongue,Cancer of Tongue,Cancer, Oral,Cancer, Tongue,Cancers, Oral,Cancers, Tongue,NEOPL ORAL,NEOPL TONGUE,neoplasm of the tongue,neoplasm of tongue,Neoplasm, Oral,Neoplasm, Tongue,Neoplasms, Oral,Neoplasms, Tongue,Oral Cancer,Oral Cancers,ORAL NEOPL,Oral Neoplasm,Oral Neoplasms,Tongue Cancer,Tongue Cancers,TONGUE NEOPL,tongue neoplasm,tongue neoplasm (disease),Tongue Neoplasms,tongue tumor,tumor of the tongue,tumor of tongue,Tongue neoplasm
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- tongue/pharyngeal cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with tongue/pharyngeal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Figure S3, Figure 5
Description: Bacterial species corresponding to the differentially abundant OTUs between tongue/pharyngeal cancer patients and control subjects
Abundance in Group 1: increased abundance in tongue/pharyngeal cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter segnis | ||
| Corynebacterium | ||
| Leptotrichia | ||
| Neisseria | ||
| Porphyromonas gingivalis | ||
| Prevotella | ||
| Streptococcus parasanguinis | ||
| Streptococcus sanguinis |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Figure S3, Figure 5
Description: Bacterial species corresponding to the differentially abundant OTUs between tongue/pharyngeal cancer patients and control subjects
Abundance in Group 1: decreased abundance in tongue/pharyngeal cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella melaninogenica | ||
| Rothia dentocariosa | ||
| Streptococcus | ||
| Streptococcus australis |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/25
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Esophageal cancer Aerodigestive tract cancer, susceptibility to,Ca lower third oesophagus,Ca middle third oesophagus,cancer of esophagus,Escc, susceptibility to,esophageal cancer,esophageal squamous cell carcinoma, susceptibility to,esophagus cancer,gastric cardia adenocarcinoma, susceptibility to,malignant esophageal neoplasm,malignant esophageal tumor,malignant esophagus neoplasm,malignant esophagus tumor,malignant neoplasm of distal third of esophagus,malignant neoplasm of esophagus,malignant neoplasm of lower third of oesophagus,malignant neoplasm of middle third of oesophagus,malignant neoplasm of proximal third of esophagus,malignant neoplasm of the esophagus,malignant neoplasm of upper third esophagus,malignant tumor of abdominal esophagus,malignant tumor of distal third of esophagus,malignant tumor of esophagus,malignant tumor of proximal third of esophagus,malignant tumor of the esophagus,malignant tumor of the middle third of the esophagus,Esophageal cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- esophageal cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with esophageal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- 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
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/25
Source: Figure S3, Figure 5
Description: Bacterial species corresponding to the differentially abundant OTUs between esophageal cancer patients and control subjects
Abundance in Group 1: increased abundance in esophageal cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter segnis | ||
| Corynebacterium | ||
| Leptotrichia hofstadii | ||
| Leptotrichia sp. | ||
| Megasphaera micronuciformis | ||
| Porphyromonas gingivalis | ||
| Streptococcus sp. |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/25
Source: Figure S3, Figure 5
Description: Bacterial species corresponding to the differentially abundant OTUs between esophageal cancer patients and control subjects
Abundance in Group 1: decreased abundance in esophageal cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Prevotella melaninogenica | ||
| Rothia dentocariosa | ||
| Streptococcus | ||
| Neisseria | ||
| Streptococcus australis |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/25
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with colorectal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
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 Claregrieve1 on 2022/07/25
Source: Figure S3, Figure 5
Description: Bacterial species corresponding to the differentially abundant OTUs between colorectal cancer patients and control subjects
Abundance in Group 1: increased abundance in colorectal cancer patients
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/25
Source: Figure S3, Figure 5
Description: Bacterial species corresponding to the differentially abundant OTUs between colorectal cancer patients and control subjects
Abundance in Group 1: decreased abundance in colorectal cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonas pasteri | ||
| Prevotella | ||
| Prevotella melaninogenica | ||
| Prevotella sp. | ||
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 5
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/25
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Differences from previous experiment shown
Subjects
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- gastric cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with gastric cancer
- 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
- 10
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 Claregrieve1 on 2022/07/25
Source: Figure S3, Figure 5
Description: Bacterial species corresponding to the differentially abundant OTUs between gastric cancer patients and control subjects
Abundance in Group 1: increased abundance in gastric cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium periodonticum | ||
| Gemella sanguinis | ||
| Haemophilus parainfluenzae | ||
| Neisseria | ||
| Porphyromonas gingivalis | ||
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/25
Source: Figure S3, Figure 5
Description: Bacterial species corresponding to the differentially abundant OTUs between gastric cancer patients and control subjects
Abundance in Group 1: decreased abundance in gastric cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Porphyromonas sp. | ||
| Prevotella | ||
| Rothia | ||
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
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