Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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
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
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
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Subjects
- Location of subjects
- China
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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
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
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
Empty strings are not accepted.
Curated date: 2021/01/10
Curator:
Revision editor(s):
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Esophageal carcinoma
- 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
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
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter segnis | ||
| Corynebacterium | ||
| Leptotrichia hofstadii | ||
| Leptotrichia sp. | ||
| Megasphaera micronuciformis | ||
| Porphyromonas gingivalis | ||
| Streptococcus sp. |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
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
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Prevotella melaninogenica | ||
| Rothia dentocariosa | ||
| Streptococcus | ||
| Neisseria | ||
| Streptococcus australis |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 4
Empty strings are not accepted.
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal carcinoma
- 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
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
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
Curated date: 2021/01/10
Curator:
Revision editor(s):
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
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
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium periodonticum | ||
| Gemella sanguinis | ||
| Haemophilus parainfluenzae | ||
| Neisseria | ||
| Porphyromonas gingivalis | ||
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
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
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Porphyromonas sp. | ||
| Prevotella | ||
| Rothia | ||
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
