Microbial biomarkers of common tongue coatings in patients with gastric cancer
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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 Uniform resource identifier for web resources.
Authors
Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J, Zhan Z
Journal
Microbial pathogenesis
Year
2019
PURPOSE: The study aims to explore the characteristic microorganisms of the common tongue coatings in patients with gastric cancer (GC). METHODS: A total of 115 GC patients were assigned to four groups: White-thin coating (W-thin) group, White-thick coating (W-thick) group, Yellow-thin coating (Y-thin) group and Yellow-thick coating (Y-thick) group. Thirty-five healthy volunteers with White-thin coating were recruit as controls. High-throughput sequencing was used to describe the microbial community of the tongue coatings based on 16S rRNA and 18S rRNA genes. Multi-factors statistical analysis was carried out to present the microbial biomarkers of the tongue coating in GC patients. RESULTS: At bacterial phylum level, Saccharibacteria had higher relative abundance in W-thick group than W-thin group, Proteobacteria was more abundant in W-thin group than Y-thick group and less abundant in Y-thick group than Y-thin group. At fungal genus level, Guehomyces and Aspergillus presented to be significantly different among the common tongue coatings. Forteen significantly increased taxa were sorted out as the microbial biomarkers of common tongue coatings by LEfSe and ROC analysis. At species level, bacterial Capnocytophaga leadbetteri and fungal Ampelomyces_sp_IRAN_1 may be the potential biomarkers of W-thin coating, four bacterial species (Megasphaera micronuciformis, Selenomonas sputigena ATCC 35185, Acinetobacter ursingii, Prevotella maculosa) may be the potential biomarkers of W-thick coating. In general, the white coatings held more complex commensal relationship than the yellow coatings. CONCLUSION: The common tongue coating owned characteristic microorganisms and special commensal relationship in the GC patients.
Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Tongue Glossus,Tongue
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- other coatings
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- white-thin tongue coating GC patient
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer with different tongue coatings
- Group 0 sample size Number of subjects in the control (unexposed) group
- 90
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
- RT-qPCR
Statistical Analysis
- 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
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
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Table 1,2,4
Description: LEfSe analysis of microbial taxa from tongue coating in GC patients
Abundance in Group 1: increased abundance in white-thin tongue coating GC patient
| NCBI | Links |
|---|---|
| Lautropia | |
| Capnocytophaga sp. | |
| Megasphaera micronuciformis |
Revision editor(s): WikiWorks
Signature 2
Needs review
Source: Table 1,2,4
Description: LEfSe analysis of microbial taxa from tongue coating in GC patients
Abundance in Group 1: decreased abundance in white-thin tongue coating GC patient
| NCBI | Links |
|---|---|
| Stomatobaculum | |
| Eubacterium sp. |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Tongue Glossus,Tongue
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- other coatings
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- white-thick tongue coating GC patient
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer with different tongue coatings
- Group 0 sample size Number of subjects in the control (unexposed) group
- 72
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
Statistical Analysis
- 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
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
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Table 1,2,4
Description: LEfSe analysis of microbial taxa from tongue coating in GC patients
Abundance in Group 1: increased abundance in white-thick tongue coating GC patient
| NCBI | Links |
|---|---|
| Candidatus Saccharibacteria | |
| Oscillospiraceae | |
| Eubacterium | |
| Megasphaera micronuciformis | |
| Selenomonas sputigena | |
| Prevotella maculosa |
Revision editor(s): WikiWorks
Signature 2
Needs review
Source: Table 1,2,4
Description: LEfSe analysis of microbial taxa from tongue coating in GC patients
Abundance in Group 1: decreased abundance in white-thick tongue coating GC patient
| NCBI | Links |
|---|---|
| Acinetobacter ursingii ⚠ | |
| Ligilactobacillus salivarius |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Tongue Glossus,Tongue
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- other coatings
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- yellow-thick tongue coating GC patient
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer with different tongue coatings
- Group 0 sample size Number of subjects in the control (unexposed) group
- 95
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
Statistical Analysis
- 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
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
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Table 1,2,4
Description: LEfSe analysis of microbial taxa from tongue coating in GC patients
Abundance in Group 1: decreased abundance in yellow-thick tongue coating GC patient
| NCBI | Links |
|---|---|
| Oscillospiraceae | |
| Lautropia | |
| Neisseria | |
| Peptostreptococcus | |
| Gemella sanguinis | |
| Capnocytophaga sputigena | |
| Haemophilus parainfluenzae |
Revision editor(s): WikiWorks
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