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
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
Keywords:
Gastric cancer, Microbiome, Tongue coating
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
Needs review
Curated date: 2021/01/10
Curator:
Revision editor(s):
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
- Tongue Glossus,Tongue,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,Gastric 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
- 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
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 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Source: Table 1
Description: LEfSe analysis of microbial taxa from tongue coating in GC patients
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Stomatobaculum | ||
| Megasphaera micronuciformis | ||
| Eubacterium sp. | ||
| Sporidiobolales | ||
| Fusarium equiseti |
Experiment 2
Needs review
Curated date: 2021/01/10
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- white-thick tongue coating GC patient
- 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
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
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Source: Table 2
Description: LEfSe analysis of microbial taxa from tongue coating in GC patients
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Saccharibacteria | ||
| Oscillospiraceae | ||
| Megasphaera micronuciformis | ||
| Selenomonas sputigena | ||
| Segatella maculosa | ||
| [Eubacterium] nodatum |
Experiment 3
Needs review
Curated date: 2021/01/10
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- yellow-thick tongue coating GC patient
- 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
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
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Source: Table 4
Description: LEfSe analysis of microbial taxa from tongue coating in GC patients
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Lautropia | ||
| Neisseria | ||
| Peptostreptococcus | ||
| Gemella sanguinis | ||
| Capnocytophaga sputigena | ||
| Haemophilus parainfluenzae | ||
| Marinobacter sp. NP39 | ||
| Burkholderiaceae |
Experiment 4
Needs review
Curated date: 2023/08/18
Curator:
Revision editor(s):
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
- yellow-thin coating GC patient
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer with yellow thin coating
- Group 0 sample size Number of subjects in the control (unexposed) group
- 88
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
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
- Richness Number of species
- unchanged
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