Microbial biomarkers of common tongue coatings in patients with gastric cancer

From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
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


Reviewed Marked as Reviewed by Atrayees on 2023-8-18

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Reviewed Marked as Reviewed by Atrayees on 2023-8-18

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks, Atrayees

Source: Table 1

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 Quality ControlLinks
Lautropia
Capnocytophaga leadbetteri
Ampelomyces

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-8-18

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks, Atrayees

Source: Table 1

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 Quality ControlLinks
Stomatobaculum
Megasphaera micronuciformis
Eubacterium sp.
Sporidiobolales
Fusarium equiseti

Revision editor(s): WikiWorks, Atrayees

Experiment 2


Reviewed Marked as Reviewed by Atrayees on 2023-8-18

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks, Atrayees

Source: Table 2

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 Quality ControlLinks
Candidatus Saccharibacteria
Oscillospiraceae
Megasphaera micronuciformis
Selenomonas sputigena
Prevotella maculosa
[Eubacterium] nodatum

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-8-18

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks, Atrayees

Source: Table 2

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 Quality ControlLinks
Acinetobacter ursingii
Ligilactobacillus salivarius
Hypocreales

Revision editor(s): WikiWorks, Atrayees

Experiment 3


Reviewed Marked as Reviewed by Atrayees on 2023-8-18

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks, Atrayees

Source: Table 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 Quality ControlLinks
Oscillospiraceae
Lautropia
Neisseria
Peptostreptococcus
Gemella sanguinis
Capnocytophaga sputigena
Haemophilus parainfluenzae
Marinobacter sp. NP39
Burkholderiaceae

Revision editor(s): WikiWorks, Atrayees

Experiment 4


Reviewed Marked as Reviewed by Atrayees on 2023-8-18

Curated date: 2023/08/18

Curator: Atrayees

Revision editor(s): Atrayees

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
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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-8-18

Curated date: 2023/08/18

Curator: Atrayees

Revision editor(s): Atrayees

Source: Table 3

Description: LEfSe analysis of microbial taxa from tongue coating in GC patients

Abundance in Group 1: decreased abundance in yellow-thin coating GC patient

NCBI Quality ControlLinks
Cladosporium halotolerans
Trichoderma

Revision editor(s): Atrayees