Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus
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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
Dong L, Yin J, Zhao J, Ma SR, Wang HR, Wang M, Chen W, Wei WQ
Journal
Frontiers in microbiology
Year
2018
Keywords:
16S rRNA gene sequencing, esophagus, microbial preference, microbial similarity, oral cavity
Human microbial communities are highly complex ecosystems, but it remains unclear if microbial compositions have any similarity in distinct sites of the oral cavity and esophagus in particular. Clinical samples were collected from three niches (saliva, tongue dorsum and supragingival plaque) of the oral cavity and three segments (upper, middle, and lower) of the esophagus in 27 healthy individuals. Bacterial V3-V4 region of 16S rRNA gene in these samples was amplified and sequenced on Illumina sequencing platform, followed by data analysis using QIIME and LEfSe softwares. Highly diverse bacterial flora with 365 genera belonging to 29 phyla resided in the oral cavity and 594 genera belonging to 29 phyla in the esophagus. The phyla Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and TM7 were most abundant in both the oral cavity and the esophagus, but the phyla Actinobacteria and Bacteroidetes were preferable in the oral cavity and Firmicutes in the esophagus. The genera Streptococcus, Neisseria, Prevotella, Actinobacillus, and Veillonella were most abundant in both oral cavity and esophagus, but Neisseria was preferable in the oral cavity and Streptococcus in the esophagus. Different niche-specific bacterial signatures were found in the oral cavity, e.g., the class Flavobacteria in the supragingival plaque, class Bacteroides in the saliva and the class Clostridia in the tongue dorsum. By contrast, no site specific bacteria for three different segments of esophagus were found. However, high variability of microbial compositions between individuals was observed. In conclusion, this study confirmed microbial diversity at different taxonomic levels in healthy oral cavity and esophagus, and identified the site-preferable bacterial signatures in six niches of the upper digestive tract. These findings provide a critical baseline for future studies interpreting microbiome-related diseases.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
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
- Oral cavity , Esophagus Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity,Gullet,Oesophagus,Esophagus,esophagus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Taxonomic microbiome measurement Taxonomic microbiome measurement,taxonomic microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Oral cavity
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Esophagus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy individual who are esophageal disease-free, confirmed by endoscopic examination and then biopsy-based pathological diagnosis if necessary.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
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
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
Source: Figure 3, Supplementary Figure S1
Description: Microbial taxa significantly different in the oral cavity compared to the esophagus with LDA score >2 using LEfse analysis
Abundance in Group 1: increased abundance in Esophagus
Revision editor(s): Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
Source: Figure 3, Supplementary Figure S1
Description: Microbial taxa significantly different in the oral cavity compared to the esophagus with LDA score >2 using LEfse analysis
Abundance in Group 1: decreased abundance in Esophagus
Revision editor(s): Scholastica
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Saliva and tongue dorsum
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Supragingival plaque
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Supragingival plaque samples of healthy individual confirmed free of periodontal diseases and no incident caries at the time of sampling by a dentist.
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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
Source: Figure 5
Description: Significantly higher relative abundance in the supragingival plaques compared to other two sites
Abundance in Group 1: increased abundance in Supragingival plaque
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Epsilonproteobacteria | ||
| Flavobacteriia | ||
| Fusobacteriota | ||
| Fusobacteriia | ||
| Spirochaetia | ||
| Spirochaetota |
Revision editor(s): Scholastica
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Tongue dorsum and supragingival plaque
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Saliva
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Saliva samples of healthy individual confirmed free of periodontal diseases and no incident caries at the time of sampling by a dentist.
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
Source: Figure 5
Description: Significantly higher relative abundance in the saliva compared to other two sites
Abundance in Group 1: increased abundance in Saliva
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidia | ||
| Coriobacteriia | ||
| Synergistia | ||
| Synergistota |
Revision editor(s): Scholastica
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Supragingival plaque and Saliva
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tongue dorsum
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tongue dorsum samples of healthy individual confirmed free of periodontal diseases and no incident caries at the time of sampling by a dentist.
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-8
Source: Figure 5
Description: Significantly higher relative abundance in the tongue dorsum compared to other two sites
Abundance in Group 1: increased abundance in Tongue dorsum
| NCBI | Quality Control | Links |
|---|---|---|
| Erysipelotrichia | ||
| Clostridia | ||
| SR1SR1 |
Revision editor(s): Scholastica
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