Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma
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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
Wang Q, Rao Y, Guo X, Liu N, Liu S, Wen P, Li S, Li Y
Journal
Scientific reports
Year
2019
To investigate the oral microflora of patients with oesophageal squamous cell carcinoma (ESCC), saliva samples were collected from 20 patients with ESCC and 21 healthy controls. The V3-V4 region of 16S rDNA was amplified and sequenced by the Illumina MiSeq high-throughput sequencing platform. The final sequences were used for OTU analysis. Alpha and beta diversity analysis showed that the bacterial diversity and richness of the ESCC group were lower than those of the control group, while the variability of the ESCC group was higher than that of the control group. According to the Metastats difference analysis and LEfSe analysis, the high risk of ESCC may be related to Actinomyces and Atopobium, while the healthy control group is closely related to Fusobacterium and Porphyromonas (the analysis was performed at the genus level). The establishment of the relationship between oral microbiota and risk of ESCC may lead to significant advances in understanding the aetiology of cancer and may open a new research paradigm for cancer prevention.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Esophageal squamous cell carcinoma ESCC,esophageal epidermoid carcinoma,esophageal scc,esophageal squamous cell cancer,esophageal squamous cell carcinoma,esophagus scc,esophagus squamous cell carcinoma,scc of esophagus,scc of the esophagus,squamous cell car. - esophagus,squamous cell carcinoma of esophagus,squamous cell carcinoma of the esophagus,Esophageal squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Oesophageal cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with oesophageal cancer diagnosed by electronic gastroscopy and histopathology, with no related surgery, radiotherapy or chemotherapy for oesophageal cancer before sampling
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- 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)
- 1 month
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
- Metastats
- 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
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
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 Folakunmi on 2024-2-26
Source: Figure 6
Description: Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC)
Abundance in Group 1: increased abundance in Oesophageal cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Actinomycetaceae | ||
| Atopobiaceae | ||
| Atopobium | ||
| Coriobacteriales | ||
| Coriobacteriia |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Source: Figure 6
Description: Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC)
Abundance in Group 1: decreased abundance in Oesophageal cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacterium | ||
| Porphyromonadaceae | ||
| Porphyromonas |
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