Microbiota in the Throat and Risk Factors for Laryngeal 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
Gong H, Shi Y, Zhou X, Wu C, Cao P, Xu C, Hou D, Wang Y, Zhou L
Journal
Applied and environmental microbiology
Year
2014
The compositions and abundances of the microbiota in the ecological niche of the human throat and the possible relationship between the microbiota and laryngeal cancer are poorly understood. To obtain insight into this, we enrolled 27 laryngeal carcinoma patients and 28 subjects with vocal cord polyps as controls. For each subject, we simultaneously collected swab samples from the upper throat near the epiglottis (site I) and tissue samples from the vestibulum laryngis to the subglottic region (site II). The microbiota of the throat were fully characterized by pyrosequencing of barcoded 16S rRNA genes. We found 14 phyla, 20 classes, 38 orders, 85 families, and 218 genera in the throats of enrolled subjects. The main phyla were Firmicutes (54.7%), Fusobacteria (14.8%), Bacteroidetes (12.7%), and Proteobacteria (10.6%). Streptococcus (37.3%), Fusobacterium (11.3%), and Prevotella (10.6%) were identified as the three most predominant genera in the throat. The relative abundances of 23 bacterial genera in site I were significantly different from those in site II (P < 0.05). The relative proportions of 12 genera largely varied between laryngeal cancer patients and control subjects (P < 0.05). Collectively, this study outlined the spatial structure of microbial communities in the human throat. The spatial structure of bacterial communities significantly varied in two anatomical sites of the throat. The bacterial profiles of the throat of laryngeal cancer patients were strongly different from those of control subjects, and several of these microorganisms may be related to laryngeal carcinoma.
Experiment 1
Reviewed Marked as Reviewed by Fatima on 2021/07/16
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
- Throat Gula,Throat,throat
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Squamous cell carcinoma carcinoma, squamous cell, malignant,epidermoid carcinoma,epidermoid cell cancer,malignant epidermoid cell neoplasm,malignant epidermoid cell tumor,malignant squamous cell neoplasm,malignant squamous cell tumor,squamous carcinoma,squamous cell cancer,squamous cell carcinoma,squamous cell carcinoma (morphologic abnormality),squamous cell carcinoma NOS (morphologic abnormality),squamous cell epithelioma,Squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- laryngeal squamous cell carcinoma (LSCC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- 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)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- T-Test
- 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)?
- Yes
Signature 1
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Table 2, Text, Supplementary Table S2
Description: Differences in bacterial communities in the throats of LSCC patients and control subjects
Abundance in Group 1: increased abundance in laryngeal squamous cell carcinoma (LSCC)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Prevotella | ||
| Parvimonas | ||
| Peptostreptococcus | ||
| Dialister | ||
| Catonella | ||
| Selenomonas | ||
| Treponema | ||
| Burkholderia | ||
| Peptostreptococcaceae |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Table 2, Text, Supplementary Table S2
Description: Differences in bacterial communities in the throats of LSCC patients and control subjects
Abundance in Group 1: decreased abundance in laryngeal squamous cell carcinoma (LSCC)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Rothia |
Revision editor(s): WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2021/07/16
Differences from previous experiment shown
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Site 2 (site below the epiglottis in the throat)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Site 1 (upper portion of throat near the epiglottis)
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Signature 1
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Table 2, Text, Supplementary Table S2
Description: Differences in bacterial communities in the throats of LSCC patients and control subjects
Abundance in Group 1: increased abundance in Site 1 (upper portion of throat near the epiglottis)
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| Leptotrichia | ||
| Actinomyces | ||
| Rothia | ||
| Granulicatella | ||
| Megasphaera | ||
| Oribacterium | ||
| Atopobium | ||
| Moryella | ||
| Candidatus Saccharibacteria |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Table 2, Text, Supplementary Table S2
Description: Differences in bacterial communities in the throats of LSCC patients and control subjects
Abundance in Group 1: decreased abundance in Site 1 (upper portion of throat near the epiglottis)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Prevotella | ||
| Parvimonas | ||
| Peptostreptococcus | ||
| Porphyromonas | ||
| Dialister | ||
| Mycoplasma | ||
| Filifactor | ||
| Catonella | ||
| Eikenella | ||
| Treponema | ||
| Aggregatibacter | ||
| Peptostreptococcaceae |
Revision editor(s): WikiWorks
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