Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy
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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.
Authors
Xu Y, Teng F, Huang S, Lin Z, Yuan X, Zeng X, Yang F
Journal
Archives of oral biology
Year
2014
Keywords:
Nasopharyngeal carcinoma, Oral microbiota, Pyrosequencing, Radiation therapy, Saliva
OBJECTIVE: A growing body of evidence has implicated human oral microbiota in the aetiology of oral and systemic diseases. Nasopharyngeal carcinoma (NPC), an epithelial-originated malignancy, has a complex aetiology not yet fully understood. Chemoradiation therapy of NPC can affect oral microbiota and is usually accompanied by plaque accumulation. Thus, the study aimed to understand the diversity, divergence and development of the oral microbiota in NPC patients and their associated treatment, which might provide useful insights into disease aetiology and treatment side effects. DESIGN: A longitudinal study was designed that included three Chinese adults with NPC. Saliva samples were collected at three time points: prior to the chemoradiation treatment (carcinoma baseline, or CB), 7 months post-treatment (carcinoma-after-therapy phase 1 or CA1) and 12 months post-treatment (carcinoma-after-therapy phase 2 or CA2). Pyrosequencing of the bacterial 16S ribosomal DNA (rDNA) V1-V3 hypervariable region was employed to characterise the microbiota. Saliva samples of three healthy subjects from our former study were employed as healthy controls. Principal coordinates analysis (PCoA), Metastats and random forest prediction models were used to reveal the key microbial members associated with NPC and its treatment programme. RESULTS: (1) In total, 412 bacterial species from at least 107 genera and 13 phyla were found in the saliva samples of the NPC patients. (2) PCoA revealed that not only were the microbiota from NPC patients distinct from those of healthy controls (p<0.001) but also that separation was found on the saliva microbiota between pre- and post-therapy (p<0.001) in the NPC samples. (3) At the genus level and the operational taxonomic unit (OTU) level, Streptococcus was found with lower abundance in NPC samples. (4) Chemoradiation therapy did not incur similar changes in microbiota structure among the three NPC patients; the microbiota in one of them stayed largely steady, while those in the other two showed significant alteration. CONCLUSIONS: This is the first study employing culture-independent techniques to interrogate the phylogenetic diversity, divergence and temporal development of oral microbiota in NPC patients. Our results indicated that certain bacterial taxa might be associated with NPC and that oral microbiota of NPC patients might respond to the chemoradiation therapy in a host-specific manner. Further investigation with larger sample size should help to validate the links between oral microbiota and NPC.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-9
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
- Nasopharyngeal squamous cell carcinoma nasopharyngeal squamous cell carcinoma,Nasopharyngeal squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls at Baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Nasopharyngeal carcinoma patients at baseline
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who have not received treatment yet
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 30 days
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- 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)?
- Yes
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
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-9
Source: Table 3
Description: Genus level comparison of the organismal composition of the saliva microbiota between Cancer patients and control groups at baseline via Metastas analysis.
Abundance in Group 1: increased abundance in Nasopharyngeal carcinoma patients at baseline
| NCBI | Quality Control | Links |
|---|---|---|
| Leptotrichia | ||
| Neisseria | ||
| Pseudomonadota | ||
| Pseudomonas |
Revision editor(s): Andre
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-9
Source: Table 3
Description: Genus level comparison of the organismal composition of the saliva microbiota between Cancer patients and control groups at baseline via Metastas analysis.
Abundance in Group 1: decreased abundance in Nasopharyngeal carcinoma patients at baseline
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Bacillota |
Revision editor(s): Andre
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-9
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Nasopharyngeal carcinoma patients at baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Nasopharyngeal carcinoma patients after treatment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who have received treatment after 7 or 12 months
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
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-9
Source: Figure 3 and within results text (under taxonomy-based characterisation of saliva microbiota, paragraph 4)
Description: Alteration of saliva microbiota between pretreatment (CB) and post-treatment (CA1 or CA2) in each patient.
Abundance in Group 1: increased abundance in Nasopharyngeal carcinoma patients after treatment
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Veillonella |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-9
Source: Figure 3 and within results text (under taxonomy-based characterisation of saliva microbiota, paragraph 4)
Description: Alteration of saliva microbiota between pretreatment (CB) and post-treatment (CA1 or CA2) in each patient.
Abundance in Group 1: decreased abundance in Nasopharyngeal carcinoma patients after treatment
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria | ||
| Prevotella |
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