Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging
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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
Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP, Chang YL
Journal
Frontiers in microbiology
Year
2018
Keywords:
16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome
Oral squamous cell carcinoma (OSCC) is a highly aggressive cancer and the fourth leading malignancy among males in Taiwan. Some pathogenic bacteria are associated with periodontitis and oral cancer. However, the comprehensive profile of the oral microbiome during the cancer's progression from the early stage to the late stage is still unclear. We profiled the oral microbiota and identified bacteria biomarkers associated with OSCC. The microbiota of an oral rinse from 51 healthy individuals and 197 OSCC patients at different stages were investigated using 16S rRNA V3V4 amplicon sequencing, followed by bioinformatics and statistical analyses. The oral microbiota communities from stage 4 patients showed significantly higher complexity than those from healthy controls. The populations also dynamically changed with the cancer's progression from stage 1 to stage 4. The predominant phyla in the oral samples showed variation in the relative abundance of Fusobacteria, Bacteroidetes, and Actinobacteria. The abundance of Fusobacteria increased significantly with the progression of oral cancer from the healthy controls (2.98%) to OSCC stage 1 (4.35%) through stage 4 (7.92%). At the genus level, the abundance of Fusobacterium increased, while the number of Streptococcus, Haemophilus, Porphyromonas, and Actinomyces decreased with cancer progression. Fusobacterium periodonticum, Parvimonas micra, Streptococcus constellatus, Haemophilus influenza, and Filifactor alocis were associated with OSCC, and they progressively increased in abundance from stage 1 to stage 4. The abundances of Streptococcus mitis, Haemophilus parainfluenzae, and Porphyromonas pasteri were inversely associated with OSCC progression. We selected a bacterial marker panel of three bacteria (upregulated F. periodonticum, down-regulated S. mitis, and P. pasteri), which had an AUC of 0.956 (95% CI = 0.925-0.986) in discriminating OSCC stage 4 from the healthy controls. Furthermore, the functional prediction of oral bacterial communities showed that genes involved in carbohydrate-related metabolism, such as methane metabolism, and energy-metabolism-related parameters, such as oxidative phosphorylation and carbon fixation in photosynthetic organisms, were enriched in late-stage OSCC, while those responsible for amino acid metabolism, such as folate biosynthesis and valine, leucine, and isoleucine biosynthesis, were significantly associated with the healthy controls. In conclusion, our results provided evidence of oral bacteria community changes during oral cancer progression and suggested the possibility of using bacteria as OSCC diagnostic markers.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-9
Subjects
- Location of subjects
- Taiwan
- 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
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- 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
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stage 4
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- OSCC confirmed by biopsy and pathological findings
- Group 0 sample size Number of subjects in the control (unexposed) group
- 51
- Group 1 sample size Number of subjects in the case (exposed) group
- 90
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics treatment at the time of sample collection.
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-9
Curated date: 2021/01/10
Curator: Utsav Patel
Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing
Source: Figure 5
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stage 4 group compared to healthy control group
Abundance in Group 1: increased abundance in Stage 4
Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-9
Curated date: 2021/01/10
Curator: Utsav Patel
Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing
Source: Figure 5
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stage 4 group compared to healthy control group
Abundance in Group 1: decreased abundance in Stage 4
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces gerencseriae | ||
| Granulicatella adiacens | ||
| Hoylesella nanceiensis | ||
| Prevotella melaninogenica | ||
| Pseudoleptotrichia goodfellowii | ||
| Schaalia georgiae |
Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-8
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stage 1
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics treatment at the time of sample collection.
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
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-8
Source: Supplementary Figure 5A
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stage 1 group compared to healthy control group
Abundance in Group 1: increased abundance in Stage 1
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-8
Source: Supplementary Figure 5A
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stage 1 group compared to healthy control group
Abundance in Group 1: decreased abundance in Stage 1
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae | ||
| Porphyromonas pasteri | ||
| Prevotella melaninogenica | ||
| Schaalia odontolytica | ||
| Veillonella parvula |
Revision editor(s): WikiWorks, ChiomaBlessing
Experiment 3
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-8
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stage 2 & 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
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
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-8
Source: Supplementary Figure 5B
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stages 2 & 3 group compared to healthy control group
Abundance in Group 1: increased abundance in Stage 2 & 3
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-8
Source: Supplementary Figure 5B
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stages 2 & 3 group compared to healthy control group
Abundance in Group 1: decreased abundance in Stage 2 & 3
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae | ||
| Porphyromonas pasteri | ||
| Prevotella melaninogenica | ||
| Schaalia odontolytica | ||
| Streptococcus mitis | ||
| Veillonella parvula | ||
| SR1 bacterium oral taxon 875 |
Revision editor(s): WikiWorks, ChiomaBlessing
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