16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment
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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
Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W, Sidransky D
Journal
Oncotarget
Year
2016
Keywords:
16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer
Systemic inflammatory events and localized disease, mediated by the microbiome, may be measured in saliva as head and neck squamous cell carcinoma (HNSCC) diagnostic and prognostic biomonitors. We used a 16S rRNA V3-V5 marker gene approach to compare the saliva microbiome in DNA isolated from Oropharyngeal (OPSCC), Oral Cavity Squamous Cell Carcinoma (OCSCC) patients and normal epithelium controls, to characterize the HNSCC saliva microbiota and examine their abundance before and after surgical resection.The analyses identified a predominance of Firmicutes, Proteobacteria and Bacteroidetes, with less frequent presence of Actinobacteria and Fusobacteria before surgery. At lower taxonomic levels, the most abundant genera were Streptococcus, Prevotella, Haemophilus, Lactobacillus and Veillonella, with lower numbers of Citrobacter and Neisseraceae genus Kingella. HNSCC patients had a significant loss in richness and diversity of microbiota species (p<0.05) compared to the controls. Overall, the Operational Taxonomic Units network shows that the relative abundance of OTU's within genus Streptococcus, Dialister, and Veillonella can be used to discriminate tumor from control samples (p<0.05). Tumor samples lost Neisseria, Aggregatibacter (Proteobacteria), Haemophillus (Firmicutes) and Leptotrichia (Fusobacteria). Paired taxa within family Enterobacteriaceae, together with genus Oribacterium, distinguish OCSCC samples from OPSCC and normal samples (p<0.05). Similarly, only HPV positive samples have an abundance of genus Gemellaceae and Leuconostoc (p<0.05). Longitudinal analyses of samples taken before and after surgery, revealed a reduction in the alpha diversity measure after surgery, together with an increase of this measure in patients that recurred (p<0.05). These results suggest that microbiota may be used as HNSCC diagnostic and prognostic biomonitors.
Experiment 1
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Lwaldron, Claregrieve1, Victoria
Subjects
- Location of subjects
- United States of America
- 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
- Oral squamous cell carcinoma mouth scc,mouth squamous cell carcinoma,OCSC,oral cavity scc,oral cavity squamous cell cancer,oral cavity squamous cell carcinoma,oral squamous cell carcinoma,scc of mouth,scc of oral cavity,scc of the mouth,scc of the oral cavity,squamous cell carcinoma of mouth,squamous cell carcinoma of oral cavity,squamous cell carcinoma of the mouth,squamous cell carcinoma of the oral cavity,Oral 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
- HNSCC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- 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).
- 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
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Figure 6, Sup Fig1
Description: Relative abundance of oral microbiome in HNSCC patients and controls
Abundance in Group 1: increased abundance in HNSCC
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Parvimonas | ||
| Peptostreptococcus | ||
| Staphylococcus | ||
| Streptococcus | ||
| Tannerella | ||
| Veillonella |
Signature 2
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Figure 6, Sup Fig1
Description: Relative abundance of oral microbiome in HNSCC patients and controls
Abundance in Group 1: decreased abundance in HNSCC
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Lautropia | ||
| Haemophilus | ||
| Neisseria | ||
| Leptotrichia |
Revision editor(s): WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Lwaldron, Claregrieve1, Victoria
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV -
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPV +
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who are HPV+
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Figure 6, Text
Description: Relative abundance of oral microbiome in HNSCC HPV + and HPV -
Abundance in Group 1: increased abundance in HPV +
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Weeksella |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Figure 6, Text
Description: Relative abundance of oral microbiome in HNSCC HPV + and HPV -
Abundance in Group 1: decreased abundance in HPV +
| NCBI | Quality Control | Links |
|---|---|---|
| Eikenella | ||
| Neisseria | ||
| Leptotrichia |
Revision editor(s): WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Lwaldron, Claregrieve1, Victoria
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- surgery
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- chemotherapy-radiation and surgery
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who received chemo/radiation and surgery
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Figure 6, Text
Description: Relative abundance of oral microbiome in chemo-radiation therapy/radiation and surgery
Abundance in Group 1: increased abundance in chemotherapy-radiation and surgery
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillaceae | ||
| Lactobacillus |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/19
Source: Figure 6, text
Description: Relative abundance of oral microbiome in chemo-radiation therapy/radiation and surgery
Abundance in Group 1: decreased abundance in chemotherapy-radiation and surgery
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Aggregatibacter | ||
| Leptotrichia |
Revision editor(s): Claregrieve1
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