The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

28725009

DOI Digital object identifier for electronic documents.

10.1038/s41598-017-06361-2

URI Uniform resource identifier for web resources.

Authors

Wolf A, Moissl-Eichinger C, Perras A, Koskinen K, Tomazic PV, Thurnher D

Journal

Scientific reports

Year

2017

This study aimed to undertake an initial, comparative analysis of the oral salivary microbiome of patients with oral and oropharyngeal squamous cell carcinoma versus healthy controls. This project, conceived as a pilot study, included 11 patients (1 female, 10 male, mean age 61.6 yrs., SD = 8.2 yrs.) and 11 healthy controls (1 female, 10 male, mean age 46.7 yrs., SD = 15.1 yrs.). Samples of saliva were analysed by high-throughput sequencing of the 16S rRNA gene using the MiSeq platform. Sequence data revealed microbial changes that may mirror disease progression and reflect clinical preconditions such as age, alcohol consumption, tumour size, lymph node status, smoking habit, and tumour HPV-positivity. Consequently, mapping microbial changes in patients with oral and oropharyngeal squamous cell carcinomas might improve our understanding of the pathobiology of the disease, and help in the design of novel diagnostic and treatment strategies.

Experiment 1

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Curated date: 2021/01/10

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Subjects

Location of subjects: Austria

Host species Species from which microbiome was sampled (if applicable): 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

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

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: Oropharyngeal Squamous Cell Carcinoma
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: diagnosed with OSCC and SCC of the oral cavity
Group 0 sample size Number of subjects in the control (unexposed) group: 11
Group 1 sample size Number of subjects in the case (exposed) group: 11
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: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: DESeq2

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
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Signature 1

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Curated date: 2021/01/10

Curator: Utsav Patel

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Source: Figure 3, Text

Description: microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma

Abundance in Group 1: increased abundance in Oropharyngeal Squamous Cell Carcinoma

NCBI	Links
Leptotrichiaceae
Desulfovibrio
Schwartzia
Moryella
Treponema
Bifidobacterium
Actinomyces
Selenomonas

Revision editor(s): WikiWorks

Signature 2

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Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Figure 3, Text

Description: microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma

Abundance in Group 1: decreased abundance in Oropharyngeal Squamous Cell Carcinoma

NCBI	Links
Pasteurellaceae
Catonella
Veillonella
Neisseria
Streptococcus
Prevotella
Haemophilus
Prevotellaceae

Revision editor(s): WikiWorks

Experiment 2

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Subjects

Location of subjects: Austria

Host species Species from which microbiome was sampled (if applicable): 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

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

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: Oropharyngeal Squamous Cell Carcinoma
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: diagnosed with OSCC and SCC of the oral cavity
Group 0 sample size Number of subjects in the control (unexposed) group: 11
Group 1 sample size Number of subjects in the case (exposed) group: 11
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

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

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: unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Signature 1

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Supplementary Figure S4

Description: microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma

Abundance in Group 1: increased abundance in Oropharyngeal Squamous Cell Carcinoma

NCBI	Links
Pseudomonadota
Spirochaetaceae
Spirochaetales
Spirochaetota
Spirochaeta
Actinomycetota
Deltaproteobacteria
Alphaproteobacteria
Bacteroidota
Bacteroidia
Bacteroidales
Selenomonadales
Negativicutes
Erysipelotrichales
Erysipelotrichia
Prevotellaceae
Pasteurellaceae
Sphingobacteriia
Sphingobacteriales
Bifidobacteriales
Flavobacteriaceae
Flavobacteriales
Flavobacteriia
Veillonella
Veillonellaceae
Corynebacteriaceae
Aeromonadales
Succinivibrionaceae