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

Study information

Reviewed Marked as Reviewed by Atrayees on 2023-7-13

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

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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Reviewed Marked as Reviewed by Atrayees on 2023-7-13

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees, Victoria

Subjects

Location of subjects: Austria

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: 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: 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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: raw counts

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

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Figure 3, Text

Description: Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls

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

NCBI	Quality Control	Links
Actinomyces
Bifidobacterium
Desulfovibrio
Leptotrichiaceae
Moryella
Schwartzia
Selenomonas
Treponema

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

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Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Figure 3, Text

Description: Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls

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

NCBI	Quality Control	Links
Catonella
Haemophilus
Neisseria
Pasteurellaceae
Prevotella
Prevotellaceae
Streptococcus
Veillonella

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 2

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Curated date: 2021/01/10

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Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

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

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Supplementary Figure S4

Description: Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls

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

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