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

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Reviewed Marked as Reviewed by Atrayees on 2023-7-13
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

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

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

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

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: increased abundance in Oropharyngeal Squamous Cell Carcinoma

NCBI Quality ControlLinks
Leptotrichiaceae
Desulfovibrio
Schwartzia
Moryella
Treponema
Bifidobacterium
Actinomyces
Selenomonas

Revision editor(s): WikiWorks

Signature 2

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

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 Quality ControlLinks
Pasteurellaceae
Catonella
Veillonella
Neisseria
Streptococcus
Prevotella
Haemophilus
Prevotellaceae

Revision editor(s): WikiWorks

Experiment 2


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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).
Not specified
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

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

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 Quality ControlLinks
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

Revision editor(s): WikiWorks

Signature 2

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

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: decreased abundance in Oropharyngeal Squamous Cell Carcinoma

NCBI Quality ControlLinks
Stomatobaculum
Bacilli
Peptostreptococcaceae
Gammaproteobacteria

Revision editor(s): WikiWorks