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, 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

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

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 ControlLinks
Actinomyces
Bifidobacterium
Desulfovibrio
Leptotrichiaceae
Moryella
Schwartzia
Selenomonas
Treponema

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

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

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 ControlLinks
Catonella
Haemophilus
Neisseria
Pasteurellaceae
Prevotella
Prevotellaceae
Streptococcus
Veillonella

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 2


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

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

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

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 ControlLinks
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

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

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

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: decreased abundance in Oropharyngeal Squamous Cell Carcinoma

NCBI Quality ControlLinks
Bacilli
Gammaproteobacteria
Peptostreptococcaceae
Stomatobaculum

Revision editor(s): WikiWorks, ChiomaBlessing