Variations in oral microbiota associated with oral cancer

From BugSigDB
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Zhao H, Chu M, Huang Z, Yang X, Ran S, Hu B, Zhang C, Liang J
Journal
Scientific reports
Year
2017
Individual bacteria and shifts in microbiome composition are associated with human disease, including cancer. To unravel the connections underlying oral bacterial dysbiosis and oral squamous cell carcinoma (OSCC), cancer lesion samples and anatomically matched normal samples were obtained from the same patients. We then profiled the bacteria within OSCC lesion surface samples at the species level using next-generation sequencing to comprehensively investigate bacterial community composition and functional genes in these samples. Significantly greater bacterial diversity was observed in the cancer samples than in the normal samples. Compared with previous studies, we identified many more taxa demonstrating remarkably different distributions between the groups. In particular, a group of periodontitis-correlated taxa, including Fusobacterium, Dialister, Peptostreptococcus, Filifactor, Peptococcus, Catonella and Parvimonas, was significantly enriched in OSCC samples. Additionally, several operational taxonomic units (OTUs) associated with Fusobacterium were highly involved in OSCC and demonstrated good diagnostic power. Our study revealed drastic changes in surface bacterial communities of OSCC. The findings enrich knowledge of the association between oral bacterial communities and oral cancer.

Experiment 1


Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Subjects

Location of subjects
China
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
oral squamous cell carcinoma (OSCC)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
subjects with oral squamous cell carcinoma and did not have detectable periodontal inflammation, visible carious lesions, oral mucosa disease or any sever systemic disorders such as diabetes, immune compromise or genetic diseases
Group 0 sample size Number of subjects in the control (unexposed) group
40
Group 1 sample size Number of subjects in the case (exposed) group
40
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 weeks

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4-V5
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
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
increased
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Figure 1c, Figure 3b, 3c, Text

Description: Variations in oral microbiota associated with oral cancer

Abundance in Group 1: increased abundance in oral squamous cell carcinoma (OSCC)

NCBI Quality ControlLinks
Mycoplasma
Treponema
Campylobacter
Eikenella
Centipeda
Alloprevotella
Fusobacterium
Selenomonas
Dialister
Peptostreptococcus
Filifactor
Peptococcus
Catonella
Parvimonas
Capnocytophaga
Peptostreptococcaceae
Lachnospiraceae
Bacteroidota
Fusobacteriota
Spirochaetota

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Figure 1c, Figure 3b, 3c, Text

Description: Variations in oral microbiota associated with oral cancer

Abundance in Group 1: decreased abundance in oral squamous cell carcinoma (OSCC)

NCBI Quality ControlLinks
Megasphaera
Stomatobaculum
Granulicatella
Lautropia
Veillonella
Streptococcus
Scardovia
Rothia
Actinomyces
Actinomycetota
Bacillota

Revision editor(s): WikiWorks