Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing

Study information

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31109865

DOI Digital object identifier for electronic documents.

10.1016/j.job.2019.03.003

URI Uniform resource identifier for web resources.

Authors

Takahashi Y, Park J, Hosomi K, Yamada T, Kobayashi A, Yamaguchi Y, Iketani S, Kunisawa J, Mizuguchi K, Maeda N, Ohshima T

Journal

Journal of oral biosciences

Year

2019

OBJECTIVES: It is important to determine the cause of increasing oral cancer occurrence and mortality rates in Japan, because the mortality rate has recently decreased in other developed countries. The impact of microbiota in carcinogenesis, especially in the digestive tract has been reported. This study aimed to clarify the relationship between oral cancer and oral microbiota in Japanese patients. METHODS: DNA was extracted from salivary samples of 60 oral cancer patients and 80 non-cancer individuals as controls. We performed metagenomic analysis using 16S rRNA amplicon sequencing. Statistical analysis in this study was performed using R (version 3.5.0). RESULTS: Oral cancer patients showed higher α-diversity compared to the control group, and the β-diversity between the two groups differed significantly. Further, there was a significant difference in the abundance ratio of bacterial genera between the two groups. Peptostreptococcus, Fusobacterium, Alloprevotella, and Capnocytophaga were more abundant in the cancer group compared to the control, whereas Rothia and Haemophilus were less abundant (p < 0.01). A negative correlation in the microbiota composition was confirmed between the operational taxonomic units (OTU) of genus Rothia and T-stage progression using the TNM classification method. We performed logistic regression analysis to investigate the impact factor for the oral cancer group, and the result showed that Chao 1 index and sex are statistically significant variables. CONCLUSIONS: In this study, we observed an increased bacterial diversity in oral cancer patients and found distribution changes for some bacteria.

Experiment 1

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Reviewed Marked as Reviewed by Fatima on 2021/07/16

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks

Subjects

Location of subjects: Japan

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: noncancer individuals
Group 1 name Corresponds to the case (exposed) group for case-control studies: Oral Squamous Cell Cancer patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: All diagnoses of oral squamous cell carcinoma were confirmed by biopsy and pathological findings.The control group was defined as individuals without any diagnosed mucosal diseases and other cancers and these individuals were over the age of 40.
Group 0 sample size Number of subjects in the control (unexposed) group: 80
Group 1 sample size Number of subjects in the case (exposed) group: 60
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 28 days

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

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

Statistical Analysis

Statistical test: T-Test

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
Chao1 Abundance-based estimator of species richness: increased
Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged
Richness Number of species: increased