Bacteriome Identified by Next Generation Sequencing in Saliva, Dental Plaque and Tumor Tissue of Patients with Oral Squamous Cell Carcinoma

Alveiro Erira1, Dabeiba A. García Robayo2, *, Andrés I. Chala3, Andrei M. Torres4, Eliana E. Muñoz Lopez5, Angel Cid Arregui6, Fabian Tobar Tosse7, Fredy Omar Gamboa Jaimes8
1 Centro de Investigaciones Odontológicas, Facultad de Odontología, Pontificia Universidad Javeriana, Bogotá D.C., Facultad de Odontología, Universidad Cooperativa de Colombia, Bogotá D.C, Colombia
2 Centro de Investigaciones Odontológicas, Facultad de Odontología, Pontificia Universidad Javeriana, Bogotá D.C., Colombia
3 Universidad de Caldas, Cirugía de Cabeza y Cuello, Manizales, Colombia
4 Instituto Nacional de Cancerología, Cirugía de Cabeza y Cuello, Bogotá D.C., Colombia, y Hospital Universitario San Ignacio, Cirugía de Cabeza y Cuello, Bogotá D.C., Colombia
5 Universidad Autónoma de Manizales, Facultad de Odontología, Manizales, Colombia
6 Targeted Tumor Vaccine, German Cancer Research Center (DKFZ) Heidelberg, Germany
7 Departamento de Ciencias Básicas de la Salud, Pontificia Universidad Javeriana, Sede Cali, Cali, Colombia
8 Departamento de Microbiología (Facultad de Ciencias) y Centro de Investigaciones Odontológicas (Facultad de Odontología), Pontificia Universidad Javeriana, Bogotá D.C., Colombia



Oral squamous cell carcinoma (OSCC) is the sixth most common cancer globally. The bacterial microbiome has been considered a risk factor that could play an essential role in carcinogenesis.


A bacteriome study was performed by next generation sequencing in dental plaque, saliva, and tumor samples of 10 OSCC patients and compared with bacteriome in dental plaque and saliva of 10 patients without OSCC.


DNA was extracted from all samples and sequenced by Illumina technology MiSeq™. Bioinformatic analyses were performed to evaluate sequence quality, alpha and beta diversity, bidirectional analysis of variance (p <0.05), and principal component analysis. After establishing bacterial profiles associated with each sample and population, intragroup and intergroup comparisons were carried out. For bacteria identification compatible with eubiosis and dysbiosis processes, a screening was performed based on the frequency of appearance in all patient samples with and without OSCC. Last, frequency, average, standard deviation, Chi-square, and Mann Whitney test were calculated.


Out of the identified 1,231 bacteria in the populations under study, 45 bacterial species were selected, of which 34 were compatible with eubiosis and 11 were compatible with dysbiosis. Among the bacteria compatible with eubiosis were Lactobacillus and Streptococcus, Chromobacterium violaceum, Enterobacter asburiae, Mycobacterium chubuense, Mycoplasma penetrans and Brachyspira intermedia. Among the species associated with dysbiosis were notable Providencia stuartii, Capnocytophaga canimorsus Legionella pneumophila and Mycoplasma hominis.


Thirty-four bacterial species may be associated with eubiosis or healthy states, and 11 bacterial species could be associated with dysbiosis or pathogenic state, OSCC”.

Key words: Microbiome, Eubiosis, Dysbiosis, Oral squamous cell carcinoma, Bacteria, Next generation sequencing.

Abstract Information

Identifiers and Pagination:

Year: 2021
Volume: 15
Publisher Item Identifier: EA-TOMICROJ-2021-2

Article History:

Electronic publication date: 14/7/2021
Collection year: 2021

© 2021 Afshar et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Correspondence: Address correspondence to this author at Centro de Investigaciones Odontológicas, Facultad de Odontología, Pontificia Universidad Javeriana, Bogotá D.C., Colombia; Tel: +05713208320; E-mails:;