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

Alveiro Erira1, 2, *, Dabeiba Adriana García Robayo1, *, Andrés Ignacio Chalá3, Andrei Moreno Torres4, 5, Eliana Elisa Muñoz Lopez6, Angel Cid Arregui7, Fabian Tobar Tosse8, Fredy Omar Gamboa Jaimes9, *
1 Centro de Investigaciones Odontológicas, Facultad de Odontología, Pontificia Universidad Javeriana, Bogotá D.C., Colombia
2 Facultad de Odontología, Universidad Cooperativa de Colombia, 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
5 Hospital Universitario San Ignacio, Cirugía de Cabeza y Cuello, Bogotá D.C., Colombia
6 Universidad Autónoma de Manizales, Facultad de Odontología, Manizales, Colombia
7 German Cancer Research Center (DKFZ), Targeted Tumor Vaccines, Heidelberg, Germany
8 Departamento de Ciencias Básicas de la Salud, Pontificia Universidad Javeriana, Sede Cali, Cali, Colombia
9 Departamento de Microbiología (Facultad de Ciencias) y Centro de Investigaciones Odontológicas (Facultad de Odontología), Pontificia Universidad Javeriana, Bogotá D.C., Colombia

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© 2021 Erira 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.

* Address correspondence to these authors at the Center for Dental Investigations, Faculty of Dentistry, Pontifical Xavierian University, Bogotá D.C., Colombia; and Department of Microbiology (Faculty of Science) and Center for Odontological Investigations (Faculty of Odontology), Pontifical Xavierian University, Bogotá D.C., Colombia; Tel: 3004678307; E-mails:,,



Oral squamous cell carcinoma (OSCC) is the sixth most common cancer in the world, and the bacterial microbiome has been considered a risk factor that could play an important 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 analyzes were performed for evaluated 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. Lastly, 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 species of Lactobacillus and Streptococcus, Chromobacterium violaceum, Enterobacter asburiae, Mycobacterium chubuense, Mycoplasma penetrans, and Brachyspira intermedia. Among the species associated with dysbiosis,  Providencia stuartii, Capnocytophaga canimorsus, Legionella pneumophila, and Mycoplasma hominis were notable.


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.

Keywords: Microbiome, Eubiosis, Dysbiosis, Oral squamous cell carcinoma, Bacteria, Next-generation sequencing.