Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture

Elisabetta Caselli,Sante Mazzacane,Irene Soffritti,Chiara Fabbri,Maria D’Accolti,Maurizio Franchi,Cristian Bassi

doi:10.1186/s12866-020-01801-y

Elisabetta Caselli, Sante Mazzacane + Show 5 more

Open Access

https://doi.org/10.1186/s12866-020-01801-y

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Journal: BMC microbiology	Publication Date: May 18, 2020
Citations: 175	License type: open-access

Affiliation: University of Ferrara

Abstract

BackgroundThe microbiome of the oral cavity is the second-largest and diverse microbiota after the gut, harboring over 700 species of bacteria and including also fungi, viruses, and protozoa. With its diverse niches, the oral cavity is a very complex environment, where different microbes preferentially colonize different habitats. Recent data indicate that the oral microbiome has essential functions in maintaining oral and systemic health, and the emergence of 16S rRNA gene next-generation sequencing (NGS) has greatly contributed to revealing the complexity of its bacterial component. However, a detailed site-specific map of oral microorganisms (including also eukaryotes and viruses) and their relative abundance is still missing. Here, we aimed to obtain a comprehensive view of the healthy oral microbiome (HOM), including its drug-resistance features.ResultsThe oral microbiome of twenty healthy subjects was analyzed by whole-genome sequencing (WGS) and real-time quantitative PCR microarray. Sampled oral micro-habitat included tongue dorsum, hard palate, buccal mucosa, keratinized gingiva, supragingival and subgingival plaque, and saliva with or without rinsing. Each sampled oral niche evidenced a different microbial community, including bacteria, fungi, and viruses. Alpha-diversity evidenced significant differences among the different sampled sites (p < 0.0001) but not among the enrolled subjects (p = 0.876), strengthening the notion of a recognizable HOM. Of note, oral rinse microbiome was more representative of the whole site-specific microbiomes, compared with that of saliva. Interestingly, HOM resistome included highly prevalent genes conferring resistance to macrolide, lincosamides, streptogramin, and tetracycline.ConclusionsThe data obtained in 20 subjects by WGS and microarray analysis provide for the first time a comprehensive view of HOM and its resistome, contributing to a deeper understanding of the composition of oral microbiome in the healthy subject, and providing an important reference for future studies, allowing to identify microbial signatures related to functional and metabolic alterations associated with diseases, potentially useful for targeted therapies and precision medicine.

Highlights

The microbiome of the oral cavity is the second-largest and diverse microbiota after the gut, harboring over 700 species of bacteria and including fungi, viruses, and protozoa
Each subject was characterized for the number of teeth, the Plaque Score (O’Leary PL, which represents the percentage of sites, four per tooth, presenting plaque; mean value ± SD, 24.15 ± 8.54), the Bleeding on Probing (BOP) index, the type of oral hygiene devices (OHD) used at home
For BOP index, the Human Microbiome Project (HMP) protocol allows a slight degree of gingivitis, for the present study we maintained the exclusion criteria for BOP≥10%, following the definition of the periodontal healthy subject of the World Workshop 2017 of the American Academy of Periodontology and European Federation of Periodontology [40]

Summary

Introduction

The microbiome of the oral cavity is the second-largest and diverse microbiota after the gut, harboring over 700 species of bacteria and including fungi, viruses, and protozoa. The oral cavity is a very complex environment, where different microbes preferentially colonize different habitats. The oral microbiome composition differs between the various micro-habitat and each individual has its “microbial identity” consisting of its own and unique microbial population [3]. These inter-individual differences, the principal function of the microbiome is the same in every person [4]. The commensal microbiome has an important role in the maintenance of oral and systemic health: its delicate balance can be altered, causing oral pathologies such as cavities endodontic disease, periodontal diseases, osteitis and tonsillitis [5,6,7] and can be associated with the development of several systemic diseases, for example cardiovascular disease [8], ictus [9], pre-term childbirth [10], diabetes [11], pneumonia [12], obesity [13, 14], colon carcinoma [15] and psychiatric issues [16]

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