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

Abstract

Background The 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. Results The 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. Conclusions The 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.

Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome

“…2b ; p < 5 × 10 −8 ) were also at least nominally significant in the other niche ( p < 0.01), consistent with our and previous findings that tongue dorsum and salivary microbiome communities exhibited high levels of similarity 38,39 , especially in micron-scale structure of oral niches 33,40 . Consistent with previous studies 24,41 , the salivary microbiome showed higher alpha diversity than tongue dorsum. In combination with the fact that saliva comes into contact with all surfaces in the oral cavity and represents a fingerprint of the general composition of the oral microbiome, these results suggested that salivary microbiome is more diverse and likely more dynamic.…”

Oral Microbiome Dysbiosis Is Associated With Symptoms Severity and Local Immune/Inflammatory Response in COVID-19 Patients: A Cross-Sectional Study

“…Oral rinse samples were collected in 5 mL of sterile phosphatebuffered saline (PBS), as previously described (Caselli et al, 2020a). The specimens were immediately inactivated with 0.1% SDS, refrigerated (2-8 • C), and processed within 4 h. Briefly, all samples were vortexed and centrifuged at 15,000 × g for 10 min at 4 • C to divide the corpuscular part from the supernatant, which were immediately frozen in liquid nitrogen and kept at −80 • C until use.…”

“…The human oral microbiome (HOM) is the second largest and complex microbial community after that of the gut in the human body ( Wade, 2013 ; Caselli et al, 2020a ). HOM dysbiosis is often associated with periodontal inflammation and has been reportedly associated with several local and systemic disease conditions ( Baghbani et al, 2020 ; Caselli et al, 2020a ), including those sustained by viral infections ( Cagna et al, 2019 ; Baghbani et al, 2020 ). Indeed, the role of HOM in the establishment of the infection of many viruses entering the body via the oropharynx has been reportedly recognized ( Baghbani et al, 2020 ).…”

Duration of gargling and rinsing among frequent mouthwash users: a cross-sectional study

“…Future studies could potentially determine if the method of mouthwash has a difference in the effectiveness of mouthwash at preventing gonorrhoea, including using a mouthwash spray. Additionally, given the complex and delicate balance of a ‘normal’ oral microbiome and its importance to overall health, 32–34 future research should ensure any recommended mouthwash use to prevent oral STIs did not have deleterious effects to the oral microbiome.…”