Oral Microbiome Studies: Potential Diagnostic and Therapeutic Implications

Abstract

Understanding the microbiology of dental caries is not a mere academic exercise; it provides the basis for preventive, diagnostic, and treatment strategies and gives the dentist a theoretical framework to become a better professional. The last years have seen the development of new research methodologies, ranging from high-throughput sequencing or "omics" techniques to new fluorescence microscopy applications and microfluidics, which have allowed the study of the oral microbiome to an unprecedented level of detail. Those studies have provided new insights about oral biofilm formation, biomarkers of caries risk, microbial etiology, appropriate sampling, identification of health-associated bacteria, and new anticaries strategies, among others. Several pitfalls are associated with the new technologies, including a small number of samples per study group, elevated cost, and genus- or species-based analyses that do not take into consideration intraspecies variability. However, the new data strongly suggest that saliva may not be an appropriate sample for etiological studies or for bacterial caries-risk tests, that microbial composition alone may be insufficient to predict caries risk, and that antimicrobial or immunization strategies targeting single species are unlikely to be effective. Strategies directed toward modulation of the oral biofilm, such as pre- and probiotics, emerge as promising new approaches to prevent tooth decay.

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

“…The choice to sample saliva was mainly due to the ease of collection and ability to obtain sufficient sample volume for analysis (particularly for the case of the host markers). While the various microenviroments of the oral cavity have highly distinct microbial residents, and an ideal sampling scenario would examine diversity on this scale, saliva bathes all oral tissues and is generally thought to represent the overall oral composition (7). Differing sampling methods are likely to account for a sizable portion of the variability seen across oral microbiome studies regarding dental caries (7).…”

“…While the various microenviroments of the oral cavity have highly distinct microbial residents, and an ideal sampling scenario would examine diversity on this scale, saliva bathes all oral tissues and is generally thought to represent the overall oral composition (7). Differing sampling methods are likely to account for a sizable portion of the variability seen across oral microbiome studies regarding dental caries (7). Another goal of this study was to examine the concentration of host immunological markers present in saliva in caries versus health, and identify microbe-metabolite co-occurrences using a recently developed machine-learning-based tool to examine such relationships in compositional data (https://github.com/biocore/mmvec).…”

“…Second-generation sequencing techniques enabled many studies characterizing the oral microbiome to distinguish healthy individuals from those with dental caries. The highlights and challenges of this progress have been the subject of several excellent recent reviews (5–7). These studies of the oral microbiome in the context of dental caries have yielded varied results, particularly vis-à-vis the association (and therefore inferred importance) of S. mutans and other taxa with the disease.…”

No differences in microbiome changes between anti‐adhesive and antibacterial ingredients in toothpastes during periodontal therapy

“…The initiation and progression of caries and periodontitis, the most prevalent diseases of mankind, are closely associated with the establishment of disease-promoting bacterial biofilms on tooth surfaces. 1,2 Their efficacious mechanical removal by properly performed oral hygiene therefore is generally regarded to be essential for predictable disease prevention. 3 Furthermore, reduction in existing cleaning deficits by structured hygiene training instructions is an indispensable necessity.…”

Chair-side saliva parameters assessment and caries experience evaluation

“…DMF-S ɛ [9][10][11][12][13][14][15][16][17][18][19][20][21] 65 DMF-S =3 2.5 DMF-S =35 5 In the studied group [12] the mean DMF-S value was 18.39, under a normal distribution. According to International Caries Assessment and Detection System examination, half of patients included in this study had no active cavities.…”