Development and validation of a new phylogenetic DNA-microarray specific for the oral microbiota

Backgrounds: The oral cavity contains hundreds of different microbial species, and their quali-quantitative characterization is crucial for an exhaustive comprehension of the oral ecology. The study of the human oral microbiota and the modifications of the microbial composition that occur during the most common odontoiatric pathologies, such as dental caries, periodontitis and perimplantitis, is of great interest. Objectives: The objective of the present study was to develop a phylogenetic DNA-microarray, named OralArray, to quickly and reliably characterize the most representative bacterial groups that colonize different sites of the oral cavity in healthy and pathological conditions. Methods: The OralArray was based on the Ligation Detection Reaction technology associated to Universal Arrays, and includes 22 probe sets targeted to bacteria belonging to the phyla Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, Fusobacteria and Spirochaete. The OralArray was tested and validated on different types of oral samples (saliva, lingual plaque, supragingival plaque and healing cap), collected from 10 healthy subjects. Conclusions: The phylogenetic microarray is characterized by high specificity, high sensitivity (down to 1 ng of PCR product) and a reproducibility of 97.7%. The OralArray was able to detect the microbial signature of different types of oral samples. Our results established the presence of an oral microbial signature specific for each subject, rather than for sample type. Moreover, the molecular tool was employed to evaluate the efficacy of a disinfectant treatment on the healing caps before their usage. The OralArray is thus suitable to study the microbiota associated with various oral sites and to monitor changes arising from therapeutic treatments.