Exploring the oral microbiome: from traditional techniques to advanced omics and databases

Abstract

The oral microbiome comprises analysis of microbes within the oral cavity. Omics, molecular, and bioinformatic methods have significant functions in examining the diversity, composition, and function of the oral microbiome. Molecular techniques, especially 16S and 18S rRNA sequencing, have transformed the study of the oral microbiome. Analysis by 16S rRNA gene sequences of the oral sample creates a broad portrait of the species composition of the oral microbiome and both existing and new species of bacteria. It is instrumental in detecting bacterial pathogens at specific levels, specifically those involved with dental caries, periodontal disease, and oral malignancy. Paralleling the above, analysis by 18S rRNA gene sequencing elicits information related to the composition of fungal as well as protist members within the oral microbiome that plays significant roles for oral health. It can detect oral cavity parasitic infections, which may lead to oral health conditions. Omics tools are general terms for the use of high-throughput approaches to study on a large scale a variety of biological molecules. Applying these technologies to the oral microbiome allows researchers to determine the genetic, transcriptomic, proteomic, and metabolomic profiles of microbes in the oral cavity. These tools help to obtain an overall picture of the oral microbiome, such as its composition, function, and interactions. There are several databases offering useful information on the oral microbiome. These databases store curated information regarding microbial communities in the oral cavity, which aid researchers in the exploration of oral microbiome diversity, composition, and functional characteristics. Some of the examples include Human Oral Microbiome Database (HOMD) and Oral Microbiome Database (OMD). In minireview, we have provided an overview of a variety of molecular and omics tools and databases utilized in the exploration of the oral microbiome.

Keywords: Database; Genomics; Microbiome; Omics; Proteomics; Transcriptomics.