Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research

Abstract

The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.

Keywords: genomics; lipidomics; metabolomics; metagenomics; oral microbiome; pangenomics; proteomics; transcriptomics.

Figure 1.

(A) Timeline of milestones in omics technologies and oral microbiome research. This timeline highlights milestones in microbiome/omics research generally (yellow), major technological advances (green), and milestones in oral microbiome research specifically (blue) over the past 33 years. (B) Omics approaches and tools. For each of the seven omics approaches discussed here, a list of the most significant and/or commonly used bioinformatics tools is provided. Note that this list is not exhaustive, and readers are referred in the main text to additional references on the specific software and benchmarking. **denotes a particularly useful or “gold standard” tool. ONT, Oxford Nanopore Technologies.