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The oral microbiome: diversity, biogeography and human health

Review article highlights recent understanding of biogeography of oral niches at the species level & summarizes the relationship between the oral #microbiota & pathology of oral diseases & systemic disease.


The human oral microbiota is highly diverse and has a complex ecology, comprising bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and highly structured biogeography that shapes metabolic exchange on a local scale and results from the diverse microenvironments present in the oral cavity. The oral microbiota also interfaces with the immune system of the human host and has an important role in not only the health of the oral cavity but also systemic health. In this Review, we highlight recent advances including novel insights into the biogeography of several oral niches at the species level, as well as the ecological role of candidate phyla radiation bacteria and non-bacterial members of the oral microbiome. In addition, we summarize the relationship between the oral microbiota and the pathology of oral diseases and systemic diseases. Together, these advances move the field towards a more holistic understanding of the oral microbiota and its role in health, which in turn opens the door to the study of novel preventive and therapeutic strategies. Introduction “I didn’t clean my teeth for three days and then took the material that had lodged in small amounts on the gums above my front teeth… I found a few living animalcules” from Antonie van Leeuwenhoek’s letter to the Royal Society on observations made from his own dental plaque, translated by Clifford Dobell) 1. The direct visual observation of bacteria in the oral cavity by Antonie van Leeuwenhoek in 1670 using his self-designed microscope marked the discovery of the oral microbiota. The diverse morphologies of the microorganisms he observed, and later depicted in his notebook, were an early indication of the complexity of the oral microbial community. Subsequent study of the human oral microbiome has revealed that the microorganisms residing in the oral cavity are a major contributor to overall host health and that dysbiosis in the oral microbiome is frequently involved in the pathogenesis of both oral and systemic diseases. The oral microbiome is acquired through both maternal transmission and the environment, in an organized pattern, with the eruption of teeth providing new ecological niches and increasing diversity2,3. The acquisition and establishment of the oral microbiome have been recently reviewed in depth4. The accessibility of the oral microbiota enables the process of biofilm and community assembly to be directly captured at the sites of interest5, and hence the oral microbiota offers a powerful model system for exploring and understanding complex microbiomes. Distinct habitats within the mouth are colonized by microbiotas that are widely different in both composition and spatial organization (Fig. 1a–e). Within the oral cavity, bacteria, archaea, eukaryotes and viruses coexist and interact with each other and with the human host (Fig. 1f). By contrast, at less accessible sites such as the human gut, microbiome structure and assembly must typically be inferred, for example, through faecal samples. Therefore, there is enormous potential in using omics approaches to examine the diverse communities of the oral microbiota both in situ and using in vitro model systems to elucidate principles of microbial community assembly and ecology. Recently developed technologies including culture-independent metagenomic sequencing, single-cell sequencing, fluorescence in situ hybridization-based microscopy (FISH-based microscopy), metatranscriptomics, metaproteomics and metabolomics have revolutionized the scale and level of resolution of oral microbiome research. These technologies have synergized with cultivation-based research, which has continued to provide the foundational model systems, whereby hypotheses generated by the new technologies can ultimately be tested and explored (Box 1). The resulting research has substantially increased our understanding of the community composition, genomic diversity, biogeography and metabolic underpinnings of the oral microbiota6,7,8,9. Read more at:

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