Single-Cell Genomics and the Oral Microbiome

Abstract

The human oral cavity is one of the first environments where microbes have been discovered and studied since the dawn of microbiology. Nevertheless, approximately 200 types of bacteria from the oral microbiota have remained uncultured in the laboratory. Some are associated with a healthy oral microbial community, while others are linked to oral diseases, from dental caries to gum disease. Single-cell genomics has enabled inferences on the physiology, virulence, and evolution of such uncultured microorganisms and has further enabled isolation and cultivation of several novel oral bacteria, including the discovery of novel interspecies interactions. This review summarizes some of the more recent advances in this field, which is rapidly moving toward physiologic characterization of single cells and ultimately cultivation of the yet uncultured. A combination of traditional microbiological approaches with genomic-based physiologic predictions and isolation strategies may lead to the oral microbiome being the first complex microbial community to have all its members cultivable in the laboratory. Studying the biology of the individual microbes when in association with other members of the community, in controlled laboratory conditions and in vivo, should lead to a better understanding of oral dysbiosis and its prevention and reversion.

Keywords: bacteria; biofilms; bioinformatics; dysbiosis; microbial ecology; microbiology.

Figure 1.

Phylogenetic tree (FastML) of human oral bacteria based on the SSU rRNA gene (HOMD V14.51 sequences). Phylum-level classification is indicated on the outer ring by individual color blocks with some of the major genera identified. Red dots indicate currently uncultured organisms, and blue squares indicate organisms for which single-cell genomes have been sequenced. The tree intends to provide a general view on the cultivation status at high taxonomic level. For the names of all oral microorganisms, and their status, see http://homd.org/.

Figure 2.

Single-cell genomics and cultivation workflow for targeted and untargeted approaches. Dotted lines indicate approaches incompatible with viable cell isolation/cultivation. FISH, fluorescence in situ hybridization.

Figure 3.

Human oral cultured bacteria resulting from the use of single-cell genomic data. (A) A coculture of Fusobacterium nucleatum (DAPI stain, blue) and Desulfobulbus oralis (stained with a green fluorescent rRNA probe). (B) Scanning electron micrograph of a pure D. oralis culture. (C) A coculture of Actinomyces sp. and TM7 HOT952 stained with rRNA probes.