A Foundation for the Oral Microbiome and Metagenome

The major objective of the proposed research is to build a foundation of genomic information and resources for the scientific community investigating how the oral microbiome contributes to human health and disease. In prior years of this project we created the expanded Human Oral Microbiome Database (eHOMD), a web accessible taxonomic and genomic database with taxon descriptions and microbiome analysis tools. We cultivated reference strains for previously uncultured oral & nasal bacteria to facilitate in vivo and in vitro experimentation, and we leveraged the sequencing power of the Human Microbiome Project as well as our laboratory's sequencing facility to generate genome sequences for the majority of oral microbial taxa. In the proposed project period, our goal is to fill in the major remaining gaps that present a barrier to full realization of the potential of `omics technologies to drive discoveries in oral microbiology. Our strategy involves three specific aims. The first Aim encompasses improvements to eHOMD itself, including a significant expansion of eHOMD to include the viruses that infect oral & nasal microbes. To allow investigators to do more rigorous microbiome research in mice, a Mouse Oral Microbiome Database (MOMD) will be released so that investigators can accurately document the composition of their mice's oral microbiome. Completion of this aim will allow investigators to link phenotypic, clinical, genomic and bibliographic information to precisely-defined bacterial and phage taxa. The Second Aim addresses the fact that nearly one-third of the 771 eHOMD bacterial taxa have no known cultivated isolates. We will bring into cultivation strains of oral bacteria that are currently refractory to cultivation and make these strains available to the research community. For bacteria that are only sporadically abundant we will use information on abundance of uncultivated bacteria in 20 subjects to guide sampling efforts, and for bacteria that are common but difficult to grow we will use co-cultivation approaches that we have previously employed successfully to isolate and grow 30 strains of the previously uncultivable Saccharibacteria. In the third Aim we will obtain genome sequences for eHOMD taxa currently lacking genome information. Using long-read sequencing we will produce closed genomes of cultivable strains, including strains isolated in Aim 2. To provide genome coverage for remaining uncultivable taxa, we will add high quality Metagenome-Assembled Genomes (MAGs) to eHOMD. Successful completion of the three Aims of this project will increase the genomic coverage of oral and nasal taxa to the point where eHOMD is an exemplary reference database that enables studies using metagenomics, transcriptomics, proteomics, and metabolomics to understand the interactions of oral microbes with one another and with their host. The genome information, tools, and strains generated by this project will serve as a permanent foundation and resource for investigations on the role of the oral microbiome in human health and disease.