# A Foundation for the Oral Microbiome and Metagenome

> **NIH NIH R01** · ADA FORSYTH INSTITUTE, INC. · 2024 · $1,181,303

## Abstract

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 f...

## Key facts

- **NIH application ID:** 10799581
- **Project number:** 5R01DE016937-19
- **Recipient organization:** ADA FORSYTH INSTITUTE, INC.
- **Principal Investigator:** Floyd E Dewhirst
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $1,181,303
- **Award type:** 5
- **Project period:** 2006-04-01 → 2026-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10799581

## Citation

> US National Institutes of Health, RePORTER application 10799581, A Foundation for the Oral Microbiome and Metagenome (5R01DE016937-19). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10799581. Licensed CC0.

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