A major goal of the oral research community is to understand how microbe-microbe and microbe- host interactions affect human health and disease. The proposed research will enable the research community to reach this goal by providing the following research resources: the Human Oral Microbiome Database (HOMD), a web accessible taxonomic and genomic database with oral taxon descriptions and microbiome analysis tools; reference strains for 150 previously uncultured oral bacteria to facilitate in vivo and in vitro experimentation; and genomes for 100 oral taxa that currently lack genetic information.
The first Aim will provide and expand a provisional naming scheme (taxonomy) for oral bacteria, including those that have not been formally named or cultivated. HOMD will be expanded to describe over 1,000 human oral taxa, and will incorporate results from the Human Microbiome Projects deep 16S rRNA sequencing of nine oral cavity sites. Completion of this aim will allow investigators to link phenotypic, clinical, genomic and bibliographic information to precisely defined oral taxa based on 16S rRNA sequences. Nearly one-third of the 400 most prevalent oral taxa have no known cultivated isolate and the Second Aim addresses this issue. Such isolates will be identified by 16S rRNA sequencing from the culture collections of investigators Tanner and Wade, and from the collection of L. V. Holdeman Moore and the late Ed Moore, Virginia Polytechnic Institute, now housed at The Forsyth Institute. Targeted isolates for diverse phyla such as TM7, Chlorobi, SR1 and others will be grown in consortia and isolated in pure culture, where possible, using methods we have described. Isolates representing previously uncultivated species will allow investigators to study of in vitro biofilm growth, develop genetic systems, and perform animal model experiments.
The Third Aim will obtain genome sequences for 150 oral taxa currently lacking genome information. It will also provide metagenome sequences for oral bacteria that can grow in consortia but not in pure culture. This project will complete the production of reference genomes for nearly all the 400 most prevalent oral bacteria. This information will be a permanent resource for interpretation of metagenome data, for the production of microarrays for transcriptome studies, and for generating protein fragment libraries from genomic coding for proteomic studies. The genome information, tool, 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.

Public Health Relevance

Oral bacteria play a key role in human health and also in diseases such as tooth decay and gum disease, and a suspected role in heart disease, stroke and pre-term birth. The proposed research will provide tools, genetic information, and bacterial strains for scientists to understand the interaction between people and their oral bacteria. Based on this information, health professionals will be better able to understand, prevent, diagnose, and treat diseases caused by oral bacteria.

National Institute of Health (NIH)
National Institute of Dental & Craniofacial Research (NIDCR)
Method to Extend Research in Time (MERIT) Award (R37)
Project #
Application #
Study Section
Oral, Dental and Craniofacial Sciences Study Section (ODCS)
Program Officer
Lunsford, Dwayne
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Forsyth Institute
Research Institutes
United States
Zip Code
Bor, Batbileg; McLean, Jeffrey S; Foster, Kevin R et al. (2018) Rapid evolution of decreased host susceptibility drives a stable relationship between ultrasmall parasite TM7x and its bacterial host. Proc Natl Acad Sci U S A 115:12277-12282
Ribeiro, Apoena Aguiar; Azcarate-Peril, Maria Andrea; Cadenas, Maria Belen et al. (2017) The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries. PLoS One 12:e0180621
Al-Hebshi, Nezar Noor; Nasher, Akram Thabet; Maryoud, Mohamed Yousef et al. (2017) Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma. Sci Rep 7:1834
Adams, S E; Arnold, D; Murphy, B et al. (2017) A randomised clinical study to determine the effect of a toothpaste containing enzymes and proteins on plaque oral microbiome ecology. Sci Rep 7:43344
Al-Hebshi, Nezar Noor; Alharbi, Fahd Ali; Mahri, Mohammed et al. (2017) Differences in the Bacteriome of Smokeless Tobacco Products with Different Oral Carcinogenicity: Compositional and Predicted Functional Analysis. Genes (Basel) 8:
Krishnan, K; Chen, T; Paster, B J (2017) A practical guide to the oral microbiome and its relation to health and disease. Oral Dis 23:276-286
Chen, Tsute; Siddiqui, Huma; Olsen, Ingar (2017) In silico Comparison of 19Porphyromonas gingivalisStrains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics. Front Cell Infect Microbiol 7:28
Johansson, I; Witkowska, E; Kaveh, B et al. (2016) The Microbiome in Populations with a Low and High Prevalence of Caries. J Dent Res 95:80-6
Siddiqui, Huma; Chen, Tsute; Aliko, Ardita et al. (2016) Microbiological and bioinformatics analysis of primary Sjogren's syndrome patients with normal salivation. J Oral Microbiol 8:31119
Al-Hebshi, Nezar Noor; Abdulhaq, Ahmed; Albarrag, Ahmed et al. (2016) Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population. J Oral Microbiol 8:31444

Showing the most recent 10 out of 41 publications