Many human diseases are polymicrobial in nature and therefore require thinking beyond the traditional one organism-one disease concept to find solutions to combating them. Of fundamental importance is the need for an understanding of how these communities evolve from a healthy to a diseased state at a community, species and gene level. Although many model species found associated with healthy or disease conditions have been characterized in vitro, it is difficult to determine if their physiology in pure cultures are maintained in vivo in the presence of a mixed microbial community. In addition, most host-associated microbes remain uncultured (estimated at ~ 50% of those identified) therefore little is known about the uncultured species except for their 16S rDNA sequence. Understanding the physiology of uncultured species has become a major limiting step in studying the ecology of these polymicrobial infections. With the advent of new approaches in high throughput sequencing, single cell genomics as well as new tools in microbial ecology, we can now achieve a deeper and more detailed understanding of the physiological and ecological principals that govern the behavior of host-associated microbial communities. In doing so, we can also reveal the functions and biological role of currently uncultured members. Specifically in this application we will investigate oral microbial communities and seek to;1) identify the active species, that are highly correlated with high and low pH microbial processes through Stable Isotope Probing (SIP);2) identify the genes and dominant pathway(s) that are expressed and also shared between these active species through metatranscriptomics;3) investigate the spatial patterns and relationships of uncultured species with the other community members using Laser Capture Microdissection and 4) sequence the genomes of key suspected pathogens that are currently uncultured, through whole genome amplification from captured single cells. The success of this study would greatly expand our knowledge of oral microbial pathogenesis as it will help us to understand the virulence properties of uncultured species as well as known pathogens, not only in pure culture, but also in multi-species dental biofilms. We are particularly focused on revealing more about how these currently uncultivated bacteria may contribute to heath and disease processes. The present lack of such information presents a major barrier to understanding polymicrobial diseases. This will have a great impact on the future clinical management of dental caries and provide a comprehensive approach for characterizing the function of species and their interactions for other host-associated communities.

Public Health Relevance

Many widespread human diseases, such as tooth decay (caries), result from the interactions of complex communities of microorganisms (polymicrobial diseases). This complexity severely complicates treatment strategies. Caries, for example, remains a major health issue in the United States and worldwide with a prevalence of more than 50% in young children, increasing to about 85% in the adult population. The majority of bacteria associated with polymicrobial diseases have not been well studied due to the fact that they cannot be grown in the laboratory. We propose to use new analytical methods to investigate the biological functions of these uncultured bacteria and their roles in human health. These approaches include generating the genomes and monitoring the physiology of these species in their natural environment. This new approach will provide a deeper understanding of disease progression and allow for the subsequent development of novel therapeutic approaches to battle these diseases.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1-GDB-2 (MC))
Program Officer
Sledjeski, Darren D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
J. Craig Venter Institute, Inc.
United States
Zip Code
Edlund, Anna; Garg, Neha; Mohimani, Hosein et al. (2017) Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules. mSystems 2:
Agnello, M; Cen, L; Tran, N C et al. (2017) Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation. J Dent Res 96:924-930
McLean, Jeffrey S; Liu, Quanhui; Bor, Batbileg et al. (2016) Draft Genome Sequence of Actinomyces odontolyticus subsp. actinosynbacter Strain XH001, the Basibiont of an Oral TM7 Epibiont. Genome Announc 4:
Zhong, Cuncong; Edlund, Anna; Yang, Youngik et al. (2016) Metagenome and Metatranscriptome Analyses Using Protein Family Profiles. PLoS Comput Biol 12:e1004991
Edlund, Anna; Liu, Quanhui; Watling, Michael et al. (2016) High-Quality Draft Genome Sequence of Low-pH-Active Veillonella parvula Strain SHI-1, Isolated from Human Saliva within an In Vitro Oral Biofilm Model. Genome Announc 4:
Shi, Baochen; Wu, Tingxi; McLean, Jeffrey et al. (2016) The Denture-Associated Oral Microbiome in Health and Stomatitis. mSphere 1:
Bor, Batbileg; Poweleit, Nicole; Bois, Justin S et al. (2016) Phenotypic and Physiological Characterization of the Epibiotic Interaction Between TM7x and Its Basibiont Actinomyces. Microb Ecol 71:243-55
Antipov, Dmitry; Korobeynikov, Anton; McLean, Jeffrey S et al. (2016) hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics 32:1009-15
To, Thao T; Liu, Quanhui; Watling, Michael et al. (2016) Draft Genome Sequence of Low-Passage Clinical Isolate Porphyromonas gingivalis MP4-504. Genome Announc 4:
Wang, Mingxun; Carver, Jeremy J; Phelan, Vanessa V et al. (2016) Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 34:828-837

Showing the most recent 10 out of 25 publications