Research
The goal of our program has been to gain an understanding for the molecular basis of bacteria-bacteria as well as bacteria-host interactions and further develop innovative methodologies, tools and integrated “omic” based approaches with wet-lab cultivation work on oral communities to understand and ultimately translate this fundamental knowledge to the overall benefit of human health. Our team has extensive experience in combining multi-omic approaches such as temporal resolved metatranscriptomic analysis in parallel with metabolomics profiling to reveal the homeostatic mechanisms of oral microbial communities. We track oral community assembly and succession, capturing the expression dynamics of key disease related species in relation to host responses .
Active Support
Mechanisms underlying the variation in rate and levels of gingival inflammatory responses among the human population
NIH/NIDCR R01
Or goal in this clinical trial is to investigate the variation in gingival inflammatory responses among the human population with multi-omics approaches.
Related to our recent publication
Bamashmous, S., Kotsakis, G. A., Kerns, K. A., Leroux, B. G., Zenobia, C., Chen, D., Trivedi, H. M., McLean, J. S*., & Darveau, R. P. (2021). Human variation in gingival inflammation. Proceedings of the National Academy of Sciences of the United States of America, 118(27), e2012578118. https://doi.org/10.1073/pnas.2012578118
Resolving Oral Bacteria Interactions with a High-Throughput Low-Cost Single-Cell Transcriptomics Approach
NIH/NIDCR R21
Here we propose to leverage a recent breakthrough in single-cell transcriptomics (scRNAseq) that has been developed for prokaryotes to study cell-cell interactions. This collaboration is with the Kuchina lab at ISB https://kuchina.isbscience.org/.
Domestication and Characterization of TM7-The Most Elusive Oral Phylum
NIH/NIDCR R01
The major goal of this project is to study the ecology, evolution and pathogenesis of human oral phlyum TM7 (Saccharibacteria) that our group has cultivated. The Saccharibacteria are now recognized as part of the Candidate Phyla Radiation and our cultivated strain TM7x was the first and only member of this large group that comprises nearly 25% of the diversity in the Domain Bacteria.
Recently Completed Support
Moving Beyond Diversity by Revealing Biological Functions of Uncultured Bacteria
NIH/NIGMS R01
We will investigate oral microbiome communities seeking to identify the species and genes that are highly correlated with microbial processes in disease state through parallel metabolomics and metatranscriptomics.
Systematic Approach to Explore the Microbial Interactome
NIH/NIDCR R21
Research in this grant will seek to provide a versatile approach for comprehensive investigation of the microbial interactome.
Making a Quantum Leap in Plaque Research with Modern Sciences
NIH/NIDCR R01
The major goals of this project are the development of new tools to study the etiology of dental caries, explore approaches for targeted elimination of cariogenic species and examine the effect on acid-production of the dental biofilm community.
Studying the Protective Effects of Normal Oral Flora
NIH/NIDCR R01
The major goal of this project is to study how normal flora can work together in a coordinated manner to prevent harmful ones from establishing themselves in our body.