Our research aims to better characterize the diversity of bacteria in natural microbial communities by type and function. Over 99% of environmental microbes are believed to be yet uncultivable, hence we rely primarily on culture-independent molecular methods to gather information on the composition and role of mixed microbial communities. Some uncultivable bacteria found in environmental samples are also present in humans, and some of those bacteria have been recently associated with human diseases. Our research attempts to discover the natural source of human-associated uncultivable bacteria and to compare the function of those bacteria in their natural environment as well as in the human body. To study function of microbes, we combine in situ hybridization with micro-autoradiography (STARFISH) to determine the types of nutrients a particular bacterium is able to take up without the need of cultivation. Such method may aid in determining more appropriate cultivation media for isolating yet uncultivable bacteria. Updates at www.ouverneylab.com.
Articles
In Search of an Uncultured Human-Associated TM7 Bacterium in the Environment, PLoS one (2011)
We have identified an environmental bacterium in the Candidate Division TM7 with ≥98.5% 16S rDNA...
Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship network perspective (with Samuel A. Smits), Faculty Publications (2010)
Background
Comparative sequence analysis of the 16S rRNA gene is frequently used to characterize the...
jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web (with Samuel A. Smits), Faculty Publications (2010)
Background
Many software packages have been developed to address the need for generating phylogenetic trees intended...
Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth (with Yann Marcy, Elisabeth M. Bik, Tina Lösekann, Natalia Ivanova, Hector Garcia Martin, Ernest Szeto, Darren Platt, Philip Hugenholtz, David A. Relman, and Stephen R. Quake), Faculty Publications (2007)
We have developed a microfluidic device that allows the isolation and genome amplification of individual...
Methanogenic Archaea and human periodontal disease (with Paul W. Lepp, Mary M. Brinig, Katherine Palm, Gary C. Armitage, and David A. Relman), Faculty Publications (2004)
Archaea have been isolated from the human colon, vagina, and oral cavity, but have not...