Exploiting chaperonin universal targets for detecting and monitoring diversity in natural microbial communities

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The ability to identify microorganisms is critical to human, animal and environmental health, as well as industries that exploit biotechnology. The development of rapid and economical methods for determining the whole genome sequence of microbes has presented new challenges to microbiologists since this information has revealed surprising amounts of diversity within traditionally defined species, and once again drawn attention to questions about what constitutes a species in the microbial world. For microbial ecologists, there is also the challenge of determining what sorts of information are valuable or informative when they are determining how a complex community of microorganisms responds to perturbation. A change in diet can have effects on the bacterial communities that live in the intestine, but are the changes to species diversity (Who is there?) worth looking at, or should we instead focus on community activity changes (What are they doing?). As with most important biological questions, there is not one simple solution and a variety of methods and approaches must be applied. Our research group is developing tools for the detection and identification of diversity among microbes and microbial populations. We are using the sequences of universally conserved chaperonin genes as "barcodes" for discriminating species and identifying functionally related subspecies groups called ecotypes. Chaperonin sequences give us a more resolving power than currently available universal targets and allow us to use a single gene sequence to discriminate phenotypically distinct groups of bacteria within traditionally defined species. We are working to apply these chaperonin-based methods to facilitate identification of microbes and to bridge the gap between structure and function in microbial communities. As part of our work, we have developed a reference database of chaperonin sequences called cpnDB, that is currently being used by clinicians, taxonomists and microbial ecologists around the world as they detect, identify, quantify and characterize microorganisms.