Evaluating Microbial Diversity and Adaptation: New Opportunities for Insight in a Data Rich World
Catherine Lozupone, University of Colorado, Boulder
Monday, September 21, 2009
4:00 p.m., 223 Weber
Advances in sequencing technology have produced exciting opportunities to understand microbial diversity and adaptation, but also challenges to interpret datasets generated on a whole new scale. UniFrac is a tool that uses phylogenetic information to compare sequences from many microbial assemblages simultaneously, and can determine the main factors, such as temperature, pH, or disease state, that explain variation between microbial assemblages. UniFrac has been used in a wide diversity of studies of both biomedical and ecological importance. By applying it to the analysis almost 100,000 sequences compiled from 181 studies of diverse microbial assemblages deposited in GenBank, I have illustrated that the bacteria that inhabit the vertebrate gut are particularly distinct from free-living communities, and that the distribution of bacterial diversity in free-living assemblages is largely governed by salinity and substrate type (i.e. whether the samples were from soil/sediment or water). I will illustrate computational enhancements that will allow for the application of UniFrac to studies containing hundreds of samples and millions of sequences, which next-generation sequencing technology has made possible. Next, I will talk about the extension of UniFrac to whole genome comparisons, allowing us to test whether horizontal gene transfer, parallel gene loss and duplications cause the repertoires of functional genes to converge in organisms that inhabit the same environment. As an example, I will illustrate how the repertoires of carbohydrate active enzymes have converged in human gut microbes compared to their non-gut relatives.