Research Projects in the Liles Laboratory

Our research group works at the intersection of environmental and clinical microbiology. We are using a combination of modern molecular biological tools and classic microbiological techniques to 1) Discover novel antibiotic compounds produced by environmental microorganisms, 2) Identify and characterize biological control agents to control disease, and 3) Study the complex microbial communities in natural environments and their response to environmental factors.

The history of microbiology as a science has traditionally relied upon microscopy and the ability to culture microorganisms on a petri dish.  The advent of molecular microbiology has brought new tools into the repertoire of microbiologists--now we are armed with whole   genome sequences of the bacteria that we study, and can use a combination of microscopy with molecular probes. Rather than supplanting the techniques that have been used for over 150 years of microbiology, the molecular era has given new life and new approaches to the field.

The work of Carl Woese and colleagues demonstrated that the 16S ribosomal RNA gene is conserved among all life forms. Molecular phylogenetic analysis now allows an objective and quantitative assessment of evolutionary relationships, and has revealed the vastness of microbial diversity on planet Earth.  Despite only being able to study a small percentage of the microbial life on Earth, cultured microorganisms have provided us with many useful natural products, such as antibiotics. Yet even to this day there remains an overwhelming diversity of microbial life that is unknown to science. Perhaps the greatest challenge for microbiologists in the 21st century is to learn more about this "silent majority" of microbial life alive on our planet.

If the phylogenetic diversity of microbial life is so vast, how much unexplored metabolic and functional diversity among microbial communities is left to discover?  To tap into this genetic potential our lab uses an approach that is designated ‘metagenomics’, which is the analysis of the collective genomes of the microorganisms in a natural environment. By cloning DNA isolated from diverse bacteria or viruses directly into a culturable host (e.g., E. coli) the genetic diversity of microorganisms in natural environments may be accessed and natural products produced by these environmental microorganisms may be expressed within a surrogate E. coli host. The metagenomic libraries can be screened by next-generation sequencing, identifying recombinant clones that contain a specific gene sequence, or by functional assays. All three of these screening methods are used in the Liles laboratory to study bacterial and viral communities in natural environments such as soils, ponds and even extreme samples like oil reservoirs over a mile below the sea floor. Although metagenomic analysis as a field is still in its infancy, a number of exciting discoveries have been made that indicate that a wealth of chemistry and biology is waiting to be unearthed!

Last updated: 11/12/2015