Research Directions

Microbes dominate planetary biomass, play essential roles in nutrient recycling, can cause disease, and are an integral part of the healthy human body. Their genomes contain records of past evolutionary events, from which we can decipher how microbes evolve and adapt to their environments. Recent advances in DNA sequencing technologies brought us an avalanche of data: thousands of genomes and terabases of environmental DNA (metagenomes). We mine these data sets (1) to assess the impact of horizontal gene transfer on microbial populations; (2) to find new ways to characterize microbial communities; and (3) to track down genomic signatures of microbial adaptations.

We are actively investigating the following questions:

Did bacteria "domesticate" viruses as an efficient means of horizontal gene exchange?
(Charcoal drawing of a gene transfer agent by Amy Zhang'17)

What genetic changes and evolutionary forces drive bacterial preference to a specific (optimal) temperature and tolerance of temperature fluctuations?


Does genome methylation play a role in bacterial temperature response?

Do Bacteria and Archaea form "species"? What are the fundamental units of prokaryotic diversity?

What is a role of horizontal gene transfer in microbial communities inhabiting an extreme environment of saturated brines (37% NaCl)?
(Isla Cristina saltern [Spain]; Photo by R. Thane Papke)