Research

The Whitaker Lab studies the dynamics of microbes and their viruses using a combination of genomics, experimental evolution, modeling, and molecular biology. 

Genomic Evolution

Viruses are obligate parasites, but the way they infect their hosts can be extraordinarily diverse and result in dynamic symbioses which protect their hosts from other viral predation and confer enormous benefits. Not much is known how this symbiosis contributes to the evolution of the communities they infect. We study this in several systems, including highly structured archaeal hot springs communities and in the pathogens infecting the human CF lung.

Plasmids and other mobile genetic elements blur the line between other and self. Our lab is very interested in the way symbioses evolve and how these elements affect the evolution of microbial populations.

 

Our lab is a part of the Genomics and Eco-evolution of Multi-Scale Symbioses (GEMS) Institute, a Biology Integration Institute funded by the National Science Foundation. GEMS aims to break down barriers between biological disciplines in the pursuit of fundamental rules that underlie symbiosis evolution.

Infection Genomics for One Health

Infectious agents cause problems for human health – but what about the infectious agents that infect the infectious agents? Viruses and other mobile genetic elements are often-overlooked pieces to the puzzle, producing nested genomes that shape the evolution of the host. We explore viral transmission dynamics in long-term P. aeruginosa infections of the CF lung using both evolutionary and bioinformatic approaches.  We take advantage of active CRISPR-Cas systems which can act as an immune “memory” for the viruses the host has encountered and use them to develop predictive models for infection in these communities.

The Infection Genomics for One Health (IGOH) theme is housed in the Carl R. Woese Institute of Genomic Biology by the South Quad and is under the fearless leadership of none other than Rachel Whitaker herself! You can find more information about research in the other labs and the theme as a whole here.

 

Model systems:

Our lab is grounded in the population and cell biology of Sulfolobus islandicus. The questions surrounding viral infection, evolution, and symbiosis are not unique to this organism, and we now have many projects going in the lab that all center around those questions. Here  are the main ones.

Sulfolobus islandicus 

S. islandicus is a hyperthermophilic archaeon of the phylum Crenarcheota which lives in the acidic hot springs (pH of 2-3 at around 80 degrees C) found in volcanically active regions. We collect wild isolates largely from Yellowstone National Park (see our Pictures tab) in order to ask questions about population dynamics, virus-host interactions, symbiosis and speciation. Hot springs are an ideal system in which to study these eco-evolutionary phenomena. The extreme environment hosts a lower species diversity, and the springs’ physical separation presents a barrier to migration. These qualities lend tractability to the system, and lack of gene flow promotes independent adaptation among different populations.

S. islandicus is also of especial interest as a model organism for crenarchaeal cell biology. A robust set of genetic methods exist for probing its physiology, several of which have been developed in our own lab by Dr. C. Zhang. In addition to the inherent interest of these unique organisms, studying crenarchaeal genetics can shed light on eukaryal-archaeal evolution. With the discovery of the Asgard archaea in recent years, increasing evidence favors the exciting hypothesis that eukaryotes evolved from within the archaeal domain. The Asgards, however, are extremely difficult or impossible to cultivate and are not genetically tractable. Crenarchaeota are relatively closely related, and share central cellular systems with both the Asgards and eukaryotes. S. islandicus is thus well positioned to aid in unraveling this profound evolutionary question.

Pseudomonas aeruginosa

P. aeruginosa is common in human-associated environments and opportunistically infects immunocompromised people. The leading cause of morbidity in cystic fibrosis patients, P. aeruginosa has been widely studied in the context of within-patient long-term evolution, where it exhibits well-described adaptation to its new environment. P. aeruginosa is infected by a wide variety of bacterial viruses (also known as bacteriophages), and we are interested in the contribution of these viruses to the evolution of P. aeruginosa in the wild – as well as the contribution of P. aeruginosa to the evolution of its viruses.

Escherichia coli

How plasmids and mobile elements evolve and spread is central to understanding the spread of antibiotic resistance.