People

Principal Investigator

Rachel Whitaker

My lab focuses on the evolutionary ecology of microbial populations. We combine field sampling of natural populations with culture and non-culture based genetic and genomic analyses. Currently we are working on understanding how the interactions between basic population genetic parameters (mutation, selection, recombination and genetic exchange, neutral genetic drift, and biogeography) shape diversity, promote ecological differentiation, and lead to speciation in the microbial world. Ultimately we will develop a comparative approach, describing natural population dynamics of different species across spatial and temporal scales, with a particular interest in how population structures reflect the unique biology and ecology of organisms in the Archaeal domain.


Graduate students

 

 Ruben Sanchez-Nieves

Horizontal gene transfer is key to understanding how microbial populations develop and evolve. I am interested in how these events occur between cells and what factors promote or discourage transfer. My research focuses on understanding the mechanisms behind DNA transfer in Sulfolobus islandicus and the molecular factors by which their populations are maintained.

 Laura Suttenfield

My project is focused on understanding the evolutionary pressures that are experienced by lysogens (bacteria carrying a latent, reactivatable virus chromosome). Both host and virus experience evolutionary pressures as the result of the other. How are transmission dynamics of the virus affected by the host lifestyle and environment? What happens to viral transmission dynamics when coevolving with infectious microbial communities and how might that impact human health? I do this work using Pseudomonas aeruginosa as a model organism.

Isabelle (Izzy) Lakis

I work with Streptomyces– a common soil bacteria known for its production of antibiotics. I’m looking at the mobile genetic elements of Streptomyces and how these elements and the related natural products impact the symbiosis between Streptomyces, plant hosts and other bacteria, such as Rhizobia. I am also a member of the GEMS Institute.

Isaiah Goertz

My project is focused on investigating the co-evolution of bacteria and plasmids. Plasmids can be costly as well as beneficial for the bacteria. Bacteria in turn can mutate to compensate for these costs. How are these changes altering bacteria within a community and how are the plasmids evolving to increase permanence?

Henry Peel

Sulfolobus islandicus is an interesting system to study due to the existence of a viral mutualist (SSV9) which fights for its persistence in the population by killing uninfected Sulfolobus cells. My research aims to focus on understanding the interactions within the “infected cell” as well as how stable this interaction is evolutionarily.

Jiayue Yang

My project is focused on exploring the CRISPR dynamics in simulated and natural microbial populations. I am looking at both infection and immunity networks mediated by CRISPR-Cas system and how the eco-evolutionary dynamics (virus-microbe symbiosis) and geographic structure (host migration) can affect the critical transitions, and stabilization of population dynamics. My research particularly applies to the thermoacidophilic crenarchaea Sulfolobus islandicus in geothermal hot springs of Yellowstone National Park (North America) and Kamchatka (Russia).

Sierra Bedwell

I am coadvised by Dr. Whitaker and Dr. Katy Heath through the GEMS Institute, and my work focuses on plasmid-host coevolution. I am working with the model nitrogen fixing bacterium Rhizobium leguminosarum, to determine if the cost of carrying symbiosis plasmids is affected by environmental conditions. In addition, I am curious if these plasmids are coevolving with the Rhizobium chromosome. My work has broad impacts on sustainable agriculture, as well as expanding knowledge about mobile genetic elements and their roles in the global ecosystem.

 


Postdocs

Kenneth Ringwald, PhD

My research focuses on horizontal gene transfer mediated by mobile genetic elements such as transposons, viruses, and plasmids.  I am particularly interested in the mobile elements that transfer antibiotic resistance genes.  My current project uses CRISPR technology to enrich complex samples for these rare but clinically and evolutionarily significant elements.

Alan Collins, PhD
My research is focused on the bacterium Pseudomonas aeruginosa and the viruses (bacteriophages) that infect it. I am
working to understand how the bacteria-bacteriophage relationship is impacted by interactions among bacterial cells and  interactions among bacteriophages. Currently I am focused on two main questions: 1) How does horizontal gene transfer influence the bacterial population immunity landscape? and 2) How does competition among bacteriophages impact their ability to infect P. aeruginosa hosts?
Giulia Orazi, PhD

My research focuses on using genomic approaches to study infectious diseases. In particular, I am investigating the interactions between bacterial pathogens and mobile genetic elements (MGEs), and the role of MGEs in spreading antimicrobial resistance. I am also involved in collaborations with local public health entities to study infection networks associated with community infectious disease outbreaks.


Lab Manager

Mindy Baughman

I am the lab manager of the BCXT, MME, and IGOH themes at the IGB. My graduate work was in conceptus effects on endometrial gene expression and decidualization of the uterus. My research interest led me to the Women’s Reproductive Health Research Center at Vanderbilt University Medical Center where I studied endometriosis using human biopsies and mouse models. Enjoying working with patients and clinical studies, I transferred to  Pulmonary and Critical Care Medicine where I studied idiopathic pulmonary fibrosis and participated in their lung biopsy program and processing of diseased lungs from transplant patients. 

 

Research Scientists

Changyi Zhang, PhD

My research encompasses the development of a set of robust genetic approaches to study the gene transfer, recombination and host-virus interactions. Specifically, I currently focus on the following two projects: 1) Chromosomal gene transfer and recombination in S. islandicus. 2). Genome-wide scale analysis of gene function in S. islandicus. This will aid in revealing unexplored genetic determinants and the underlying mechanisms of various biological processes, particularly DNA repair, replication and recombination, in S. islandicus.

Jayadevi Chandrashekhar, PhD

 


Undergraduate assistants

Amelia Steinlein
Eddie Andrews
Ahmad Hassan


Former graduate students

  • Alex Phillips, PhD – Postdoc, Schmid Lab, Duke
  • Sam Dewerff, PhD
  • Elizabeth Rowland, PhD – Postdoc, Kieffer Lab, UIUC
  • Danielle Campbell – PhD – Postdoc, Baldridge Lab, Washington University in St. Louis
  • Maria Bautista, PhD – Postdoc, Geomicrobiology Group, University of Calgary
  • Whitney England, PhD – Research Specialist, Spitale Lab, UC Irvine
  • Dave Krause, PhD – Postdoc, University of Wisconsin-Madison
  • Nicholas Youngblut, PhD – MPI Project Leader, Ley Lab, Max Planck Institute for Developmental Biology
  • Nicole Held, PhD – Sr. Research Scientist, Southwest Research Institute

Former postdocs

  • Dr. Matt Pauly – CDC
  • Dr. Mohamed Zeineldin – Postdoctoral Researcher, USDA
  • Dr. Mohea Couturier – Postdoctoral Researcher, 

Former undergraduate assistants

Rachel and Changyi (third and fourth from left) with Changyi’s amazing undergraduates! (from left) Pranav Akhand, Rebecca Wipfler, Emmy Hallet, Allison Narlock. May 2019.
  • Allison Narlock
  • Pranav Akhand
  • Tianyu Lu
  • Rebecca Wipfler – Graduate Student, Division of Geological and Planetary Sciences, California Institute of Technology 
  • Joseph Demuro – Associate QC Analyst at Scientific Protein Laboratories, LLC
  • Serina Teluja
  • Lauren Paddock
  • Marika Maggos
  • Emmy Hallett – MCB MS program, UIUC
  • Jesse Black – University of Hawaii
  • Kimberly Allen – Indiana University Purdue University
  • Carlos A Vega – Indiana University Purdue University
  • Angelo Raphael Blancaflor
  • Jarrett Wade
  • Gita Golonzka
  • Yuan Li – Graduate Student, Dept. of Microbiology and Immunology, University of Michigan