The lab after Ruben’s defense in Fall 2023

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.

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.


Thomas Cowell

My research focuses on applying droplet microfluidics to enable novel measurements of the thermophilic archaea S. islandicus and its viruses. I currently focus on two approaches: 1) massively pararllelized in-drop cultivation of diverse environmental samples, and 2) high-throughput single virus measurements using ddPCR. Precise characterization of host and virus diversity will contribute to an understanding of complex virus-host interactions present in hot springs ecosystems.

Graduate Students

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.


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?

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.


Abigail Finn

I am the resident microscopist, my project focuses on the cell biology of the hyperthermophillic archaeon Sulfolobus islandicus using high heat live imaging and the excellent resources and instruments at the IGB core facilities! More precisely, I am investigating an interesting phenotype displayed by a mutant lacking its outermost protein barrier- the S-layer- which appears to have connections to ancestral eukaryotic cell division mechanics and may be an avenue through which to explore potentially novel methods of homologous gene transfer similar to eukaryotic meiosis.

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. 

Visiting Researcher

Eddie Andrews

Undergraduate assistants

Mia Mercado
Sanjana Jose
Aiden Allenfort

Former graduate students

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

Former postdocs

  • Ken Ringwald – Fermentation Specialist, Riggs Brewing Company
  • Alan Collins – Bioinformatician at IHRC Inc
  • Guilia Orazi – APHL-CDC Infectious Disease Laboratory Fellow
  • Mohamed Zeineldin – Postdoctoral Researcher, USDA
  • Mohea Couturier – Postdoctoral Researcher, Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel
  • Matt Pauly – ORISE fellow in the Division of Viral Hepatitis at the CDC

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.
  • Ahmad Hassan
  • Catherine Koterba
  • Amelia Steinlein – Dermatology Medical Assistant, Derick Dermatology
  • Allison Narlock – Senior Research Associate at CinderBio
  • Pranav Akhand
  • Tianyu Lu – Bioinformatician, University of Pennsylvania School of Medicine
  • 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 Taluja – PhD Student, Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University
  • Emmy Hallett – PhD Candidate, INRS ETE
  • Jesse Black – Research Associate with Fisheries Collaborative Program, University of California, Santa Cruz
  • Lauren Paddock – Microbiology Graduate Student, University of Rochester School of Medicine and Dentistry
  • Marika Maggos, MD – Resident, Department of Obstetrics and Gynecology, UIC College of Medicine
  • Kimberly Allen – Indiana University Purdue University
  • Carlos A Vega – Indiana University Purdue University
  • Angelo Raphael Blancaflor – Staff, InterVarsity
  • Jarrett Wade
  • Gita Golonzka – Clinical Research Coordinator at OHSU Department of Neurology
  • Yuan Li, PhD – Dept. of Microbiology and Immunology, University of Michigan