Rachel Whitaker

Co-PI; Professor of Microbiology

University of Illinois Urbana-Champaign

Lab Website

Projects

CRISPR dynamics in Bombella strains isolated from longitudinal sampling of honey bee larvae

Core Project

CRISPR-Cas immunity tracks host-microbe interactions. Researchers aim to study CRISPR dynamics in natural populations and their impact on symbiont evolution using Bombella from bee larvae.
Establishing a GEMS culture collection

Core Project

Microbial diversity, particularly from complex communities like soil, is still underexplored. Researchers are working to culture microbes from field sites at the KBS Biological Station in Michigan.
From sequence to structure workflow for analysis of CRISPR-Cas immunity dynamics in microbial populations

Core Project

Researchers are developing a genomics tool to analyze CRISPR population diversity in bacterial genomes, aiming to enhance predictive models for microbial infection epidemiology.
GEMS Education Curriculum Development and Professional Learning

Core Project

The GEMS education and outreach team studies the impact of their efforts through various research projects, which occur during professional development experiences and in teachers’ classrooms.
Influence of the mobilome on the honey bee microbiome via longitudinal metagenomics and reverse ecology

Core Project

Researchers study how ecological and evolutionary factors shape the honey bee gut microbiome, focusing on mobile gene interactions through a longitudinal analysis of apiaries.
Multi-scale structure of natural variation in Streptomyces in rhizophere of long-term nitrogen addition experiment

Core Project

Isabelle Lakis studies how long-term nitrogen addition affects Streptomyces populations in the rhizosphere. They aim to understand community dynamics and variation in pangenomic elements.
Multipartite genome evolution in E. coli

Core Project

Isaiah Goertz and his team study E. coli genomic diversity and plasmid distributions in wastewater samples over 20 months. They aim to model gene flow and understand barriers to plasmid transmission.
Plasmid population biology across environments in Rhizobium leguminosarum

Core Project

Sierra Bedwell studies how changes in Rhizobium plasmid dynamics affect legume-rhizobia mutualism decline due to nitrogen fertilization, using soil and nodule samples.
Viral infection changes the outcome of bacterial evolution

Core Project

Researchers aim to understand how viruses impact bacterial evolution, focusing on viral fitness in environments where vertical transmission is enforced due to a lack of susceptible hosts.

Publications

Ganote et al., 2025

Ganote, C., Caesar, L., Rice, D. W., Whitaker, R. J., & Newton, I. L. G. (2025). Evolutionary trends in Bombella apis CRISPR-Cas systems. bioRxiv.
https://doi.org/10.1101/2025.02.05.636693
Liaghat et al., 2024

Liaghat, A., Yang, J., Whitaker, R., & Pascual, M. (2024). Punctuated virus-driven succession generates dynamical alternations in CRISPR-mediated microbe-virus coevolution. Journal of The Royal Society Interface, 21(217), 20240195.
https://doi.org/10.1098/rsif.2024.0195
Suttenfield et al., 2024

Suttenfield, L. C., Rapti, Z., Chandrashekhar, J. H., Steinlein, A. C., Vera, J. C., Kim, T., & Whitaker, R. J. (2024). Phage-mediated resolution of genetic conflict alters the evolutionary trajectory of Pseudomonas aeruginosa lysogens. mSystems, 9:e00801-24.
https://doi.org/10.1128/msystems.00801-24
Vereau Gorbitz et al., 2024

Vereau Gorbitz, D., Schwarz, C., McMullen, J. G., Cerón-Romero, M., Doyle, R. T., Lau, J. A., Whitaker, R. J., Vanderpool, C. K., & Heath, K. (2024). Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum. bioRxiv.
https://doi.org/10.1101/2024.10.17.618979
Collins & Whitaker, 2023

Collins, A. J., & Whitaker, R. J. (2023). CRISPR Comparison Toolkit: Rapid identification, visualization, and analysis of CRISPR array diversity. The CRISPR Journal, 6(4), 386–400.
https://doi.org/10.1089/crispr.2022.0080