The Thoms Lab at Florida State University studies how plants use their innate immune systems to build and maintain healthy relationships with the microbes that live on and around their roots. Our work focuses on a central question: How do hosts distinguish beneficial microbes from harmful pathogens?
The lab offers extensive hands-on research opportunities for undergraduate and graduate students and postdoctoral fellows interested in plant biology, microbiomes, or host–microbe evolution.
Our research investigates how innate immune pathways shape microbial communities and influence host health. We work with beneficial and pathogenic strains within the Pseudomonas fluorescens species complex that are nearly genetically identical—yet interact with the plant in completely different ways. These powerful models allow us to discover which microbial signals activate immune responses, and how immunity prevents microbiome imbalance (dysbiosis).
We use molecular genetics, biochemical fractionation of microbial metabolites, immune signaling assays, fluorescence microscopy, and evolution-based approaches to uncover how innate immunity:
This work provides foundational insights needed to develop sustainable microbiome-informed agricultural strategies and improves our understanding of host–microbe interactions across all organisms.
Principal Investigator
Research Focus: Understanding the role of innate immunity in shaping healthy microbiomes.
Dr. Thoms received his PhD in Genome, Cell, and Developmental Biology at Indiana University, and completed an NSF postdoctoral fellowship in Dr. Cara Haney's Lab at the University of British Columbia. He started his lab at FSU in 2023.
Postdoctoral Researcher
Project: Identifying novel bacterial metabolites that indicate bacterial symbiotic lifestyle.
Email: gnd25@fsu.edu
PhD Student
Project: Determining how plant immunity is an evolutionary force on symbiotic lifestyles.
Email: deh23@fsu.edu
PhD Student
Project: Identifying the spatiotemporal mechanisms that govern host-microbe interactions.
Email: maq19@fsu.edu
Master's Student (Thesis-Based)
Project: Determining the role of toxin-triggered immunity in host-microbe interactions.
Email: cat22@fsu.edu
Lab Technician
Role: Identifying bacterial metabolites that indicate bacterial symbiotic lifestyle.
Email: mpw21@fsu.edu
Authors: Thoms D, et al.
Journal: Cell Reports (2025)
Abstract: For optimal growth and development, hosts must promote healthy symbiotic interactions while restricting pathogens. To ask whether hosts can distinguish phylogenetically similar pathogens and beneficial bacteria, we used two closely related plant root-associated strains within the Pseudomonas fluorescens species complex. Despite having similar immunogenic microbe-associated molecular patterns, one strain is beneficial and the other exhibits exotoxin-dependent virulence...
Read Full PaperAuthors: Thoms D, et al.
Journal: MPMI (2021)
Abstract: This article is part of the Top 10 Unanswered Questions in MPMI invited review series. That plants recruit beneficial microbes while simultaneously restricting pathogens is critical to their survival. Plants must exclude pathogens; however, most land plants are able to form mutualistic symbioses with arbuscular mycorrhizal fungi. Plants also associate with the complex microbial communities that form the microbiome. The outcome of each symbiotic interaction—whether a specific microbe is pathogenic, commensal, or mutualistic—relies on...
Read Full Paper
Prospective PhD graduate students should apply through the FSU Graduate Admissions Portal.
Graduate student applicants may apply to the Cell & Molecular Biology or Ecology & Evolution programs.
Priority Application Deadline: December 1
(Please verify deadlines on the official FSU portal for the relevant application year)