Research Bench Lab

Microbiology & Immunology

John Kirby, PhD

John R. Kirby, PhD

Chair, Microbiology & Immunology; Walter Schroeder Professor in Microbiology and Immunology; Associate Director, Microbiome, Genomic Sciences and Precision Medicine Center; Associate Director, Center for Microbiome Research


  • Microbiology & Immunology
    BSB B2140

Contact Information

General Interests

Bacterial Signal Transduction, Microbial Communities, Predator-Prey Dynamics, Xenobiotic Disruption of Microbiomes


PhD, Biochemistry, University of Illinois Urbana-Champaign, 1998

Research Experience

  • Bacteria
  • Biofilms
  • Chemotaxis
  • Computational Biology
  • Gastrointestinal Microbiome
  • Microbial Interactions
  • Microbiota
  • Signal Transduction
  • Xenobiotics

Methodologies and Techniques

  • Cloning, Molecular
  • DNA, Bacterial
  • Fecal Microbiota Transplantation
  • Gene Expression Regulation, Bacterial
  • Genome, Bacterial
  • Microbial Interactions
  • Molecular Sequence Data
  • Sequence Alignment
  • Sequence Analysis, DNA

Leadership Positions

  • Associate Director, Center for Microbiome Research
  • Associate Director, Microbiome, Genomic Sciences and Precision Medicine Center
  • Chair, Department of Microbiology & Immunology
  • Member, Finance Committee, Board of Trustees

Educational Expertise

  • Bacterial Physiological Phenomena
  • Microbiology
  • Microbiota

Research Interests

Our major areas of investigation focus on signal transduction in diverse bacteria ranging from soil dwelling spore formers, Bacillus subtilis and Myxococcus xanthus, to biofilm forming pathogens, to microbial communities in the gut.

We are taking a systems biology approach to characterize a family of two-component system homologs for their role during biofilm formation and predation by M. xanthus. Our primary area of interest aims to decipher cross-regulation between highly similar pairs of NtrB-NtrC homologs for their control of motility and development in M. xanthus.

In addition, we are actively investigating interactions between M. xanthus and B. subtilis as a model for predator-prey interactions in vivo. Our primary goal here is to assess the role of production of secondary metabolites on both sides of the predator-prey equation.

Finally, we have also been examining the role of xenobiotics for their capacity to disrupt the gut microbiota with deleterious consequences on metabolism. Currently, we utilize the Illumina platform to obtain 16s rDNA sequence information and analyze those data using QIIME (Quantitative Insights Into Microbial Ecology) open source software. We are employing the use of total calorimetry to assess metabolic defects in mice following perturbation with xenobiotics.

For all projects, we are working with collaborators to generate mathematical models to describe how small molecules can elicit shifts in microbial populations.