Research Bench Lab
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

We are examining the role of xenobiotics for their capacity to disrupt the gut microbiota with deleterious consequences on host physiology and metabolism. Disease models used in the lab are a salt-sensitive rat model for hypertension, a mouse model of diet-induced obesity, and a mouse model of obesity induced by the second-generation antipsychotic risperidone. We perform physiological measurements related to each disease model, fecal material transfers to establish a causal link between the microbiota and disease, and 16S rDNA and metagenomic sequencing to analyze taxonomic and functional composition of the microbiota. Metagenomic analyses allow us to identify and test candidate probiotic strains of bacteria with specific metabolic features that influence the progression of disease. We have filed a patent (US 2020/0016124 A1) based on our work leading to reduction of weight gain and are in discussions to create a startup company.

Predator-Prey Interactions
The above work is a direct product of our understanding of bacterial interactions between Myxococcus xanthus and Bacillus subtilis as a model for microbial predator-prey interactions. Our primary goal is to assess the role of specialized metabolites produced by both the predator and the prey. Detailed molecular mechanisms for predator-prey interactions in vitro provide insights into gut-based systems in rodents and humans.