John R. Kirby, PhD


Professor of Microbiology

Contact Information

Office: 3-352 Bowen Science Building
51 Newton Rd
Iowa City, IA 52242
Phone: 319-335-7818

Lab: 3-315 Bowen Science Building
51 Newton Rd
Iowa City, IA 52242
Phone: 319-335-8866

Email: john-kirby@uiowa.edu
Web: Kirby Lab Website


BS, Biochemistry, University of Illinois at Urbana-Champaign
PhD, Biochemistry, University of Illinois at Urbana-Champaign

Post Doctorate, Molecular Cell Biology, University of California, Berkeley

Education/Training Program Affiliations

Department of Microbiology Graduate Program
Interdisciplinary Graduate Program in Genetics
Interdisciplinary Graduate Program in Informatics
Interdisciplinary Graduate Program in Translational Biomedicine
Medical Scientist Training Program

Research Summary

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.

Center, Program and Institute Affiliations

Alfred P. Sloan Center for Exemplary Mentoring
Center for Biocatalysis and Bioprocessing

Selected Publications

Show All

Müller S, Strack S, Ryan S, Kearns D, Kirby J.  Predation by Myxococcus xanthus induces Bacillus subtilis to form spore-filled megastructures.  Appl Environ Microbiol.  2015 January. 81(1):203-10.

Müller S, Strack S, Hoefler B, Straight P, Kearns D, Kirby J.  Bacillaene and sporulation protect Bacillus subtilis from predation by Myxococcus xanthus.  Appl Environ Microbiol.  2014 September 15. 80(18):5603-10.

Darnell C, Wilson J, Tiwari N, Fuentes E, Kirby J.  Chemosensory regulation of a HEAT-repeat protein couples aggregation and sporulation in Myxococcus xanthus.  J Bacteriol.  2014 September. 196(17):3160-8.

Willett J, Tiwari N, Müller S, Hummels K, Houtman J, Fuentes E, Kirby J.  Specificity residues determine binding affinity for two-component signal transduction systems.  MBio.  2013 November 5. 4(6):e00420-13.

Willett J, Kirby J.  Genetic and Biochemical Dissection of a HisKA Domain Identifies Residues Required Exclusively for Kinase and Phosphatase Activities.  PLoS Genet.  2012 November. 8(11):e1003084.

Willett J, Kirby J.  CrdS and CrdA comprise a two-component system that is cooperatively regulated by the Che3 chemosensory system in Myxococcus xanthus.  MBio.  2011 August 2. 2(4):e00110-11.

Berleman J, Scott J, Chumley T, Kirby J.  Predataxis behavior in Myxococcus xanthus.  Proc Natl Acad Sci U S A.  2008 November 4. 105(44):17127-32.

Berleman J, Kirby J.  Multicellular development in Myxococcus xanthus is stimulated by predator-prey interactions.  J Bacteriol.  2007 August. 189(15):5675-82.

Müller S, Shen H, Hofmann D, Schairer H, Kirby J.  Integration into the phage attachment site, attB, impairs multicellular differentiation in Stigmatella aurantiaca.  J Bacteriol.  2006 March. 188(5):1701-9.

Rao C, Kirby J, Arkin A.  Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis.  PLoS Biol.  2004 February. 2(2):E49.

Date Last Modified: 09/01/2016 - 09:35:46