Microbiology

John R. Kirby, PhD

Portrait

Professor of Microbiology

Contact Information

Office: 3-632 Bowen Science Building
51 Newton Rd
Iowa City, IA 52242
Office Phone: 319-335-7818

Lab: 3-615D Bowen Science Building
51 Newton Rd
Iowa City, IA 52242
Phone: 319-335-7938

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

Education

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

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

Education/Training Program Affiliations

Biosciences Graduate Program
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

All Publications

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.
[Link]

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.
[Link]

Moine A, Agrebi R, Espinosa L, Kirby J, Zusman D, Mignot T, Mauriello E.  Functional organization of a multimodular bacterial chemosensory apparatus.  PLoS Genet.  2014 March 6. 10(3):e1004164.
[Link]

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.  2014. Epub ahead of print.
[Link]

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.
[Link]

Schlievert P, Merriman J, Salgado-Pabón W, Mueller E, Spaulding A, Vu B, Chuang-Smith O, Kohler P, Kirby J.  Menaquinone analogs inhibit growth of bacterial pathogens.  Antimicrob Agents Chemother.  2013 November. 57(11):5432-7.
[Link]

Müller S, Willett J, Bahr S, Scott J, Wilson J, Darnell C, Vlamakis H, Kirby J.  Draft Genome of a Type 4 Pilus Defective Myxococcus xanthus Strain, DZF1.  Genome Announc.  2013 June 20. 1(3):pii: e00392-13.
[Link]

Müller S, Willett J, Bahr S, Darnell C, Hummels K, Dong C, Vlamakis H, Kirby J.  Draft Genome Sequence of Myxococcus xanthus Wild-Type Strain DZ2, a Model Organism for Predation and Development.  Genome Announc.  2013 May 9. 1(3):pii: e00217-13.
[Link]

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.
[Link]

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.
[Link]

Kirby J.  Designer bacteria degrades toxin.  Nat Chem Biol.  2010 June. 6(6):398-9.
[Link]

Berleman J, Kirby J.  Deciphering the hunting strategy of a bacterial wolfpack.  FEMS Microbiol Rev.  2009 September. 33(5):942-57.
[Link]

Scharf B, Aldridge P, Kirby J, Crane B.  Upward mobility and alternative lifestyles: a report from the 10th biennial meeting on Bacterial Locomotion and Signal Transduction.  Mol Microbiol.  2009 July. 73(1):5-19.
[Link]

Kirby J.  Chemotaxis-like regulatory systems: unique roles in diverse bacteria.  Annu Rev Microbiol.  2009. 63:45-59.
[Link]

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.
[Link]

Mignot T, Kirby J.  Genetic circuitry controlling motility behaviors of Myxococcus xanthus.  Bioessays.  2008 August. 30(8):733-43.
[Link]

Thomas S, Wagner R, Arakaki A, Skolnick J, Kirby J, Shimkets L, Sanford R, Löffler F.  The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria.  PLoS One.  2008 May 7. 3(5):e2103.
[Link]

Kirby J, Berleman J, Müller S, Li D, Scott J, Wilson J.  Chemosensory Signal Transduction Systems in Myxococcus xanthus.  ASM Press.  2008. 

Zusman D, Scott A, Yang Z, Kirby J.  Chemosensory pathways, motility and development in Myxococcus xanthus.  Nat Rev Microbiol.  2007 November. 5(11):862-72.
[Link]

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

Kirby J.  In vivo mutagenesis using EZ-Tn5.  Methods Enzymol.  2007. 421:17-21.
[Link]

Berleman J, Chumley T, Cheung P, Kirby J.  Rippling is a predatory behavior in Myxococcus xanthus.  J Bacteriol.  2006 August. 188(16):5888-95.
[Link]

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.
[Link]

Rao C, Kirby J, Arkin A.  Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles.  Phys Biol.  2005 July 14. 2(3):148-58.
[Link]

Vlamakis H, Kirby J, Zusman D.  The Che4 pathway of Myxococcus xanthus regulates type IV pilus-mediated motility.  Mol Microbiol.  2004 June. 52(6):1799-811.
[Link]

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.
[Link]

Kirby J, Zusman D.  Chemosensory regulation of developmental gene expression in Myxococcus xanthus.  Proc Natl Acad Sci U S A.  2003 February 18. 100(4):2008-13.
[Link]

Kirby J, Kristich C, Saulmon M, Zimmer M, Garrity L, Zhulin I, Ordal G.  CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis.  Mol Microbiol.  2001 November. 42(3):573-85.
[Link]

Kirby J.  Chemotaxis genes, fibrils and PE taxis in Myxococcus xanthus.  Trends Microbiol.  2001 May. 9(5):205.
[Link]

Kirby J, Niewold T, Maloy S, Ordal G.  CheB is required for behavioural responses to negative stimuli during chemotaxis in Bacillus subtilis.  Mol Microbiol.  2000 January. 35(1):44-57.
[Link]

Kirby J, Saulmon M, Kristich C, Ordal G.  CheY-dependent methylation of the asparagine receptor, McpB, during chemotaxis in Bacillus subtilis.  J Biol Chem.  1999 April 16. 274(16):11092-100.
[Link]

Ordal G, Kirby J.  Chemotaxis.  John Wiley & Sons, New York.  1999. 1:413-5.

Ordal G, Kirby J.  Methyltransferase.  John Wiley & Sons, New York.  1999. 3:1491-2.

Ordal G, Kirby J.  Protein Methylation.  John Wiley & Sons, New York.  1999. 3:1486-8.

Ordal G, Kirby J.  Transducer Proteins.  John Wiley & Sons, New York.  1999. 4:2593-995.

Kirby J, Kristich C, Feinberg S, Ordal G.  Methanol production during chemotaxis to amino acids in Bacillus subtilis.  Mol Microbiol.  1997 May. 24(4):869-78.
[Link]

Rasario M, Kirby J, Bochar D, Ordal G.  Chemotactic methylation and behavior in Bacillus subtilis: role of two unique proteins, CheC and CheD.  Biochemistry.  1995 March 21. 34(11):3823-31.
[Link]

Kirsch M, Peters P, Hanlon D, Kirby J, Ordal G.  Chemotactic methylesterase promotes adaptation to high concentrations of attractant in Bacillus subtilis.  J Biol Chem.  1993 September 5. 268(25):18610-6.
[Link]

Thoelke M, Kirby J, Ordal G.  Novel methyl transfer during chemotaxis in Bacillus subtilis.  Biochemistry.  1989 June 27. 28(13):5585-9.
[Link]

Ordal G, Parker H, Kirby J.  Complementation and characterization of chemotaxis mutants of Bacillus subtilis.  J Bacteriol.  1985 November. 164(2):802-10.
[Link]

Date Last Modified: 12/19/2014 - 08:32:38