John Kirby Laboratory

  • Research

    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.

    Two-Component Signaling

    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 and chemosensory systems for their control of motility and development in M. xanthus.

    See recent publications:

    Willett, JW and Kirby, JR. (2011) CrdS and CrdA Comprise a Two-Component System That Is Cooperatively Regulated by the Che3 Chemosensory System in Myxococcus xanthus. mBio 2(4): e00110-11.

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

    Willett, JW, Tiwari, N, Müller, S, Hummels, KR, Houtman, J, Fuentes, EJ and Kirby JR. (2013) Specificity Residues Determine Binding Affinity for Two-Component Signal Transduction Systems. mBio 4(6):e00420-13.

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

    Predator-Prey Interactions

    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.

    See recent publications:

    Müller, S, Strack, SN, Hoefler, BC, Straight, P, Kearns DB and Kirby, JR. (2014) Bacillaene and sporulation protects Bacillus subtilis from predation by Myxococcus xanthus. Appl. Environ. Microbiol. 80(18):5603-10.

    Müller, S, Strack, SN, Ryan SE, Kearns DB and Kirby, JR. (2015) Predation by Myxococcus xanthus Induces Bacillus subtilis to Form Spore-Filled Megastructures. Appl. Environ. Microbiol. pii: AEM.02448-14.

    Microbiome

    We are 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.

    Manuscripts in preparation:

    Bahr, S, O’Brien E, and Kirby JR. “The Human Microbiome is Altered in Patients with Chronic Rhinosinusitus.”

    Bahr, S, Grobe, J, Calarge, C, Kirby JR. “Risperidone Disrupts the Microbiome to Alter Resting Metabolic Rates.”