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John Kirby PhD

John Kirby PhD profile photo picture

Chair, Center Associate Director, Professor

Institution: Medical College of Wisconsin
Department: Microbiology and Immunology

Member of the Cardiovascular Center
Member of the Center for Immunology
Member of the Center for Microbiome Research
Member of the Mellowes Center for Genomic Sciences and Precision Medicine

View Curriculum Vitae

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

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

    • Educational Expertise

  • Bacterial Physiological Phenomena
  • Microbiology
  • Microbiota

    • Publications (54)

  • Thiocillin contributes to the ecological fitness of Bacillus cereus ATCC 14579 during interspecies interactions with Myxococcus xanthus. (Müller S, DeLeon O, Atkinson SN, Saravia F, Kellogg S, Shank EA, Kirby JR) Front Microbiol 2023;14:1295262 PMID: 38075900 PMCID: PMC10704990 SCOPUS ID: 2-s2.0-85178917053 12/11/2023    
  • A single, peri-operative antibiotic can persistently alter the post-operative gut microbiome after Roux-en-Y gastric bypass. (Fernando DG, Saravia FL, Atkinson SN, Barron M, Kirby JR, Kindel TL) Surg Endosc 2023 Feb;37(2):1476-1486 PMID: 35768736 SCOPUS ID: 2-s2.0-85133186635 06/30/2022    
  • Methods for the Comprehensive in vivo Analysis of Energy Flux, Fluid Homeostasis, Blood Pressure, and Ventilatory Function in Rodents. (Reho JJ, Nakagawa P, Mouradian GC Jr, Grobe CC, Saravia FL, Burnett CML, Kwitek AE, Kirby JR, Segar JL, Hodges MR, Sigmund CD, Grobe JL) Front Physiol 2022;13:855054 PMID: 35283781 PMCID: PMC8914175 SCOPUS ID: 2-s2.0-85126220642 03/15/2022       13 Citations
  • Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice. (Lozada-Fernández VV, deLeon O, Kellogg SL, Saravia FL, Hadiono MA, Atkinson SN, Grobe JL, Kirby JR) mSystems 2022 Feb 22;7(1):e0023021 PMID: 35076278 PMCID: PMC8788325 SCOPUS ID: 2-s2.0-85123715407 01/26/2022       11 Citations
  • Gut Microbiota Represent a Major Thermogenic Biomass. (Riedl RA, Burnett CML, Pearson NA, Reho JJ, Mokadem M, Edwards RA, Kindel TL, Kirby JR, Grobe JL) Function (Oxf) 2021;2(3):zqab019 PMID: 33939772 PMCID: PMC8055641 SCOPUS ID: 2-s2.0-85114762228 05/04/2021       18 Citations
  • Dietary influences on the Dahl SS rat gut microbiota and its effects on salt-sensitive hypertension and renal damage. (Abais-Battad JM, Saravia FL, Lund H, Dasinger JH, Fehrenbach DJ, Alsheikh AJ, Zemaj J, Kirby JR, Mattson DL) Acta Physiol (Oxf) 2021 Aug;232(4):e13662 PMID: 33866692 PMCID: PMC9835005 SCOPUS ID: 2-s2.0-85104879371 04/19/2021       24 Citations
  • Sleeve gastrectomy prevents hypertension associated with unique shifts in the gut microbiome. (Barron M, Atkinson SN, Kirby J, Kindel T) Surg Endosc 2021 Oct;35(10):5461-5467 PMID: 32989546 PMCID: PMC8004532 SCOPUS ID: 2-s2.0-85091609559 09/30/2020       3 Citations
  • Achromobacter xylosoxidans Cellular Pathology Is Correlated with Activation of a Type III Secretion System. (Pickrum AM, DeLeon O, Dirck A, Tessmer MH, Riegert MO, Biller JA, Ledeboer NA, Kirby JR, Frank DW) Infect Immun 2020 Jun 22;88(7) PMID: 32366575 PMCID: PMC7309624 SCOPUS ID: 2-s2.0-85088536617 05/06/2020       17 Citations
  • The SrrAB two-component system regulates Staphylococcus aureus pathogenicity through redox sensitive cysteines. (Tiwari N, López-Redondo M, Miguel-Romero L, Kulhankova K, Cahill MP, Tran PM, Kinney KJ, Kilgore SH, Al-Tameemi H, Herfst CA, Tuffs SW, Kirby JR, Boyd JM, McCormick JK, Salgado-Pabón W, Marina A, Schlievert PM, Fuentes EJ) Proc Natl Acad Sci U S A 2020 May 19;117(20):10989-10999 PMID: 32354997 PMCID: PMC7245129 SCOPUS ID: 2-s2.0-85084961758 05/02/2020       50 Citations
  • Suppressor mutations reveal an NtrC-like response regulator, NmpR, for modulation of Type-IV Pili-dependent motility in Myxococcus xanthus. (Bretl DJ, Ladd KM, Atkinson SN, Müller S, Kirby JR) PLoS Genet 2018 Oct;14(10):e1007714 PMID: 30346960 PMCID: PMC6211767 SCOPUS ID: 2-s2.0-85055910992 10/23/2018       4 Citations
  • Ancient Regulatory Role of Lysine Acetylation in Central Metabolism. (Nakayasu ES, Burnet MC, Walukiewicz HE, Wilkins CS, Shukla AK, Brooks S, Plutz MJ, Lee BD, Schilling B, Wolfe AJ, Müller S, Kirby JR, Rao CV, Cort JR, Payne SH) mBio 2017 Nov 28;8(6) PMID: 29184018 PMCID: PMC5705920 SCOPUS ID: 2-s2.0-85039922037 12/01/2017       86 Citations
  • The Gut Microbiome, Energy Homeostasis, and Implications for Hypertension. (Riedl RA, Atkinson SN, Burnett CML, Grobe JL, Kirby JR) Curr Hypertens Rep 2017 Apr;19(4):27 PMID: 28316052 PMCID: PMC5773096 SCOPUS ID: 2-s2.0-85015782153 03/21/2017       41 Citations
  • The Gut Microbiome of the Vector Lutzomyia longipalpis Is Essential for Survival of Leishmania infantum. (Kelly PH, Bahr SM, Serafim TD, Ajami NJ, Petrosino JF, Meneses C, Kirby JR, Valenzuela JG, Kamhawi S, Wilson ME) mBio 2017 Jan 17;8(1) PMID: 28096483 PMCID: PMC5241394 SCOPUS ID: 2-s2.0-85014830318 01/18/2017       97 Citations
  • Identification of Functions Affecting Predator-Prey Interactions between Myxococcus xanthus and Bacillus subtilis. (Müller S, Strack SN, Ryan SE, Shawgo M, Walling A, Harris S, Chambers C, Boddicker J, Kirby JR) J Bacteriol 2016 Dec 15;198(24):3335-3344 PMID: 27698086 PMCID: PMC5116937 SCOPUS ID: 2-s2.0-84996939200 10/05/2016       26 Citations
  • Molecular Mechanisms of Signaling in Myxococcus xanthus Development. (Bretl DJ, Kirby JR) J Mol Biol 2016 Sep 25;428(19):3805-30 PMID: 27430596 SCOPUS ID: 2-s2.0-84986915805 07/20/2016       37 Citations
  • Type IV-pili dependent motility is co-regulated by PilSR and PilS2R2 two-component systems via distinct pathways in Myxococcus xanthus. (Bretl DJ, Müller S, Ladd KM, Atkinson SN, Kirby JR) Mol Microbiol 2016 Oct;102(1):37-53 PMID: 27393239 SCOPUS ID: 2-s2.0-84988461449 07/10/2016       10 Citations
  • Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure. (Bahr SM, Weidemann BJ, Castro AN, Walsh JW, deLeon O, Burnett CM, Pearson NA, Murry DJ, Grobe JL, Kirby JR) EBioMedicine 2015 Nov;2(11):1725-34 PMID: 26870798 PMCID: PMC4740326 SCOPUS ID: 2-s2.0-84958879311 02/13/2016       105 Citations
  • Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure. (Bahr SM, Weidemann BJ, Castro AN, Walsh JW, deLeon O, Burnett CML, Pearson NA, Murry DJ, Grobe JL, Kirby JR) EBioMedicine 2015 Nov;2(11):1725-1734 PMID: 28958498 SCOPUS ID: 2-s2.0-84958879311 11/01/2015       105 Citations
  • Use of the second-generation antipsychotic, risperidone, and secondary weight gain are associated with an altered gut microbiota in children. (Bahr SM, Tyler BC, Wooldridge N, Butcher BD, Burns TL, Teesch LM, Oltman CL, Azcarate-Peril MA, Kirby JR, Calarge CA) Transl Psychiatry 2015 Oct 06;5(10):e652 PMID: 26440540 PMCID: PMC4930121 SCOPUS ID: 2-s2.0-84943422862 10/07/2015       150 Citations
  • Predation by Myxococcus xanthus induces Bacillus subtilis to form spore-filled megastructures. (Müller S, Strack SN, Ryan SE, Kearns DB, Kirby JR) Appl Environ Microbiol 2015 Jan;81(1):203-10 PMID: 25326308 PMCID: PMC4272737 SCOPUS ID: 2-s2.0-84917705880 10/19/2014       58 Citations
  • Bacillaene and sporulation protect Bacillus subtilis from predation by Myxococcus xanthus. (Müller S, Strack SN, Hoefler BC, Straight PD, Kearns DB, Kirby JR) Appl Environ Microbiol 2014 Sep;80(18):5603-10 PMID: 25002419 PMCID: PMC4178607 SCOPUS ID: 2-s2.0-84906330901 07/09/2014       96 Citations
  • Chemosensory regulation of a HEAT-repeat protein couples aggregation and sporulation in Myxococcus xanthus. (Darnell CL, Wilson JM, Tiwari N, Fuentes EJ, Kirby JR) J Bacteriol 2014 Sep;196(17):3160-8 PMID: 24957622 PMCID: PMC4135651 SCOPUS ID: 2-s2.0-84905472288 06/25/2014       8 Citations
  • Functional organization of a multimodular bacterial chemosensory apparatus. (Moine A, Agrebi R, Espinosa L, Kirby JR, Zusman DR, Mignot T, Mauriello EM) PLoS Genet 2014 Mar;10(3):e1004164 PMID: 24603697 PMCID: PMC3945109 SCOPUS ID: 2-s2.0-84897463421 03/08/2014       23 Citations
  • Specificity residues determine binding affinity for two-component signal transduction systems. (Willett JW, Tiwari N, Müller S, Hummels KR, Houtman JC, Fuentes EJ, Kirby JR) mBio 2013 Nov 05;4(6):e00420-13 PMID: 24194534 PMCID: PMC3892784 SCOPUS ID: 2-s2.0-84891612853 11/07/2013       34 Citations
  • Menaquinone analogs inhibit growth of bacterial pathogens. (Schlievert PM, Merriman JA, Salgado-Pabón W, Mueller EA, Spaulding AR, Vu BG, Chuang-Smith ON, Kohler PL, Kirby JR) Antimicrob Agents Chemother 2013 Nov;57(11):5432-7 PMID: 23959313 PMCID: PMC3811306 SCOPUS ID: 2-s2.0-84885908612 08/21/2013       39 Citations
  • Draft Genome of a Type 4 Pilus Defective Myxococcus xanthus Strain, DZF1. (Müller S, Willett JW, Bahr SM, Scott JC, Wilson JM, Darnell CL, Vlamakis HC, Kirby JR) Genome Announc 2013 Jun 20;1(3) PMID: 23788552 PMCID: PMC3707601 06/22/2013    
  • Draft Genome Sequence of Myxococcus xanthus Wild-Type Strain DZ2, a Model Organism for Predation and Development. (Müller S, Willett JW, Bahr SM, Darnell CL, Hummels KR, Dong CK, Vlamakis HC, Kirby JR) Genome Announc 2013 May 09;1(3) PMID: 23661486 PMCID: PMC3650445 05/11/2013    
  • Genetic and biochemical dissection of a HisKA domain identifies residues required exclusively for kinase and phosphatase activities. (Willett JW, Kirby JR) PLoS Genet 2012;8(11):e1003084 PMID: 23226719 PMCID: PMC3510030 SCOPUS ID: 2-s2.0-84870660891 12/12/2012       80 Citations
  • CrdS and CrdA comprise a two-component system that is cooperatively regulated by the Che3 chemosensory system in Myxococcus xanthus. (Willett JW, Kirby JR) mBio 2011;2(4) PMID: 21810965 PMCID: PMC3147164 SCOPUS ID: 2-s2.0-80052568134 08/04/2011       25 Citations
  • Designer bacteria degrades toxin. (Kirby JR) Nat Chem Biol 2010 Jun;6(6):398-9 PMID: 20479747 SCOPUS ID: 2-s2.0-77952515515 05/19/2010       10 Citations
  • Deciphering the hunting strategy of a bacterial wolfpack. (Berleman JE, Kirby JR) FEMS Microbiol Rev 2009 Sep;33(5):942-57 PMID: 19519767 PMCID: PMC2774760 SCOPUS ID: 2-s2.0-68149094083 06/13/2009       177 Citations
  • Upward mobility and alternative lifestyles: a report from the 10th biennial meeting on Bacterial Locomotion and Signal Transduction. (Scharf BE, Aldridge PD, Kirby JR, Crane BR) Mol Microbiol 2009 Jul;73(1):5-19 PMID: 19496930 PMCID: PMC2724751 SCOPUS ID: 2-s2.0-67649418053 06/06/2009       2 Citations
  • Chemotaxis-like regulatory systems: unique roles in diverse bacteria. (Kirby JR) Annu Rev Microbiol 2009;63:45-59 PMID: 19379070 SCOPUS ID: 2-s2.0-70349538976 04/22/2009       97 Citations
  • Predataxis behavior in Myxococcus xanthus. (Berleman JE, Scott J, Chumley T, Kirby JR) Proc Natl Acad Sci U S A 2008 Nov 04;105(44):17127-32 PMID: 18952843 PMCID: PMC2579389 SCOPUS ID: 2-s2.0-55949134132 10/28/2008       87 Citations
  • Genetic circuitry controlling motility behaviors of Myxococcus xanthus. (Mignot T, Kirby JR) Bioessays 2008 Aug;30(8):733-43 PMID: 18623059 SCOPUS ID: 2-s2.0-48949097122 07/16/2008       17 Citations
  • The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. (Thomas SH, Wagner RD, Arakaki AK, Skolnick J, Kirby JR, Shimkets LJ, Sanford RA, Löffler FE) PLoS One 2008 May 07;3(5):e2103 PMID: 18461135 PMCID: PMC2330069 SCOPUS ID: 2-s2.0-47749126600 05/08/2008       124 Citations
  • Chemosensory pathways, motility and development in Myxococcus xanthus. (Zusman DR, Scott AE, Yang Z, Kirby JR) Nat Rev Microbiol 2007 Nov;5(11):862-72 PMID: 17922045 SCOPUS ID: 2-s2.0-35348833523 10/09/2007       229 Citations
  • Multicellular development in Myxococcus xanthus is stimulated by predator-prey interactions. (Berleman JE, Kirby JR) J Bacteriol 2007 Aug;189(15):5675-82 PMID: 17513469 PMCID: PMC1951827 SCOPUS ID: 2-s2.0-34547645982 05/22/2007       53 Citations
  • In vivo mutagenesis using EZ-Tn5. (Kirby JR) Methods Enzymol 2007;421:17-21 PMID: 17352911 SCOPUS ID: 2-s2.0-33847678145 03/14/2007       12 Citations
  • Rippling is a predatory behavior in Myxococcus xanthus. (Berleman JE, Chumley T, Cheung P, Kirby JR) J Bacteriol 2006 Aug;188(16):5888-95 PMID: 16885457 PMCID: PMC1540073 SCOPUS ID: 2-s2.0-33748639464 08/04/2006       99 Citations
  • Integration into the phage attachment site, attB, impairs multicellular differentiation in Stigmatella aurantiaca. (Müller S, Shen H, Hofmann D, Schairer HU, Kirby JR) J Bacteriol 2006 Mar;188(5):1701-9 PMID: 16484181 PMCID: PMC1426541 SCOPUS ID: 2-s2.0-33644783109 02/18/2006       7 Citations
  • Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles. (Rao CV, Kirby JR, Arkin AP) Phys Biol 2005 Jul 14;2(3):148-58 PMID: 16224120 SCOPUS ID: 2-s2.0-26944472780 10/15/2005       22 Citations
  • The Che4 pathway of Myxococcus xanthus regulates type IV pilus-mediated motility. (Vlamakis HC, Kirby JR, Zusman DR) Mol Microbiol 2004 Jun;52(6):1799-811 PMID: 15186426 SCOPUS ID: 2-s2.0-3042590307 06/10/2004       51 Citations
  • Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. (Rao CV, Kirby JR, Arkin AP) PLoS Biol 2004 Feb;2(2):E49 PMID: 14966542 PMCID: PMC340952 SCOPUS ID: 2-s2.0-19344376625 02/18/2004       123 Citations
  • Chemosensory regulation of developmental gene expression in Myxococcus xanthus. (Kirby JR, Zusman DR) Proc Natl Acad Sci U S A 2003 Feb 18;100(4):2008-13 PMID: 12566562 PMCID: PMC149949 SCOPUS ID: 2-s2.0-0037452669 02/05/2003       92 Citations
  • CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis. (Kirby JR, Kristich CJ, Saulmon MM, Zimmer MA, Garrity LF, Zhulin IB, Ordal GW) Mol Microbiol 2001 Nov;42(3):573-85 PMID: 11722727 SCOPUS ID: 2-s2.0-0035168279 11/28/2001       53 Citations
  • Chemotaxis genes, fibrils and PE taxis in Myxococcus xanthus. (Kirby JR) Trends Microbiol 2001 May;9(5):205 PMID: 11393181 SCOPUS ID: 2-s2.0-0035340420 06/08/2001    
  • CheB is required for behavioural responses to negative stimuli during chemotaxis in Bacillus subtilis. (Kirby JR, Niewold TB, Maloy S, Ordal GW) Mol Microbiol 2000 Jan;35(1):44-57 PMID: 10632876 SCOPUS ID: 2-s2.0-0033963325 01/13/2000       43 Citations
  • CheY-dependent methylation of the asparagine receptor, McpB, during chemotaxis in Bacillus subtilis. (Kirby JR, Saulmon MM, Kristich CJ, Ordal GW) J Biol Chem 1999 Apr 16;274(16):11092-100 PMID: 10196193 SCOPUS ID: 2-s2.0-0033574575 04/10/1999       31 Citations
  • Methanol production during chemotaxis to amino acids in Bacillus subtilis. (Kirby JR, Kristich CJ, Feinberg SL, Ordal GW) Mol Microbiol 1997 May;24(4):869-78 PMID: 9194713 SCOPUS ID: 2-s2.0-0030905518 05/01/1997       27 Citations
  • Chemotactic methylation and behavior in Bacillus subtilis: role of two unique proteins, CheC and CheD. (Rosario MM, Kirby JR, Bochar DA, Ordal GW) Biochemistry 1995 Mar 21;34(11):3823-31 PMID: 7893679 SCOPUS ID: 2-s2.0-0028937662 03/21/1995       54 Citations
  • Chemotactic methylesterase promotes adaptation to high concentrations of attractant in Bacillus subtilis. (Kirsch ML, Peters PD, Hanlon DW, Kirby JR, Ordal GW) J Biol Chem 1993 Sep 05;268(25):18610-6 PMID: 8395512 SCOPUS ID: 2-s2.0-0027194322 09/05/1993       49 Citations
  • Novel methyl transfer during chemotaxis in Bacillus subtilis. (Thoelke MS, Kirby JR, Ordal GW) Biochemistry 1989 Jun 27;28(13):5585-9 PMID: 2505839 SCOPUS ID: 2-s2.0-0024354885 06/27/1989       27 Citations
  • Complementation and characterization of chemotaxis mutants of Bacillus subtilis. (Ordal GW, Parker HM, Kirby JR) J Bacteriol 1985 Nov;164(2):802-10 PMID: 3932330 PMCID: PMC214322 SCOPUS ID: 2-s2.0-0022345182 11/01/1985       20 Citations
    • Last update: 04/22/2024