Date of Document: March 28, 2024
CURRICULUM VITAE

John Kirby PhD
Chair, Center Associate Director, Professor
Department of Microbiology and Immunology

OFFICE ADDRESS:
Basic Science Building
8701 Watertown Plank Road
Milwaukee, WI 53226

EDUCATION:
- 1992 B.S. Biochemistry, University of Illinois at Urbana-Champaign
- 1998 Ph.D. Biochemistry, University of Illinois at Urbana-Champaign

POSTGRADUATE TRAINING AND FELLOWSHIP APPOINTMENTS:
1998 - 2002 Postdoctoral Fellow, University of California, Berkeley

FACULTY APPOINTMENTS:
2002 - 2006 Assistant Professor, School of Biology, Georgia Institute of Technology
2007 - 2014 Associate Professor, Department of Microbiology, University of Iowa
2014 - 2016 Professor, Department of Microbiology, University of Iowa
2017 - Present Professor & Chair, Department of Microbiology & Immunology, Medical College of Wisconsin

RESEARCH ADMINISTRATIVE APPOINTMENTS:
2017 - Present Associate Director, Center for Microbiome Research, Medical College of Wisconsin
2017 - Present Associate Director, Genome Sciences & Precision Medicine Center, Medical College of Wisconsin

MEMBERSHIPS IN HONORARY AND PROFESSIONAL SOCIETIES:
2006 - 2010 Cold Spring Harbor Laboratory: Advanced Bacterial Genetics (Instructor )
2006 - 2007 American Society for Microbiology: Cell & Structural Biology (Division Chair)
2007 - 2008 American Society for Microibology : Cell & Structural Biology (Division Advisor)
2012 - Present Hennepin Life Sciences (Science Advisor)
2013 - Present PLOS ONE (Academic Editor)
2014 - Present Molecular Microbiology (Editorial Advisory Board)
2015 - Present Frontiers in Microbiology (Editorial Advisory Board)


BIBLIOGRAPHY
Refereed Journal Publications/Original Papers
1. Ordal GW, Parker HM, Kirby JR. Complementation and characterization of chemotaxis mutants of Bacillus subtilis. J Bacteriol. 1985 Nov;164(2):802-10. PMCID: PMC214322
2. Thoelke MS, Kirby JR, Ordal GW. Novel methyl transfer during chemotaxis in Bacillus subtilis. Biochemistry. 1989 Jun 27;28(13):5585-9.
3. Kirsch ML, Peters PD, Hanlon DW, Kirby JR, Ordal GW. Chemotactic methylesterase promotes adaptation to high concentrations of attractant in Bacillus subtilis. J Biol Chem. 1993 Sep 05;268(25):18610-6.
4. Rosario MM, Kirby JR, Bochar DA, Ordal GW. Chemotactic methylation and behavior in Bacillus subtilis: role of two unique proteins, CheC and CheD. Biochemistry. 1995 Mar 21;34(11):3823-31.
5. Kirby JR, Kristich CJ, Feinberg SL, Ordal GW. Methanol production during chemotaxis to amino acids in Bacillus subtilis. Mol Microbiol. 1997 May;24(4):869-78.
6. Kirby JR, Saulmon MM, Kristich CJ, Ordal GW. CheY-dependent methylation of the asparagine receptor, McpB, during chemotaxis in Bacillus subtilis. J Biol Chem. 1999 Apr 16;274(16):11092-100.
7. Kirby JR, Niewold TB, Maloy S, Ordal GW. CheB is required for behavioural responses to negative stimuli during chemotaxis in Bacillus subtilis. Mol Microbiol. 2000 Jan;35(1):44-57.
8. Kirby JR. Chemotaxis genes, fibrils and PE taxis in Myxococcus xanthus. Trends Microbiol. 2001 May;9(5):205.
9. Kirby JR, Kristich CJ, Saulmon MM, Zimmer MA, Garrity LF, Zhulin IB, Ordal GW. CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis. Mol Microbiol. 2001 Nov;42(3):573-85.
10. Kirby JR, Zusman DR. Chemosensory regulation of developmental gene expression in Myxococcus xanthus. Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):2008-13. PMCID: PMC149949
11. Rao CV, Kirby JR, Arkin AP. Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. PLoS Biol. 2004 Feb;2(2):E49. PMCID: PMC340952
12. Vlamakis HC, Kirby JR, Zusman DR. The Che4 pathway of Myxococcus xanthus regulates type IV pilus-mediated motility. Mol Microbiol. 2004 Jun;52(6):1799-811.
13. Rao CV, Kirby JR, Arkin AP. Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles. Phys Biol. 2005 Jul 14;2(3):148-58.
14. Müller S, Shen H, Hofmann D, Schairer HU, Kirby JR. Integration into the phage attachment site, attB, impairs multicellular differentiation in Stigmatella aurantiaca. J Bacteriol. 2006 Mar;188(5):1701-9. PMCID: PMC1426541
15. Berleman JE, Chumley T, Cheung P, Kirby JR. Rippling is a predatory behavior in Myxococcus xanthus. J Bacteriol. 2006 Aug;188(16):5888-95. PMCID: PMC1540073
16. Kirby JR. In vivo mutagenesis using EZ-Tn5. Methods Enzymol. 2007;421:17-21.
17. Berleman JE, Kirby JR. Multicellular development in Myxococcus xanthus is stimulated by predator-prey interactions. J Bacteriol. 2007 Aug;189(15):5675-82. PMCID: PMC1951827
18. Zusman DR, Scott AE, Yang Z, Kirby JR. Chemosensory pathways, motility and development in Myxococcus xanthus. Nat Rev Microbiol. 2007 Nov;5(11):862-72.
19. Thomas SH, Wagner RD, Arakaki AK, Skolnick J, Kirby JR, Shimkets LJ, Sanford RA, Löffler FE. The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. PLoS One. 2008 May 07;3(5):e2103. PMCID: PMC2330069
20. Mignot T, Kirby JR. Genetic circuitry controlling motility behaviors of Myxococcus xanthus. Bioessays. 2008 Aug;30(8):733-43.
21. Berleman JE, Scott J, Chumley T, Kirby JR. Predataxis behavior in Myxococcus xanthus. Proc Natl Acad Sci U S A. 2008 Nov 04;105(44):17127-32. PMCID: PMC2579389
22. Kirby JR. Chemotaxis-like regulatory systems: unique roles in diverse bacteria. Annu Rev Microbiol. 2009;63:45-59.
23. Scharf BE, Aldridge PD, Kirby JR, Crane BR. Upward mobility and alternative lifestyles: a report from the 10th biennial meeting on Bacterial Locomotion and Signal Transduction. Mol Microbiol. 2009 Jul;73(1):5-19. PMCID: PMC2724751
24. Berleman JE, Kirby JR. Deciphering the hunting strategy of a bacterial wolfpack. FEMS Microbiol Rev. 2009 Sep;33(5):942-57. PMCID: PMC2774760
25. Kirby JR. Designer bacteria degrades toxin. Nat Chem Biol. 2010 Jun;6(6):398-9.
26. Willett JW, Kirby JR. CrdS and CrdA comprise a two-component system that is cooperatively regulated by the Che3 chemosensory system in Myxococcus xanthus. mBio. 2011;2(4). PMCID: PMC3147164
27. Willett JW, Kirby JR. Genetic and biochemical dissection of a HisKA domain identifies residues required exclusively for kinase and phosphatase activities. PLoS Genet. 2012;8(11):e1003084. PMCID: PMC3510030
28. Müller S, Willett JW, Bahr SM, Darnell CL, Hummels KR, Dong CK, Vlamakis HC, Kirby JR. Draft Genome Sequence of Myxococcus xanthus Wild-Type Strain DZ2, a Model Organism for Predation and Development. Genome Announc. 2013 May 09;1(3). PMCID: PMC3650445
29. Müller S, Willett JW, Bahr SM, Scott JC, Wilson JM, Darnell CL, Vlamakis HC, Kirby JR. Draft Genome of a Type 4 Pilus Defective Myxococcus xanthus Strain, DZF1. Genome Announc. 2013 Jun 20;1(3). PMCID: PMC3707601
30. Schlievert PM, Merriman JA, Salgado-Pabón W, Mueller EA, Spaulding AR, Vu BG, Chuang-Smith ON, Kohler PL, Kirby JR. Menaquinone analogs inhibit growth of bacterial pathogens. Antimicrob Agents Chemother. 2013 Nov;57(11):5432-7. PMCID: PMC3811306
31. Willett JW, Tiwari N, Müller S, Hummels KR, Houtman JC, Fuentes EJ, Kirby JR. Specificity residues determine binding affinity for two-component signal transduction systems. mBio. 2013 Nov 05;4(6):e00420-13. PMCID: PMC3892784
32. Moine A, Agrebi R, Espinosa L, Kirby JR, Zusman DR, Mignot T, Mauriello EM. Functional organization of a multimodular bacterial chemosensory apparatus. PLoS Genet. 2014 Mar;10(3):e1004164. PMCID: PMC3945109
33. Darnell CL, Wilson JM, Tiwari N, Fuentes EJ, Kirby JR. Chemosensory regulation of a HEAT-repeat protein couples aggregation and sporulation in Myxococcus xanthus. J Bacteriol. 2014 Sep;196(17):3160-8. PMCID: PMC4135651
34. Müller S, Strack SN, Hoefler BC, Straight PD, Kearns DB, Kirby JR. Bacillaene and sporulation protect Bacillus subtilis from predation by Myxococcus xanthus. Appl Environ Microbiol. 2014 Sep;80(18):5603-10. PMCID: PMC4178607
35. Müller S, Strack SN, Ryan SE, Kearns DB, Kirby JR. Predation by Myxococcus xanthus induces Bacillus subtilis to form spore-filled megastructures. Appl Environ Microbiol. 2015 Jan;81(1):203-10. PMCID: PMC4272737
36. Bahr SM, Tyler BC, Wooldridge N, Butcher BD, Burns TL, Teesch LM, Oltman CL, Azcarate-Peril MA, Kirby JR, Calarge CA. Use of the second-generation antipsychotic, risperidone, and secondary weight gain are associated with an altered gut microbiota in children. Transl Psychiatry. 2015 Oct 06;5(10):e652. PMCID: PMC4930121
37. Bahr SM, Weidemann BJ, Castro AN, Walsh JW, deLeon O, Burnett CML, Pearson NA, Murry DJ, Grobe JL, Kirby JR. Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure. EBioMedicine. 2015 Nov;2(11):1725-1734.
38. Bahr SM, Weidemann BJ, Castro AN, Walsh JW, deLeon O, Burnett CM, Pearson NA, Murry DJ, Grobe JL, Kirby JR. Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure. EBioMedicine. 2015 Nov;2(11):1725-34. PMCID: PMC4740326
39. Bretl DJ, Müller S, Ladd KM, Atkinson SN, Kirby JR. Type IV-pili dependent motility is co-regulated by PilSR and PilS2R2 two-component systems via distinct pathways in Myxococcus xanthus. Mol Microbiol. 2016 Oct;102(1):37-53.
40. Bretl DJ, Kirby JR. Molecular Mechanisms of Signaling in Myxococcus xanthus Development. J Mol Biol. 2016 Sep 25;428(19):3805-30.
41. Müller S, Strack SN, Ryan SE, Shawgo M, Walling A, Harris S, Chambers C, Boddicker J, Kirby JR. Identification of Functions Affecting Predator-Prey Interactions between Myxococcus xanthus and Bacillus subtilis. J Bacteriol. 2016 Dec 15;198(24):3335-3344. PMCID: PMC5116937
42. Kelly PH, Bahr SM, Serafim TD, Ajami NJ, Petrosino JF, Meneses C, Kirby JR, Valenzuela JG, Kamhawi S, Wilson ME. The Gut Microbiome of the Vector Lutzomyia longipalpis Is Essential for Survival of Leishmania infantum. mBio. 2017 Jan 17;8(1). PMCID: PMC5241394
43. Riedl RA, Atkinson SN, Burnett CML, Grobe JL, Kirby JR. The Gut Microbiome, Energy Homeostasis, and Implications for Hypertension. Curr Hypertens Rep. 2017 Apr;19(4):27. PMCID: PMC5773096
44. 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. Ancient Regulatory Role of Lysine Acetylation in Central Metabolism. mBio. 2017 Nov 28;8(6). PMCID: PMC5705920
45. Bretl DJ, Ladd KM, Atkinson SN, Müller S, Kirby JR. Suppressor mutations reveal an NtrC-like response regulator, NmpR, for modulation of Type-IV Pili-dependent motility in Myxococcus xanthus. PLoS Genet. 2018 Oct;14(10):e1007714. PMCID: PMC6211767
46. 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. The SrrAB two-component system regulates <i>Staphylococcus aureus</i> pathogenicity through redox sensitive cysteines. Proc Natl Acad Sci U S A. 2020 May 19;117(20):10989-10999. PMCID: PMC7245129
47. Pickrum AM, DeLeon O, Dirck A, Tessmer MH, Riegert MO, Biller JA, Ledeboer NA, Kirby JR, Frank DW. Achromobacter xylosoxidans Cellular Pathology Is Correlated with Activation of a Type III Secretion System. Infect Immun. 2020 Jun 22;88(7). PMCID: PMC7309624
48. Barron M, Atkinson SN, Kirby J, Kindel T. Sleeve gastrectomy prevents hypertension associated with unique shifts in the gut microbiome. Surg Endosc. 2021 Oct;35(10):5461-5467. PMCID: PMC8004532
49. Abais-Battad JM, Saravia FL, Lund H, Dasinger JH, Fehrenbach DJ, Alsheikh AJ, Zemaj J, Kirby JR, Mattson DL. Dietary influences on the Dahl SS rat gut microbiota and its effects on salt-sensitive hypertension and renal damage. Acta Physiol (Oxf). 2021 Aug;232(4):e13662. PMCID: PMC9835005
50. Riedl RA, Burnett CML, Pearson NA, Reho JJ, Mokadem M, Edwards RA, Kindel TL, Kirby JR, Grobe JL. Gut Microbiota Represent a Major Thermogenic Biomass. Function (Oxf). 2021;2(3):zqab019. PMCID: PMC8055641
51. Lozada-Fernández VV, deLeon O, Kellogg SL, Saravia FL, Hadiono MA, Atkinson SN, Grobe JL, Kirby JR. Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice. mSystems. 2022 Feb 22;7(1):e0023021. PMCID: PMC8788325
52. 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. Methods for the Comprehensive <i>in vivo</i> Analysis of Energy Flux, Fluid Homeostasis, Blood Pressure, and Ventilatory Function in Rodents. Front Physiol. 2022;13:855054. PMCID: PMC8914175
53. Fernando DG, Saravia FL, Atkinson SN, Barron M, Kirby JR, Kindel TL. A single, peri-operative antibiotic can persistently alter the post-operative gut microbiome after Roux-en-Y gastric bypass. Surg Endosc. 2023 Feb;37(2):1476-1486.
54. Fernando DG, Saravia FL, Atkinson SN, Barron M, Kirby JR, Kindel TL. Correction: A single, peri-operative antibiotic can persistently alter the post-operative gut microbiome after Roux-en-Y gastric bypass. Surg Endosc. 2023 Feb;37(2):1614.
55. Müller S, DeLeon O, Atkinson SN, Saravia F, Kellogg S, Shank EA, Kirby JR. Thiocillin contributes to the ecological fitness of <i>Bacillus cereus</i> ATCC 14579 during interspecies interactions with <i>Myxococcus xanthus</i>. Front Microbiol. 2023;14:1295262. PMCID: PMC10704990