John R. Kirby, PhD
Chair, Microbiology & Immunology; Walter Schroeder Professor in Microbiology and Immunology; Associate Director, Microbiome, Genomic Sciences and Precision Medicine Center; Associate Director, Center for Microbiome Research
- Computational Biology
- Gastrointestinal Microbiome
- Microbial Interactions
- Signal Transduction
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
- Associate Director, Center for Microbiome Research
- Associate Director, Microbiome, Genomic Sciences and Precision Medicine Center
- Chair, Department of Microbiology & Immunology
- Member, Finance Committee, Board of Trustees
- Bacterial Physiological Phenomena
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.
(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 05/06/2020
(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
(Bretl DJ, Ladd KM, Atkinson SN, Müller S, Kirby JR.) PLoS Genet. 2018 10;14(10):e1007714 PMID: 30346960 PMCID: PMC6211767 SCOPUS ID: 2-s2.0-85055910992 10/23/2018
(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 11 28;8(6) PMID: 29184018 PMCID: PMC5705920 SCOPUS ID: 2-s2.0-85039922037 12/01/2017
(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
(Kelly PH, Bahr SM, Serafim TD, Ajami NJ, Petrosino JF, Meneses C, Kirby JR, Valenzuela JG, Kamhawi S, Wilson ME.) mBio. 2017 01 17;8(1) PMID: 28096483 PMCID: PMC5241394 SCOPUS ID: 2-s2.0-85014830318 01/18/2017
(Müller S, Strack SN, Ryan SE, Shawgo M, Walling A, Harris S, Chambers C, Boddicker J, Kirby JR.) J Bacteriol. 2016 12 15;198(24):3335-3344 PMID: 27698086 PMCID: PMC5116937 SCOPUS ID: 2-s2.0-84996939200 10/05/2016
(Bretl DJ, Müller S, Ladd KM, Atkinson SN, Kirby JR.) Mol Microbiol. 2016 10;102(1):37-53 PMID: 27393239 SCOPUS ID: 2-s2.0-84988461449 07/10/2016
(Bretl DJ, Kirby JR.) J Mol Biol. 2016 09 25;428(19):3805-30 PMID: 27430596 SCOPUS ID: 2-s2.0-84986915805 07/20/2016
(Bahr SM, Weidemann BJ, Castro AN, Walsh JW, deLeon O, Burnett CM, Pearson NA, Murry DJ, Grobe JL, Kirby JR.) EBioMedicine. 2015 11;2(11):1725-34 PMID: 26870798 PMCID: PMC4740326 SCOPUS ID: 2-s2.0-84958879311 02/13/2016
(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:e652 PMID: 26440540 PMCID: PMC4930121 SCOPUS ID: 2-s2.0-84943422862 10/07/2015