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
- 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.
(Bretl DJ, Ladd KM, Atkinson SN, Müller S, Kirby JR.) PLoS Genet. 2018 10;14(10):e1007714.
(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).
(Riedl RA, Atkinson SN, Burnett CML, Grobe JL, Kirby JR.) Curr Hypertens Rep. 2017 Apr;19(4):27.
(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).
(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.
(Bretl DJ, Müller S, Ladd KM, Atkinson SN, Kirby JR.) Mol Microbiol. 2016 10;102(1):37-53.
(Bretl DJ, Kirby JR.) J Mol Biol. 2016 09 25;428(19):3805-30.
(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.
(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.
(Müller S, Strack SN, Ryan SE, Kearns DB, Kirby JR.) Appl Environ Microbiol. 2015 Jan;81(1):203-10.
(Müller S, Strack SN, Hoefler BC, Straight PD, Kearns DB, Kirby JR.) Appl Environ Microbiol. 2014 Sep;80(18):5603-10.