John R. Kirby, PhD
Chair, Microbiology & Immunology; Walter Schroeder Professor in Microbiology and Immunology; Associate Director, Microbiome, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine; Associate Director, Center for Microbiome Research
Locations
- Microbiology & Immunology
BSB B2140
Contact Information
General Interests
Education
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
- 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
Educational Expertise
- Bacterial Physiological Phenomena
- Microbiology
- Microbiota
Research Interests
Microbiome
We are examining the role of xenobiotics for their capacity to disrupt the gut microbiota with deleterious consequences on host physiology and metabolism. Disease models used in the lab are a salt-sensitive rat model for hypertension, a mouse model of diet-induced obesity, and a mouse model of obesity induced by the second-generation antipsychotic risperidone. We perform physiological measurements related to each disease model, fecal material transfers to establish a causal link between the microbiota and disease, and 16S rDNA and metagenomic sequencing to analyze taxonomic and functional composition of the microbiota. Metagenomic analyses allow us to identify and test candidate probiotic strains of bacteria with specific metabolic features that influence the progression of disease. We have filed a patent (US 2020/0016124 A1) based on our work leading to reduction of weight gain and are in discussions to create a startup company.
Predator-Prey Interactions
The above work is a direct product of our understanding of bacterial interactions between Myxococcus xanthus and Bacillus subtilis as a model for microbial predator-prey interactions. Our primary goal is to assess the role of specialized metabolites produced by both the predator and the prey. Detailed molecular mechanisms for predator-prey interactions in vitro provide insights into gut-based systems in rodents and humans.
Publications
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(Barron M, Fernando DG, Atkinson SN, Kirby J, Kindel TL.) Journal of Surgical Research. September 2024;301:118-126 SCOPUS ID: 2-s2.0-85196756485 09/01/2024
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(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
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(Müller S, DeLeon O, Atkinson SN, Saravia F, Kellogg S, Shank EA, Kirby JR.) Front Microbiol. 2023;14:1295262 PMID: 38075900 PMCID: PMC10704990 12/11/2023
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(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 01/26/2022
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(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
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(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
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(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
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(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 05/04/2021
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(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
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(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
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(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
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(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