David Guttman

faculty_img Academic Title: Professor

Campus: St. George

CSB Appointment: Full

Primary Undergraduate Department:
Cell & Systems Biology

Graduate Programs:
Cell & Systems Biology
Genome Biology & Bioinformatics

Titles and Honors:
Canada Research Chair in Comparative Genomics

Academic or Administrative Appointments:
Associate Chair for Research
Director, Centre for the Analysis of Genome Evolution & Function

Education:
Ph.D. Stony Brook University 1994
B.Sc. Washington University in St. Louis 1987
Mailing Address
Department of Cell & Systems Biology
University of Toronto
25 Willcocks St.
Toronto, ON M5S 3B2
Canada
Contact Information
Office phone: 416-978-6865
Office: ESC 4041
Lab: ESC 4039
Lab phone: 416-946-7121
Email: david.guttman@utoronto.ca
URL: http://guttman.csb.utoronto.ca/
Research Areas
Bioinformatics & Computational Biology
Comparative Genomics
Evolutionary Biology
Functional Genomics
Genetics
Microbiology
Pathology
Plant Biology
Research

The Guttman lab has two major foci. First, we are studying the evolution of host specificity and virulence in pathogenic bacteria. We are specifically interested in identifying the genetic determinants of host specificity, and determining what factors determine if a particular bacterial-host interaction is benign or results in disease. Our work will lead to a better understanding of where the genetic potential for virulence originates and how is it maintained in bacterial populations. Most of this work is done with the agriculturally important plant pathogen Pseudomonas syringae and the model plant Arabidopsis thaliana. Our second focus is on the structure, dynamics, and function of bacterial communities (microbiomes) associated with both humans and plants. We are specifically interested in understanding how polymicrobial communities influence the expression and course of disease. Microbiomes have been shown to dramatically influence immune development and disease resistance and progression. Most of this work is focused on cystic fibrosis, and plant resistance, although we also study a number of other human pathologies such as inflammatory bowel disease. We use a wide range of comparative, evolutionary and functional genomic approaches in the group. We have a particularly strong emphasis on using evolutionary and bioinformatic approaches to generate hypotheses that can then be functionally validated through traditional molecular and biochemical assays.

Selected Publications

2019

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Perturbations of the ZED1 pseudokinase activate plant immunity..Bastedo DP, Khan M, Martel A, Seto D, Kireeva I, Zhang J, Masud W, Millar D, Lee JY, Lee AH, Gong Y, Santos-Severino A, Guttman DS, Desveaux D. PLoS Pathog. 2019 Jul; 15(7):e1007900
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Diversity and Evolution of Type III Secreted Effectors: A Case Study of Three Families..Bastedo DP, Lo T, Laflamme B, Desveaux D, Guttman DS. Curr. Top. Microbiol. Immunol. 2019 Jun 26; ():
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Molecular Evolution of Type III Secreted Effector Proteins..Dillon MM, Almeida RND, Laflamme B, Martel A, Weir BS, Desveaux D, Guttman DS. Front Plant Sci 2019; 10():418
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Mycobiome Sequencing and Analysis Applied to Fungal Community Profiling of the Lower Respiratory Tract During Fungal Pathogenesis..McTaggart LR, Copeland JK, Surendra A, Wang PW, Husain S, Coburn B, Guttman DS, Kus JV. Front Microbiol 2019; 10():512
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Map of physical interactions between extracellular domains of Arabidopsis leucine-rich repeat receptor kinases..Mott GA, Smakowska-Luzan E, Pasha A, Parys K, Howton TC, Neuhold J, Lehner A, Grünwald K, Stolt-Bergner P, Provart NJ, Mukhtar MS, Desveaux D, Guttman DS, Belkhadir Y. Sci Data 2019 02 26; 6():190025
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Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations..Layeghifard M, Li H, Wang PW, Donaldson SL, Coburn B, Clark ST, Caballero JD, Zhang Y, Tullis DE, Yau YCW, Waters V, Hwang DM, Guttman DS. NPJ Biofilms Microbiomes 2019; 5():4
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Penicillin-binding protein 3 is a common adaptive target among Pseudomonas aeruginosa isolates from adult cystic fibrosis patients treated with β-lactams..Clark ST, Sinha U, Zhang Y, Wang PW, Donaldson SL, Coburn B, Waters VJ, Yau YCW, Tullis DE, Guttman DS, Hwang DM. Int. J. Antimicrob. Agents 2019 May; 53(5):620-628
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Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex..Dillon MM, Thakur S, Almeida RND, Wang PW, Weir BS, Guttman DS. Genome Biol. 2019 01 03; 20(1):3
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Identifying Type III Secreted Effector Function via a Yeast Genomic Screen..Lee AH, Bastedo DP, Youn JY, Lo T, Middleton MA, Kireeva I, Lee JY, Sharifpoor S, Baryshnikova A, Zhang J, Wang PW, Peisajovich SG, Constanzo M, Andrews BJ, Boone CM, Desveaux D, Guttman DS. G3 (Bethesda) 2019 02 07; 9(2):535-547
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2018

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Design and application of a novel two-amplicon approach for defining eukaryotic microbiota..Popovic A, Bourdon C, Wang PW, Guttman DS, Voskuijl W, Grigg ME, Bandsma RHJ, Parkinson J. Microbiome 2018 12 20; 6(1):228
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A genome-wide association analysis reveals a potential role for recombination in the evolution of antimicrobial resistance in Burkholderia multivorans..Diaz Caballero J, Clark ST, Wang PW, Donaldson SL, Coburn B, Tullis DE, Yau YCW, Waters VJ, Hwang DM, Guttman DS. PLoS Pathog. 2018 12; 14(12):e1007453
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Constructing and Analyzing Microbiome Networks in R..Layeghifard M, Hwang DM, Guttman DS. Methods Mol. Biol. 2018; 1849():243-266
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Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies..Fitzpatrick CR, Lu-Irving P, Copeland J, Guttman DS, Wang PW, Baltrus DA, Dlugosch KM, Johnson MTJ. Microbiome 2018 08 18; 6(1):144
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Population genomics of bacterial host adaptation..Sheppard SK, Guttman DS, Fitzgerald JR. Nat. Rev. Genet. 2018 09; 19(9):549-565
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Epidemiology of Clonal Pseudomonas aeruginosa Infection in a Canadian Cystic Fibrosis Population..Middleton MA, Layeghifard M, Klingel M, Stanojevic S, Yau YCW, Zlosnik JEA, Coriati A, Ratjen FA, Tullis ED, Stephenson A, Wilcox P, Freitag A, Chilvers M, McKinney M, Lavoie A, Wang PW, Guttman DS, Waters VJ. Ann Am Thorac Soc 2018 07; 15(7):827-836
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Diversification of Pseudomonas aeruginosa within the cystic fibrosis lung and its effects on antibiotic resistance..Clark ST, Guttman DS, Hwang DM. FEMS Microbiol. Lett. 2018 03 01; 365(6):
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An extracellular network of Arabidopsis leucine-rich repeat receptor kinases..Smakowska-Luzan E, Mott GA, Parys K, Stegmann M, Howton TC, Layeghifard M, Neuhold J, Lehner A, Kong J, Grünwald K, Weinberger N, Satbhai SB, Mayer D, Busch W, Madalinski M, Stolt-Bergner P, Provart NJ, Mukhtar MS, Zipfel C, Desveaux D, Guttman DS, Belkhadir Y. Nature 2018 01 18; 553(7688):342-346
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A High-Sensitivity, Microtiter-Based Plate Assay for Plant Pattern-Triggered Immunity..Mott GA, Desveaux D, Guttman DS. Mol. Plant Microbe Interact. 2018 05; 31(5):499-504
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2017

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interaction with biofilm enhances tobramycin resistance..Beaudoin T, Yau YCW, Stapleton PJ, Gong Y, Wang PW, Guttman DS, Waters V. NPJ Biofilms Microbiomes 2017; 3():25
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A Practical Guide to Quantitative Interactor Screening with Next-Generation Sequencing (QIS-Seq)..Gong Y, Desveaux D, Guttman DS, Lewis JD. Methods Mol. Biol. 2017; 1613():1-20
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Draft Genome Sequences of 10 Environmental Strains Isolated from Soils, Sediments, and Waters..Shrestha SD, Guttman DS, Perron GG. Genome Announc 2017 Aug 24; 5(34):
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Topo-phylogeny: Visualizing evolutionary relationships on a topographic landscape..Waese J, Provart NJ, Guttman DS. PLoS ONE 2017; 12(5):e0175895
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Expanded type III effector recognition by the ZAR1 NLR protein using ZED1-related kinases..Seto D, Koulena N, Lo T, Menna A, Guttman DS, Desveaux D. Nat Plants 2017 03 13; 3():17027
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Navigating social and ethical challenges of biobanking for human microbiome research..Chuong KH, Hwang DM, Tullis DE, Waters VJ, Yau YC, Guttman DS, O\'Doherty KC. BMC Med Ethics 2017 01 11; 18(1):1
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Disentangling Interactions in the Microbiome: A Network Perspective..Layeghifard M, Hwang DM, Guttman DS. Trends Microbiol. 2017 03; 25(3):217-228
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Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology..Baltrus DA, McCann HC, Guttman DS. Mol. Plant Pathol. 2017 01; 18(1):152-168
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The HopF family of Pseudomonas syringae type III secreted effectors..Lo T, Koulena N, Seto D, Guttman DS, Desveaux D. Mol. Plant Pathol. 2017 04; 18(3):457-468
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2016

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Image-Based Quantification of Plant Immunity and Disease..Laflamme B, Middleton M, Lo T, Desveaux D, Guttman DS. Mol. Plant Microbe Interact. 2016 12; 29(12):919-924
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Association of host genome with intestinal microbial composition in a large healthy cohort..Turpin W, Espin-Garcia O, Xu W, Silverberg MS, Kevans D, Smith MI, Guttman DS, Griffiths A, Panaccione R, Otley A, Xu L, Shestopaloff K, Moreno-Hagelsieb G, , Paterson AD, Croitoru K. Nat. Genet. 2016 11; 48(11):1413-1417
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Gene Slider: sequence logo interactive data-visualization for education and research..Waese J, Pasha A, Wang TT, van Weringh A, Guttman DS, Provart NJ. Bioinformatics 2016 12 01; 32(23):3670-3672
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A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies..Thakur S, Guttman DS. BMC Bioinformatics 2016 Jun 30; 17(1):260
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Genomic screens identify a new phytobacterial microbe-associated molecular pattern and the cognate Arabidopsis receptor-like kinase that mediates its immune elicitation..Mott GA, Thakur S, Smakowska E, Wang PW, Belkhadir Y, Desveaux D, Guttman DS. Genome Biol. 2016 May 09; 17():98
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Phytopathogen Genome Announcement: Draft Genome Sequences of 62 Pseudomonas syringae Type and Pathotype Strains..Thakur S, Weir BS, Guttman DS. Mol. Plant Microbe Interact. 2016 Apr; 29(4):243-6
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Chronic infection phenotypes of Pseudomonas aeruginosa are associated with failure of eradication in children with cystic fibrosis..Vidya P, Smith L, Beaudoin T, Yau YC, Clark S, Coburn B, Guttman DS, Hwang DM, Waters V. Eur. J. Clin. Microbiol. Infect. Dis. 2016 Jan; 35(1):67-74
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2015

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Elevated Temperature Differentially Influences Effector-Triggered Immunity Outputs in Arabidopsis..Menna A, Nguyen D, Guttman DS, Desveaux D. Front Plant Sci 2015; 6():995
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Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung..Diaz Caballero J, Clark ST, Coburn B, Zhang Y, Wang PW, Donaldson SL, Tullis DE, Yau YC, Waters VJ, Hwang DM, Guttman DS. MBio 2015 Sep 01; 6(5):e00981-15
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Phenotypic diversity within a Pseudomonas aeruginosa population infecting an adult with cystic fibrosis..Clark ST, Diaz Caballero J, Cheang M, Coburn B, Wang PW, Donaldson SL, Zhang Y, Liu M, Keshavjee S, Yau YC, Waters VJ, Elizabeth Tullis D, Guttman DS, Hwang DM. Sci Rep 2015 Jun 05; 5():10932
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The human microbiome..Coburn B, Guttman DS. CMAJ 2015 Aug 11; 187(11):825
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Lung microbiota across age and disease stage in cystic fibrosis..Coburn B, Wang PW, Diaz Caballero J, Clark ST, Brahma V, Donaldson S, Zhang Y, Surendra A, Gong Y, Elizabeth Tullis D, Yau YC, Waters VJ, Hwang DM, Guttman DS. Sci Rep 2015 May 14; 5():10241
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Seasonal community succession of the phyllosphere microbiome..Copeland JK, Yuan L, Layeghifard M, Wang PW, Guttman DS. Mol. Plant Microbe Interact. 2015 Mar; 28(3):274-85
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2014

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Immunomodulation by the Pseudomonas syringae HopZ type III effector family in Arabidopsis..Lewis JD, Wilton M, Mott GA, Lu W, Hassan JA, Guttman DS, Desveaux D. PLoS ONE 2014; 9(12):e116152
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Proteomics of effector-triggered immunity (ETI) in plants..Hurley B, Subramaniam R, Guttman DS, Desveaux D. Virulence 2014; 5(7):752-60
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Peptides and small molecules of the plant-pathogen apoplastic arena..Mott GA, Middleton MA, Desveaux D, Guttman DS. Front Plant Sci 2014; 5():677
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The Pseudomonas syringae type III effector HopF2 suppresses Arabidopsis stomatal immunity..Hurley B, Lee D, Mott A, Wilton M, Liu J, Liu YC, Angers S, Coaker G, Guttman DS, Desveaux D. PLoS ONE 2014; 9(12):e114921
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Opinion: Conservation and stewardship of the human microbiome..O\'Doherty KC, Neufeld JD, Brinkman FS, Gardner H, Guttman DS, Beiko RG. Proc. Natl. Acad. Sci. U.S.A. 2014 Oct 07; 111(40):14312-3
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Proteomics of effector-triggered immunity (ETI) in plants.Hurley B, Subramaniam R, Guttman DS, Desveaux D. Virulence 2014 Sep;5(7)
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Microbial genome-enabled insights into plant-microorganism interactions..Guttman DS, McHardy AC, Schulze-Lefert P. Nat. Rev. Genet. 2014 Dec; 15(12):797-813
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Gut microbial metabolism drives transformation of MSH2-deficient colon epithelial cells..Belcheva A, Irrazabal T, Robertson SJ, Streutker C, Maughan H, Rubino S, Moriyama EH, Copeland JK, Surendra A, Kumar S, Green B, Geddes K, Pezo RC, Navarre WW, Milosevic M, Wilson BC, Girardin SE, Wolever TMS, Edelmann W, Guttman DS, Philpott DJ, Martin A. Cell 2014 Jul 17; 158(2):288-299
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The rise of the undead: pseudokinases as mediators of effector-triggered immunity..Lewis JD, Lo T, Bastedo P, Guttman DS, Desveaux D. Plant Signal Behav 2014; 9(1):e27563
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Next-generation mapping of genetic mutations using bulk population sequencing..Austin RS, Chatfield SP, Desveaux D, Guttman DS. Methods Mol. Biol. 2014; 1062():301-15
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2013

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The Arabidopsis ZED1 pseudokinase is required for ZAR1-mediated immunity induced by the Pseudomonas syringae type III effector HopZ1a..Lewis JD, Lee AH, Hassan JA, Wan J, Hurley B, Jhingree JR, Wang PW, Lo T, Youn JY, Guttman DS, Desveaux D. Proc. Natl. Acad. Sci. U.S.A. 2013 Nov 12; 110(46):18722-7
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Phytopathogen type III effectors as probes of biological systems..Lee AH, Middleton MA, Guttman DS, Desveaux D. Microb Biotechnol 2013 May; 6(3):230-40
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