Professor David Guttman

David S. Guttman



St. George (downtown)

CSB Appointment


Research Areas

Bioinformatics / Computational Biology, Evolutionary Biology, Genetics / Genomics, Microbiology, Molecular Biology, Pathology, Plant Biology, Systems Biology


Ph.D. Stony Brook University 1994
B.Sc. Washington University in St. Louis 1987

Titles and Honors

Canada Research Chair in Comparative Genomics

Primary Undergraduate Department

Cell & Systems Biology

Graduate Programs

Cell & Systems Biology
Genome Biology & Bioinformatics

Academic or Administrative Appointments

Director, Centre for the Analysis of Genome Evolution & Function

Research Description

The Guttman lab focuses on deciphering how bacteria adapt to, and manipulate their hosts. We study questions related to the evolution of bacterial host specificity and virulence, how pathogen populations and communities (i.e. microbiomes) adapt to the host environment over the course of disease development, and how secreted pathogen effectors evolve and interact with the immune system to determine the outcome of host-microbe interactions. I am particularly fascinated by the scope and impact of natural genetic diversity on these interactions. We use a multidisciplinary approach that harnesses evolutionary genetics, genomics, molecular biology, microbiology, plant biology, pathology, bioinformatics, and statistical genetics to gain insight into how pathogen evolution influences the outcome of host-pathogen interactions.

There are two big research directions in the Guttman lab. The first is focuses on understanding the basis of pathogen host specificity. We study how evolutionary processes drive the diversification of pathogenic bacterial strains, and identify host specificity factors and study how these factors evolve and interact with the host immune system to either promote pathogenesis or trigger the immune response. This project is focused on the plant pathogen Pseudomonas syringae, which is a highly diverse species complex consisting of many specialized strains that cause important diseases on nearly all major crops. We are particularly interested in how the type III secreted effector proteins of this species determine the course and fate of the disease process.

The second focus centers on human lung pathogens, with an emphasis on the opportunistic pathogen Pseudomonas aeruginosa, which causes numerous drug-resistant, hospital-associated infections, and is the leading cause of death in Cystic Fibrosis patients. These projects primarily focus on understanding how bacterial pathogens evolve over very short time-scales in response to changes in the clinical state or treatment of patients. We want to understand the source of genomic diversity in these populations, how this diversity enables clones to respond to selective pressures imposed by antimicrobial treatments or competition with other species in the microbiome, and novel ways to use this diversity to predict antimicrobial susceptibility and clinical outcomes.

Our work is leading to a better understanding of where the genetic potential for virulence originates, how this potential is maintained in bacterial populations, and how pathogen evolution impacts the fitness of their eukaryotic hosts.

Contact Information

Office Phone: 416-978-6865
Office: ESC4041
Lab: ESC4039
Lab Phone: 416-946-7121

Mailing Address

Department of Cell & Systems Biology
University of Toronto
25 Willcocks St.
Toronto, ON M5S 3B2

Visit lab’s website

Recent News

Life sciences students honour CSB Teaching Assistants with Teaching Excellence Award

Congratulations to this year’s TA Teaching Excellence Award winners, Ruby He, Mary-Elizabeth Raymond, Andrea-Aditi Taylor and Kathryn McTavish!…

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Benign bacteria can cooperatively cause virulence

“In science, we often focus on a single ‘wild type’ organism, but even a single species of bacteria has as much variation as the instruments in a…

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Cooperative virulence via the collective action of secreted pathogen effectors

Ruiz-Bedoya T, Wang PW, Desveaux D, Guttman DS
2023, Nature Microbiology, 10.1038/s41564-023-01328-8

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RecPD: A Recombination-aware measure of phylogenetic diversity

Coelho LP, Bundalovic-Torma C, Desveaux D, Guttman DS
2022, PLOS Computational Biology, 10.1371/journal.pcbi.1009899

Metaeffector interactions modulate the type III effector-triggered immunity load of Pseudomonas syringae

Dinesh-Kumar SP, Martel A, Laflamme B, Breit-McNally C, Wang P, Lonjon F, Desveaux D, Guttman DS
2022, PLOS Pathogens, 10.1371/journal.ppat.1010541

Predictive modeling of Pseudomonas syringae virulence on bean using gradient boosted decision trees

Baltrus DA, Almeida RND, Greenberg M, Bundalovic-Torma C, Martel A, Wang PW, Middleton MA, Chatterton S, Desveaux D, Guttman DS
2022, PLOS Pathogens, 10.1371/journal.ppat.1010716

ZAR1: Guardian of plant kinases

Breit-McNally C, Laflamme B, Singh RA, Desveaux D, Guttman DS
2022, Frontiers in Plant Science, 10.3389/fpls.2022.981684

The Arabidopsis effector-triggered immunity landscape is conserved in oilseed crops

Breit-McNally C, Desveaux D, Guttman DS
2022, Scientific Reports, 10.1038/s41598-022-10410-w

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The role of Psl in the failure to eradicate Pseudomonas aeruginosa biofilms in children with cystic fibrosis

Morris AJ, Jackson L, CW Yau Y, Reichhardt C, Beaudoin T, Uwumarenogie S, Guttman KM, Lynne Howell P, Parsek MR, Hoffman LR, Nguyen D, DiGiandomenico A, Guttman DS, Wozniak DJ, Waters VJ
2021, npj Biofilms and Microbiomes, 10.1038/s41522-021-00234-3

Comparative genomic insights into the epidemiology and virulence of plant pathogenic pseudomonads from Turkey

Dillon MM, Ruiz-Bedoya T, Bundalovic-Torma C, Guttman KM, Kwak H, Middleton MA, Wang PW, Horuz S, Aysan Y, Guttman DS
2021, Microbial Genomics, 10.1099/mgen.0.000585

Evaluation of digital dispense-assisted broth microdilution antimicrobial susceptibility testing for Pseudomonas aeruginosa isolates

Clark ST, Stapleton PJ, Wang PW, Yau YCW, Waters VJ, Hwang DM, Guttman DS
2021, Scientific Reports, 10.1038/s41598-021-88423-0

The Impact of Migration on the Gut Metagenome of South Asian Canadians

Copeland JK, Chao G, Vanderhout S, Acton E, Wang PW, Benchimol EI, El-Sohemy A, Croitoru K, Gommerman JL, Guttman DS
2021, Gut Microbes, 10.1080/19490976.2021.1902705

The ETS-ETI cycle: evolutionary processes and metapopulation dynamics driving the diversification of pathogen effectors and host immune factors

Martel A, Ruiz-Bedoya T, Breit-McNally C, Laflamme B, Desveaux D, Guttman DS
2021, Current Opinion in Plant Biology, 10.1016/j.pbi.2021.102011

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Pseudomonas aeruginosa Strain-sharing in Early Infection Among Children With Cystic Fibrosis

Stapleton PJ, Izydorcyzk C, Clark S, Blanchard A, Wang PW, Yau Y, Waters V, Guttman DS
2020, Clinical Infectious Diseases, 10.1093/cid/ciaa788

Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways

Khanolkar RA, Clark ST, Wang PW, Hwang DM, Yau YCW, Waters VJ, Guttman DS, Cleary DW
2020, mSystems, 10.1128/mSystems.00809-20

The Arabidopsis ZED1-Related Kinase Genomic Cluster Is Specifically Required for Effector-Triggered Immunity

Seto D, Laflamme B, Guttman DS, Desveaux D
2020, Plant Physiology, 10.1104/pp.20.00447

Immunodiversity of the Arabidopsis ZAR1 NLR Is Conveyed by Receptor-Like Cytoplasmic Kinase Sensors

Martel A, Laflamme B, Seto D, Bastedo DP, Dillon MM, Almeida RND, Guttman DS, Desveaux D
2020, Frontiers in Plant Science, 10.3389/fpls.2020.01290

Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide

Isabel S, Graña-Miraglia L, Gutierrez JM, Bundalovic-Torma C, Groves HE, Isabel MR, Eshaghi A, Patel SN, Gubbay JB, Poutanen T, Guttman DS, Poutanen SM
2020, Scientific Reports, 10.1038/s41598-020-70827-z

A High-Throughput, Seedling Screen for Plant Immunity

Martel A, Lo T, Desveaux D, Guttman DS
2020, Molecular Plant-Microbe Interactions®, 10.1094/MPMI-10-19-0295-TA

The pan-genome effector-triggered immunity landscape of a host-pathogen interaction

Laflamme B, Dillon MM, Martel A, Almeida RND, Desveaux D, Guttman DS
2020, Science, 10.1126/science.aax4079

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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
2019, PLoS pathogens, 15, e1007900, 31269090

Diversity and Evolution of Type III Secreted Effectors: A Case Study of Three Families.

Bastedo DP, Lo T, Laflamme B, Desveaux D, Guttman DS
2019, Current topics in microbiology and immunology, 31240408

Molecular Evolution of Type III Secreted Effector Proteins.

Dillon MM, Almeida RND, Laflamme B, Martel A, Weir BS, Desveaux D, Guttman DS
2019, Frontiers in plant science, 10, 418, 31024592

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
2019, Frontiers in microbiology, 10, 512, 30930884

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
2019, Scientific data, 6, 190025, 30806640

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
2019, G3 (Bethesda, Md.), 9, 535-547, 30573466

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
2019, NPJ biofilms and microbiomes, 5, 4, 30675371

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
2019, International journal of antimicrobial agents, 53, 620-628, 30664925

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
2019, Genome biology, 20, 3, 30606234

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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
2018, Microbiome, 6, 228, 30572961

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
2018, PLoS pathogens, 14, e1007453, 30532201

Population genomics of bacterial host adaptation.

Sheppard SK, Guttman DS, Fitzgerald JR
2018, Nature reviews. Genetics, 19, 549-565, 29973680

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
2018, Microbiome, 6, 144, 30121081

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
2018, Annals of the American Thoracic Society, 15, 827-836, 29911888

Diversification of Pseudomonas aeruginosa within the cystic fibrosis lung and its effects on antibiotic resistance.

Clark ST, Guttman DS, Hwang DM
2018, FEMS microbiology letters, 365, 29401362

A High-Sensitivity, Microtiter-Based Plate Assay for Plant Pattern-Triggered Immunity.

Mott GA, Desveaux D, Guttman DS
2018, Molecular plant-microbe interactions : MPMI, 31, 499-504, 29199888

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
2018, Nature, 553, 342-346, 29320478

Constructing and Analyzing Microbiome Networks in R.

Layeghifard M, Hwang DM, Guttman DS
2018, Methods in molecular biology (Clifton, N.J.), 1849, 243-266, 30298259

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interaction with biofilm enhances tobramycin resistance.

Beaudoin T, Yau YCW, Stapleton PJ, Gong Y, Wang PW, Guttman DS, Waters V
2017, NPJ biofilms and microbiomes, 3, 25, 29062489

Draft Genome Sequences of 10 Environmental Strains Isolated from Soils, Sediments, and Waters.

Shrestha SD, Guttman DS, Perron GG
2017, Genome announcements, 5, 28839021

Topo-phylogeny: Visualizing evolutionary relationships on a topographic landscape.

Waese J, Provart NJ, Guttman DS
2017, PloS one, 12, e0175895, 28459802

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
2017, Nature plants, 3, 17027, 28288096

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
2017, BMC medical ethics, 18, 1, 28077127

A Practical Guide to Quantitative Interactor Screening with Next-Generation Sequencing (QIS-Seq).

Gong Y, Desveaux D, Guttman DS, Lewis JD
2017, Methods in molecular biology (Clifton, N.J.), 1613, 1-20, 28849555

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Image-Based Quantification of Plant Immunity and Disease.

Laflamme B, Middleton M, Lo T, Desveaux D, Guttman DS
2016, Molecular plant-microbe interactions : MPMI, 29, 919-924, 27996374

Disentangling Interactions in the Microbiome: A Network Perspective.

Layeghifard M, Hwang DM, Guttman DS
2017, Trends in microbiology, 25, 217-228, 27916383

Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology.

Baltrus DA, McCann HC, Guttman DS
2017, Molecular plant pathology, 18, 152-168, 27798954

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
2016, Nature genetics, 48, 1413-1417, 27694960

Gene Slider: sequence logo interactive data-visualization for education and research.

Waese J, Pasha A, Wang TT, van Weringh A, Guttman DS, Provart NJ
2016, Bioinformatics (Oxford, England), 32, 3670-3672, 27522081

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.

Thakur S, Guttman DS
2016, BMC bioinformatics, 17, 260, 27363390

The HopF family of Pseudomonas syringae type III secreted effectors.

Lo T, Koulena N, Seto D, Guttman DS, Desveaux D
2017, Molecular plant pathology, 18, 457-468, 27061875

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
2016, Genome biology, 17, 98, 27160854

Phytopathogen Genome Announcement: Draft Genome Sequences of 62 Pseudomonas syringae Type and Pathotype Strains.

Thakur S, Weir BS, Guttman DS
2016, Molecular plant-microbe interactions : MPMI, 29, 243-6, 26883489

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
2016, European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, 35, 67-74, 26492874

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Elevated Temperature Differentially Influences Effector-Triggered Immunity Outputs in Arabidopsis.

Menna A, Nguyen D, Guttman DS, Desveaux D
2015, Frontiers in plant science, 6, 995, 26617631

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
2015, mBio, 6, e00981-15, 26330513

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
2015, Scientific reports, 5, 10932, 26047320

The human microbiome.

Coburn B, Guttman DS
2015, CMAJ : Canadian Medical Association journal = journal de l\'Association medicale canadienne, 187, 825, 25991836

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
2015, Scientific reports, 5, 10241, 25974282

Seasonal community succession of the phyllosphere microbiome.

Copeland JK, Yuan L, Layeghifard M, Wang PW, Guttman DS
2015, Molecular plant-microbe interactions : MPMI, 28, 274-85, 25679538

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Proteomics of effector-triggered immunity (ETI) in plants

Hurley B, Subramaniam R, Guttman DS, Desveaux D
2014, Virulence, 5, 25290905

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
2014, PloS one, 9, e116152, 25546415

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
2014, PloS one, 9, e114921, 25503437

Peptides and small molecules of the plant-pathogen apoplastic arena.

Mott GA, Middleton MA, Desveaux D, Guttman DS
2014, Frontiers in plant science, 5, 677, 25506352

Opinion: Conservation and stewardship of the human microbiome.

O\'Doherty KC, Neufeld JD, Brinkman FS, Gardner H, Guttman DS, Beiko RG
2014, Proceedings of the National Academy of Sciences of the United States of America, 111, 14312-3, 25294925

Microbial genome-enabled insights into plant-microorganism interactions.

Guttman DS, McHardy AC, Schulze-Lefert P
2014, Nature reviews. Genetics, 15, 797-813, 25266034

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
2014, Cell, 158, 288-299, 25036629

The rise of the undead: Pseudokinases as mediators of effector-triggered immunity

Lewis JD, Lo T, Bastedo P, Guttman DS, Desveaux D
2014, Plant signaling & behavior, 9, 24398910

Next-generation mapping of genetic mutations using bulk population sequencing.

Austin RS, Chatfield SP, Desveaux D, Guttman DS
2014, Methods in molecular biology (Clifton, N.J.), 1062, 301-15, 24057374

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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
2013, Proceedings of the National Academy of Sciences of the United States of America, 110, 18722-7, 24170858

Phytopathogen type III effectors as probes of biological systems

Lee AH, Middleton MA, Guttman DS, Desveaux D
2013, Microbial biotechnology, 6, 230-40, 23433088

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