Jesse Shapiro

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Jesse Shapiro

Associate Professor, Department of Microbiology and Immunology

Email: jesse.shapiro@umontreal.ca
Phone: TBA

740 Dr Penfield Ave, Room 7006
Montréal, Québec, Canada, H3A 0G1


Jesse Shapiro did his undergrad in Biology at McGill, followed by an MSc in Integrative Bioscience at Oxford. He then completed a PhD in Computational and Systems Biology at MIT with Eric Alm, where he developed methods to detect signatures of natural selection, recombination, and speciation in bacterial genomes. He went on to a postdoc with Pardis Sabeti at the Broad Institute and Harvard University, where he studied the evolutionary genomics of Mycobacterium tuberculosis and Lassa virus. After seven years as Canada Research Chair in Microbial Evolutionary Genomics at Université de Montréal, he returned to McGill as an associate professor in the Department of Microbiology and Immunology and the Genome Centre. 

Research Interests

Jesse’s research uses genomics to understand the ecology and evolution of microbes, ranging from freshwater bacterioplankton to the human gut microbiome. His work has helped elucidate the origins of bacterial species, leading to a more unified species concept across domains of life, and has developed genome-wide association study (GWAS) methods tailored for bacteria. He is particularly interested in pathogen evolution, and their evolution within patients, and interactions with members of the resident  microbiome. His laboratory currently has projects on the ecology and evolution of toxic cyanobacterial blooms, cholera infections, and antimicrobial resistance, among others.

Recent Publications

  • N'Guessan, A, Kailasam, S, Mostefai, F, Poujol, R, Grenier, JC, Ismailova, N et al.. Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping and sequence analysis. iScience. 2023;26 (8):107394. doi: 10.1016/j.isci.2023.107394. PubMed PMID:37599818 PubMed Central PMC10433132.
  • Madi, N, Cato, ET, Sayeed, A, Islam, K, Khabir, IU, Bhuiyan, TR et al.. Phage predation and antibiotic exposure are inversely associated with disease severity and shape pathogen genetic diversity in cholera patients. bioRxiv. 2023; :. doi: 10.1101/2023.06.14.544933. PubMed PMID:37398242 PubMed Central PMC10312676.
  • Saber, MM, Donner, J, Levade, I, Acosta, N, Parkins, MD, Boyle, B et al.. Single nucleotide variants in Pseudomonas aeruginosa populations from sputum correlate with baseline lung function and predict disease progression in individuals with cystic fibrosis. Microb Genom. 2023;9 (4):. doi: 10.1099/mgen.0.000981. PubMed PMID:37052589 PubMed Central PMC10210962.
  • Naderi, S, Chen, PE, Murall, CL, Poujol, R, Kraemer, S, Pickering, BS et al.. Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis. Elife. 2023;12 :. doi: 10.7554/eLife.83685. PubMed PMID:37014792 PubMed Central PMC10072876.
  • Madi, N, Chen, D, Wolff, R, Shapiro, BJ, Garud, NR. Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome. Elife. 2023;12 :. doi: 10.7554/eLife.78530. PubMed PMID:36757364 PubMed Central PMC9977275.
  • Creasy-Marrazzo, A, Saber, MM, Kamat, M, Bailey, LS, Brinkley, L, Cato, E et al.. Genome-wide association studies reveal distinct genetic correlates and increased heritability of antimicrobial resistance in Vibrio cholerae under anaerobic conditions. Microb Genom. 2022;8 (12):. doi: 10.1099/mgen.0.000905. PubMed PMID:36748512 PubMed Central PMC9837564.
  • Douglas, GM, Kim, S, Langille, MGI, Shapiro, BJ. Efficient computation of contributional diversity metrics from microbiome data with FuncDiv. Bioinformatics. 2023;39 (1):. doi: 10.1093/bioinformatics/btac809. PubMed PMID:36519836 PubMed Central PMC9825779.
  • Jalili, F, Trigui, H, Maldonado, JFG, Dorner, S, Zamyadi, A, Shapiro, BJ et al.. Impact of Stagnation on the Diversity of Cyanobacteria in Drinking Water Treatment Plant Sludge. Toxins (Basel). 2022;14 (11):. doi: 10.3390/toxins14110749. PubMed PMID:36355999 PubMed Central PMC9697381.
  • Le, KTN, Maldonado, JFG, Goitom, E, Trigui, H, Terrat, Y, Nguyen, TL et al.. Shotgun Metagenomic Sequencing to Assess Cyanobacterial Community Composition following Coagulation of Cyanobacterial Blooms. Toxins (Basel). 2022;14 (10):. doi: 10.3390/toxins14100688. PubMed PMID:36287957 PubMed Central PMC9607033.
  • Leducq, JB, Sneddon, D, Santos, M, Condrain-Morel, D, Bourret, G, Martinez-Gomez, NC et al.. Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity. Genome Biol Evol. 2022;14 (8):. doi: 10.1093/gbe/evac123. PubMed PMID:35906926 PubMed Central PMC9364378.
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