Jesse Shapiro

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

Website

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

• Tromas, N, Simon, DF, Fortin, N, Hernández-Zamora, M, Pereira, A, Mazza, A et al.. Metagenomic insights into cyanotoxin dynamics in a Mexican subtropical lake. Chemosphere. 2025;376 :144285. doi: 10.1016/j.chemosphere.2025.144285. PubMed PMID:40058228 .
• Xu, CCY, Fugère, V, Barbosa da Costa, N, Beisner, BE, Bell, G, Cristescu, ME et al.. Pre-exposure to stress reduces loss of community and genetic diversity following severe environmental disturbance. Curr Biol. 2025;35 (5):1061-1073.e4. doi: 10.1016/j.cub.2025.01.037. PubMed PMID:39933522 .
• Naderi, S, Sagan, SM, Shapiro, BJ. Within-host genetic diversity of SARS-CoV-2 across animal species. Virus Evol. 2025;11 (1):veae117. doi: 10.1093/ve/veae117. PubMed PMID:39830312 PubMed Central PMC11739616.
• Qin, C, Lypaczewski, P, Sayeed, A, Cuénod, AC, Brinkley, L, Creasy-Marrazzo, A et al.. Vibrio cholerae lineage and pangenome diversity varies geographically across Bangladesh over one year. bioRxiv. 2024; :. doi: 10.1101/2024.11.12.623281. PubMed PMID:39605465 PubMed Central PMC11601304.
• Gill, EE, Jia, B, Murall, CL, Poujol, R, Anwar, MZ, John, NS et al.. The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology. Microb Genom. 2024;10 (10):. doi: 10.1099/mgen.0.001293. PubMed PMID:39401061 PubMed Central PMC11472881.
• Jayme, G, Liu, JL, Galvez, JH, Reiling, SJ, Celikkol, S, N'Guessan, A et al.. Combining Short- and Long-Read Sequencing Technologies to Identify SARS-CoV-2 Variants in Wastewater. Viruses. 2024;16 (9):. doi: 10.3390/v16091495. PubMed PMID:39339971 PubMed Central PMC11437403.
• Derrick, E, Shapiro, BJ. One Health: Urban birds peck up resistant pathogens. Curr Biol. 2024;34 (17):R829-R831. doi: 10.1016/j.cub.2024.07.075. PubMed PMID:39255768 .
• Lypaczewski, P, Chac, D, Dunmire, CN, Tandoc, KM, Chowdhury, F, Khan, AI et al.. Vibrio cholerae O1 experiences mild bottlenecks through the gastrointestinal tract in some but not all cholera patients. Microbiol Spectr. 2024;12 (8):e0078524. doi: 10.1128/spectrum.00785-24. PubMed PMID:38916318 PubMed Central PMC11302224.
• Sutcliffe, SG, Kraemer, SA, Ellmen, I, Knapp, JJ, Overton, AK, Nash, D et al.. Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data. Microb Genom. 2024;10 (5):. doi: 10.1099/mgen.0.001249. PubMed PMID:38785221 PubMed Central PMC11165662.
• Gill, EE, Jia, B, Murall, CL, Poujol, R, Anwar, MZ, John, NS et al.. The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology. ArXiv. 2024; :. . PubMed PMID:38764594 PubMed Central PMC11100916.