
Jesse Shapiro
Assistant Professor,McGill University
Department of Microbiology & Immunology
E-mail: jesse.shapiro@umontreal.ca
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EducationPostdoc, 2012, Harvard (Organismic & Evolutionary Biology and The Center for Communicable Disease Dynamics)
PhD, 2010, MIT (Computational & Systems Biology)
MSc, 2004, Oxford (Integrative Bioscience)
BSc, 2003, McGill (Biology) ResearchMost of the genetic and metabolic diversity that exists on earth – and has existed for billions of years – is microbial. Arguably more impressive than the sheer quantity of microbial diversity is its dynamic nature: microbes are constantly evolving and adapting. Our ongoing research tracks evolving microbial populations in real time, using whole-genome and whole-community DNA sequencing to understand their evolution and predict how they adapt to changing environments. For example: (1) freshwaters subject to seasonal cyanobacterial blooms, (2) the human gut, focusing on cholera infections, (3) viral hemorrhagic fevers (Lassa and Ebola), (4) evolution of antibiotic resistance in Mycobacterium tuberculosis.QCBS studentsNaíla Barbosa da CostaPh.D. Previous students (since 2009)Nicolas TROMASPostdoctoral fellow Geneviève DuboisM.Sc. Kiri SternM.Sc. Relevant QCBS research themesExamples of species studiedVibrio cholerae Streptococcus pyogenes Mycobacterium tuberculosis Saccharomyces cerevisiae Trypanosoma brucei Publications50- Translational activity is uncoupled from nucleic acid content in bacterial cells of the human gut microbiota Taguer M , Shapiro B J , Maurice C F , 2021 Gut Microbes (Date Added: 2021-04-11) 49- Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study Levade I , Saber M M , Midani F S , Chowdhury F , Khan A I , Begum Y A , Ryan E T , David L A , Calderwood S B , Harris J B , LaRocque R C , Qadri F , Shapiro B J , Weil A A , 2021 The Journal of infectious diseases (Date Added: 2021-03-19) 48- Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France Seguin-Orlando A , Donat R , Der Sarkissian C , Southon J , Thèves C , Manen C , Tchérémissinoff Y , Crubézy E , Shapiro B , Deleuze J , Dalén L , Guilaine J , Orlando L , 2021 Current Biology (Date Added: 2021-02-07) 47- Can Cyanobacterial Diversity in the Source Predict the Diversity in Sludge and the Risk of Toxin Release in a Drinking Water Treatment Plant? Jalili F , Trigui H , Guerra Maldonado J F , Dorner S , Zamyadi A , Shapiro B J , Terrat Y , Fortin N , Sauvé S , Prévost M , 2021 Toxins (Date Added: 2021-01-27) 46- Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics Spielman S J , 2020 Molecular Biology and Evolution (Date Added: 2020-12-24) 45- Does diversity beget diversity in microbiomes? Madi N , Vos M , Murall C L , Legendre P , Shapiro B J , 2020 eLife (Date Added: 2020-12-22) 44- A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities Kraemer S A , Barbosa da Costa N , Shapiro B J , Fradette M , Huot Y , Walsh D A , 2020 ISME Journal (Date Added: 2020-08-17) 43- Two cases of type-a haemophilus influenzae meningitis within the same week in the same hospital are phylogenetically unrelated but recently exchanged capsule genes Terrat Y , Farnaes L , Bradley J , Tromas N , Shapiro B J , 2020 Microbial Genomics (Date Added: 2020-05-30) 42- Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes Saber M M , Shapiro B J , 2020 Microbial genomics (Date Added: 2020-04-10) 41- Community rescue in experimental phytoplankton communities facing severe herbicide pollution Fugère, V, Hébert, M-P, da Costa, NB, Xu, CCY, Barrett, RDH, Beisner, BE, Bell, G, Fussmann, GF, Shapiro, BJ, Yargeau, V, Gonzalez, A 2020 Nature Ecology and Evolution (Date Added: 2020-03-24) 40- The evolution of realized niches within freshwater Synechococcus Tromas N , Taranu Z E , Castelli M , Pimentel J S M , Pereira D A , Marcoz R , Shapiro B J , Giani A , 2020 Environmental Microbiology (Date Added: 2020-02-24) 39- Functional Diversity: An Epistemic Roadmap Malaterre C , Dussault A C , Rousseau-Mermans S , Barker G , Beisner B E , Bouchard F , Desjardins E , Handa I T , Kembel S W , Lajoie G , Maris V , Munson A D , Odenbaugh J , Poisot T , Shapiro B J , Suttle C A , 2019 BioScience (Date Added: 2019-10-25) 38- Coherence of Microcystis species revealed through population genomics Pérez-Carrascal O M , Terrat Y , Giani A , Fortin N , Greer C W , Tromas N , Shapiro B J , 2019 ISME Journal (Date Added: 2019-08-08) 37- Microbial evolutionary medicine: from theory to clinical practice Andersen S B , Shapiro B J , Vandenbroucke-Grauls C , de Vos M G J , 2019 The Lancet Infectious Diseases (Date Added: 2019-08-03) 36- Reuniting ecology and evolution Shapiro B J , 2018 Environmental Microbiology Reports (Date Added: 2018-12-26) 35- Niche separation increases with genetic distance among bloom-forming cyanobacteria Tromas N , Taranu Z E , Martin B D , Willis A , Fortin N , Greer C W , Shapiro B J , 2018 Frontiers in Microbiology (Date Added: 2018-04-04) 34- The Inuit gut microbiome is dynamic over time and shaped by traditional foods Dubois G , Girard C , Lapointe F , Shapiro B J , 2017 Microbiome (Date Added: 2018-08-08) 33- The population genetics of pangenomes Shapiro B J , 2017 Nature Microbiology (Date Added: 2017-12-06) 32- Cooking and co-ingested polyphenols reduce in vitro methylmercury bioaccessibility from fish and may alter exposure in humans Girard, C, Charette, T, Leclerc M , Shapiro, J, Amyot, M 2017 Science of the Total Environment (Date Added: 2017-11-10) 31- Mitochondrial recombination and introgression during speciation by hybridization Leducq J , Henault M , Charron G , Nielly-Thibault L , Terrat Y , Fiumera H L , Shapiro B J , Landry C R , 2017 Molecular Biology and Evolution (Date Added: 2017-09-09) 30- Gut Microbiome of the Canadian Arctic Inuit Girard, C, Tromas, N, Amyot, M, Shapiro, BJ 2017 MSphere (Date Added: 2017-08-16) 29- Characterising and predicting cyanobacterial blooms in an 8-year amplicon sequencing time course Tromas N , Fortin N , Bedrani L , Terrat Y , Cardoso P , Bird D , Greer C W , Shapiro B J , 2017 ISME Journal (Date Added: 2017-08-03) 28- AD-LIBS: Inferring ancestry across hybrid genomes using low-coverage sequence data Schaefer N K , Shapiro B , Green R E , 2017 BMC Bioinformatics (Date Added: 2017-04-20) 27- The evolutionary and phylogeographic history of woolly mammoths: A comprehensive mitogenomic analysis Chang D , Knapp M , Enk J , Lippold S , Kircher M , Lister A , MacPhee R D E , Widga C , Czechowski P , Sommer R , Hodges E , Stümpel N , Barnes I , Dalén L , Derevianko A , Germonpré M , Hillebrand-Voiculescu A , Constantin S , Kuznetsova T , Mol D , Rathgeber T , Rosendahl W , Tikhonov A N , Willerslev E , Hannon G , Lalueza-Fox C , Joger U , Poinar H , Hofreiter M , Shapiro B , 2017 Scientific Reports (Date Added: 2017-04-05) 26- Origins of pandemic Vibrio cholerae from environmental gene pools Shapiro, BJ, Levade, I, Kovacikova, G, Taylor, RK, Almagro-Moreno, S 2016 Nature Microbiology (Date Added: 2017-02-14) 25- Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps Bao, Y-J, Shapiro, BJ, Lee, SW, Ploplis, VA, Castellino, FJ 2016 Scientific Reports (Date Added: 2017-02-14) 24- How clonal are bacteria over time? Shapiro, BJ 2016 Current Opinion in Microbiology (Date Added: 2017-02-14) 23- What Is Speciation? Shapiro, BJ, Leducq, J-B, Mallet, J 2016 PLoS Genetics (Date Added: 2017-02-14) 22- Environment and host species shape the skin microbiome of captive neotropical bats Lemieux-Labonte, V, Tromas, N, Shapiro, BJ, Lapointe, F-J 2016 PeerJ (Date Added: 2016-11-28) 21- The advent of genome-wide association studies for bacteria Chen, PE, Shapiro, BJ 2015 Current Opinion in Microbiology (Date Added: 2017-02-15) 20- Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus Andersen, KG, Shapiro, BJ, Matranga, CB, Sealfon, R, Lin, AE, Moses, LM, Folarin, OA, Goba, A, Odia, I, Ehiane, PE, Momoh, M, England, EM, Winnicki, S, Branco, LM, Gire, SK, Phelan, E, Tariyal, R, Tewhey, R, Omoniwa, O, Fullah, M, Fonnie, R, Fonnie, M, Kanneh, L, Jalloh, S, Gbakie, M, Saffa, S, Karbo, K, Gladden, AD, Qu, J, Stremlau, M, Nekoui, M, Finucane, HK, Tabrizi, S, Vitti, JJ, Birren, B, Fitzgerald, M, McCowan, C, Ireland, A, Berlin, AM, Bochicchio, J, Tazon-Vega, B, Lennon, NJ, Ryan, EM, Bjornson, Z, Milner, DA, Lukens, AK, Broodie, N, Rowland, M, Heinrich, M, Akdag, M, Schieffelin, JS, Levy, D, Akpan, H, Bausch, DG, Rubins, K, McCormick, JB, Lander, ES, Günther, S, Hensley, L, Okogbenin, S, Schaffner, SF, Okokhere, PO, Khan, SH, Grant, DS, Akpede, GO, Asogun, DA, Gnirke, A, Levin, JZ, Happi, CT, Garry, RF, Sabeti, PC 2015 Cell (Date Added: 2017-02-15) 19- Microbial speciation Shapiro, BJ, Polz, MF 2015 Cold Spring Harbor Perspectives in Biology (Date Added: 2017-02-15) 18- What is speciation? Studying closely related natural bacterial populations is leading to a more unified concept of speciation across the tree of life Shapiro, BJ 2015 Microbe (Date Added: 2017-02-15) 17- A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens Farhat, MR, Shapiro, BJ, Sheppard, SK, Colijn, C, Murray, M 2014 Genome Medicine (Date Added: 2017-02-15) 16- Ordering microbial diversity into ecologically and genetically cohesive units Shapiro, BJ, Polz, MF 2014 Trends in Microbiology (Date Added: 2017-02-15) 15- Evolutionary consequences of intra-patient phage predation on microbial populations Seed, KD, Yen, M, Shapiro, BJ, Hilaire, IJ, Charles, RC, Teng, JE, Ivers, LC, Boncy, J, Harris, JB, Camilli, A 2014 eLife (Date Added: 2017-02-15) 14- Reproducibility of Vibrionaceae population structure in coastal bacterioplankton Szabo, G, Preheim, SP, Kauffman, KM, David, LA, Shapiro, J, Alm, EJ, Polz, MF 2013 The ISME Journal (Date Added: 2017-07-31) 13- Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis Farhat, MR, Shapiro, BJ, Kieser, KJ, Sultana, R, Jacobson, KR, Victor, TC, Warren, RM, Streicher, EM, Calver, A, Sloutsky, A, Kaur, D, Posey, JE, Plikaytis, B, Oggioni, MR, Gardy, JL, Johnston, JC, Rodrigues, M, Tang, PKC, Kato-Maeda, M, Borowsky, ML, Muddukrishna, B, Kreiswirth, BN, Kurepina, N, Galagan, J, Gagneux, S, Birren, B, Rubin, EJ, Lander, ES, Sabeti, PC, Murray, M 2013 Nature Genetics (Date Added: 2017-02-15) 12- Sympatric Speciation: When Is It Possible in Bacteria? Friedman, J, Alm, EJ, Shapiro, BJ 2013 PLoS ONE (Date Added: 2017-02-15) 11- Population genomics of early events in the ecological differentiation of bacteria Shapiro, BJ, Friedman, J, Cordero, OX, Preheim, SP, Timberlake, SC, Szabó, G, Polz, MF, Alm, EJ 2012 Science (Date Added: 2017-02-15) 10- The slow:fast substitution ratio reveals changing patterns of natural selection in γ-proteobacterial genomes Shapiro, BJ, Alm, E 2009 ISME Journal (Date Added: 2017-02-15) 9- Looking for Darwin's footprints in the microbial world Shapiro, BJ, David, LA, Friedman, J, Alm, EJ 2009 Trends in Microbiology (Date Added: 2017-02-15) 8- Comparing patterns of natural selection across species using selective signatures Shapiro, BJ, Alm, EJ 2008 PLoS Genetics (Date Added: 2017-02-15) 7- Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients Kapoor, A, Shapiro, B, Shafer, RW, Shulman, N, Rhee, S-Y, Delwart, EL 2008 Retrovirology (Date Added: 2017-02-15) 6- Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: Subtype G is a circulating recombinant form Abecasis, AB, Lemey, P, Vidal, N, De Oliveira, T, Peeters, M, Camacho, R, Shapiro, B, Rambaut, A, Vandamme, A-M 2007 Journal of Virology (Date Added: 2017-02-15) 5- An experimental test of the causes of small-scale phenotypic differentiation in a population of great tits Shapiro, BJ, Garant, D, Wilkin, TA, Sheldon, BC 2006 Journal of Evolutionary Biology (Date Added: 2017-02-16) 4- An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae Lesage, G, Shapiro, J, Specht, CA, Sdicu, A-M, Menard, P, Hussein, S, Tong, AHY, Boone, C, Bussey, H 2005 BMC Genetics (Date Added: 2017-02-16) 3- VSG switching in Trypanosoma brucei: antigenic variation analysed using RNAi in the absence of immune selection Aitcheson, N, Talbot, S, Shapiro, J, Hughes, K, Adkin, C, Butt, T, Sheader, K, Rudenko, G 2005 Molecular Microbiology (Date Added: 2017-02-16) 2- Analysis of -1,3-Glucan Assembly in Saccharomyces cerevisiae Using a Synthetic Interaction Network and Altered Sensitivity to Caspofungin Lesage, G 2004 Genetics (Date Added: 2017-02-16) 1- Global mapping of the yeast genetic interaction network Tong, AHY, Lesage, G, Bader, GD, Ding, H, Xu, H, Xin, X, Young, J, Berriz, GF, Brost, RL, Chang, M, Chen, YQ, Cheng, X, Chua, G, Friesen, H, Goldberg, DS, Haynes, J, Humphries, C, He, G, Hussein, S, Ke, L, Krogan, N, Li, Z, Levinson, JN, Lu, H, Menard, P, Munyana, C, Parsons, AB, Ryan, O, Tonikian, R, Roberts, T, Sdicu, A-M, Shapiro, J, Sheikh, B, Suter, B, Wong, SL, Zhang, LV, Zhu, H, Burd, CG, Munro, S, Sander, C, Rine, J, Greenblatt, J, Peter, M, Bretscher, A, Bell, G, Roth, FP, Brown, GW, Andrews, B, Bussey, H, Boone, C 2004 Science (New York, N.Y.) (Date Added: 2017-02-16) In the mediaCustom Diets—But Do They Work? (John Ortved) 2019-08-19 SFU-led team fights drug-resistant tuberculosis with artificial intelligence 2019-03-25 L’UdeM obtient huit nouvelles chaires de recherche du Canada et quatre renouvellements 2018-05-04 Deux nouvelles options en sciences biologiques 2017-02-22 |