Jesse Shapiro

Assistant Professor,
McGill University

Department of Microbiology & Immunology
Institution page
Personal page


Postdoc, 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)


Most 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 students

Naíla Barbosa da Costa

Other (co-)supervisor: Jesse Shapiro
(Start: 2016)
Other QCBS (co-)supervisor: Gregor Fussmann
Eco-evolutionary dynamics of microbial communities in disturbed freshwater ecosystems
Personal page

Inès Levade

(Start: 2014)
Genomic analysis of cholera micro-evolution and transmission

Previous students (since 2009)

Nicolas TROMAS

Postdoctoral fellow
Other (co-)supervisor: Angus Buckling, Exeter University
(Start: 2014, End: 2017)

Examples of species studied

Vibrio cholerae
Streptococcus pyogenes
Mycobacterium tuberculosis
Saccharomyces cerevisiae
Trypanosoma brucei


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)

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)

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)

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)