jesse Principal investigator:
B. Jesse Shapiro

Associate professor
Department of Microbiology & Immunology
McGill University
Investigator, McGill Genome Centre
jesse dot shapiro at mcgill dot ca

                                                                           Graduate students


Emma Derrick
Research interests: Most of our current knowledge of bacterial evolution comes from laboratory experiments. I am interested in how bacteria evolve in a semi-natural aquatic community where bacteria can interact with each other and their environment. Using LEAP at McGill Gault Nature Reserve, we are studying the evolutionary responses of bacteria after herbicide contamination.
Background: I completed my B.Sc. at McGill University in Microbiology and Immunology. During my undergrad I joined the Shapiro lab and worked on a project on susceptibility to cholera infection using metagenomes.


Akhil Kholwadwala
Research Interests: For my PhD, using the LEAP system as a model, I am interested in the rapid adaptation of aquatic communities and individual species to a plurality of anthropogenic stressors and their synergistic effects. I am also interested in looking at the predictability of evolution within the context of this system.
Previous Research: I graduated with a B.S. in Ecology and Evolutionary Biology and a B.A. in French from the University of Rochester in 2022. As an undergraduate, I conducted research with Dr. Jennifer Brisson on the evolution of polymorphic and polyphenic traitsin aphids. I also worked with the U.S. Fish and Wildlife Service to test the ability of eDNA technologies to detect the presence of rare and endangered bumblebee species.


Chuhan Qin
Research interests: For my PhD, I would like to understand how the interaction of different biological processes such as selection, mutation and recombination has resulted in different population structures in different bacteria. Built upon this, I want to develop novel population genomic models that can be used to predict population dynamics and guide the clinical usage of drugs.
Previous research: The first project I worked on is with Prof. Stephen Gordon, during which I used whole genome sequencing data to trace the transmission of Mycobacterium avium in cows from several Irish farms. I then moved on to work with Prof. Matthew Fisher on a population genomics study of the pathogenic fungus Aspergillus fumigatus, and with Dr Nicholas Croucher exploring the mechanisms controlling the population structure of Streptococcus pneumoniae and Helicobacter pylori.


Sana Naderi
I am a graduate student at the McGill Genome Centre and the Department of Microbiology and Immunology. My research focuses on the genomic epidemiology of SARS-CoV-2, specifically its transmission and adaptation in animal hosts. Additionally, I am interested in time series analyses of SARS-CoV-2 wastewater sequences. I use population genetics and statistical approaches to assess the ability of such data to predict pathogen blooms. I did my undergraduate studies in electrical engineering and system control at Sharif University of Technology in Tehran. During my undergrad, I interned at the Vienna school of population genetics at the University of Vienna, the McGill Genome Center, and the Vienna Biocenter at the Austrian Academy of Sciences. I have been a graduate student in the Shapiro Lab since January 2022 and will be transferring to the PhD program in 2023.

                                                                           Postdocs & Research Associates


Nicolas Tromas
Research interests: My main interests are to solve fundamental questions in microbial ecology and evolution; tracking 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. One of my objectives is to improve prediction of cyanobacterial blooms and toxicity using microbial interaction information. One of my favorite things is to connect with people and develop new projects.
Background: I did my PhD with Santiago F. Elena at the Polytechnic University of Valencia, Spain where I used the plant virus TEV as a model to address evolutionary questions. And after? To make it short: I moved to Montréal in 2014 to work on Cyanobacteria with Jesse - was a Marie S. Curie fellow with Angus Buckling and Jesse - worked (and still working on!!) one of the biggest Cyano genomics project (ATRAPP) - currently working with Sam Chaffron (LS2N, Nantes) on Tara oceans data - and reducing my stress by writing volume 2 of Fila&Bubbee (children’s book).


Aline Cuénod
Research interests: I am fascinated by infectious diseases and the interplay of pathogenic bacteria with their human host. Cholera is one of the most important infectious diseases, yearly affecting millions of people and frequently arising where sanitary infrastructure is inadequate. Pandemic cholera is caused by a pathogenic lineage of the aquatic bacterial species V. cholerae. While V. cholerae infections can be very virulent and lead to severe dehydration and death within hours, most infections cause no or only mild diarrhoeal symptoms. In my current project, for which I received a Postdoc.Mobility fellowship from the Swiss National Science Foundation, I investigate the interplay of patient characteristics and bacterial genetic factors promoting Cholera symptoms and transmission.
Background: During my PhD, which I did in the research group of Prof. Adrian Egli at the University of Basel (Switzerland), I worked in close collaboration with clinical diagnostics. I analysed Matrix-assisted laser desorption/ionisation time of flight (MALDI-TOF) mass spectra, bacterial genomes and patient related clinical data, to increase the resolution of bacterial identification in diagnostics for Klebsiella and E. coli.


Gavin Douglas
Research interests: I study a broad range of questions related to microbial evolutionary genetics. Currently I am focused on applying standard population genetics approaches to prokaryotic strains found in natural communities. I would like to leverage this approach to assess the strength of selection acting on accessory genes across different strains. This work is currently focused on strains found in the honey bee gut microbiome, which has low taxonomic richness and so somewhat simplifies the task of profiling strain-level variation. I am also interested more generally in the importance of gene-level vs. individual-level selection in shaping prokaryotic pangenomes.
Background: I did my PhD at Dalhousie University with Morgan Langille, where my work focused on integrating functional and taxonomic data types for microbiome data analysis. Prior to that, I worked as a bioinformatician for a year at the Integrated Microbiome Resource at Dalhousie University. I completed my BSc and MSc degrees both at the University of Toronto. I worked with Alan Moses during my MSc project, which involved investigating the evolutionary forces acting upon primate transcription factor binding sites.


Steven G. Sutcliffe
Research interests: Wastewater based epidemiology (WBE) has been used to track pathogens circulating in the community (e.g., Polio in the UK) and is receiving more interest than ever with SARS-CoV-2 being efficiently tracked in wastewater across the globe. My interest is in both understanding how to improve SARS-CoV-2 monitoring for WBE, and in how these tools can improve our pandemic preparedness beyond SARS-CoV-2. In the Shapiro Lab we are working on building the bioinformatic infrastructure to efficiently handle the large-quantities of sequence data from WBE, and its translation to inform public health.
Background: I received a PhD from McGill in Microbiology and Immunology for my work in the lab of Dr. Corinne Maurice. My thesis was on the role of bacteriophages (viruses of bacteria) in shaping the human gut microbiota. We showed that phages persist in the healthy human gut through integrating within the bacterial genome but this balance can be disrupted by exposure to various medications. Prior to that I had worked in food safety microbiology laboratory (Mérieux NutriSciences), and did research on diatoms (microalgae) in the laboratory of Dr. Irena Kaczmarska at Mount Allison University. It is a microbial world, we just live in it!

Join the lab!

Applicants should be excited about microbiology, genomics, computational biology or evolutionary biology – and ideally have a background in one or more of these areas.

The lab has very limited funding for salaries, so applicants are expected to apply for external scholarships or fellowships, such as NSERC, FQRNT and CIHR. Prospective students can apply to either the Microbiology or Quantitative Life Sciences graduate programs.

Email Jesse to apply. Please include:

  • a description of your background and research interests
  • what you would like to work on in the lab
  • contact information for 2 references

Lab Alumni:

  • Dr. Naima Madi, PhD 2023
  • Dr. Naíla Barbosa da Costa, PhD 2022
  • Dr. Carmen Lía Murall (postdoc 2019-2021): Now COVID-19 Genomics Lead at Public Health Agency of Canada
  • Dr. Morteza M. Saber (postdoc 2018-2021): Now a bioinformatician/data scientist at MIMS
  • Arnaud N’Guessan (MSc 2021): Now a PhD candidate at the University of Toronto
  • Dr. Peter Chen (PhD 2021): Now a postdoc with Jesse and Michael Reed at RI-MUHC
  • Dr. Olga Pérez Carrascal (postdoc 2017-2021): Now a postdoc with Michael Shapira at UC Berkeley
  • Dr. Yves Terrat (postdoc 2015-2021): Now a data scientist at UdeM/IVADO
  • Dr. Inès Levade (PhD, 2020): Now a scientist at the Quebec Institute for Public Health (INSPQ)
  • Kiri Stern (MSc, 2020). Now a PhD student in Quantitative Life Sciences at McGill.
  • Dr. Jean-Baptiste Leducq (postdoc 2016-2021): Now an assistant professor at Université Laval
  • Dr. ​Catherine Girard (PhD, 2017): Now a faculty member at UQAC​
  • Elisa Moreno (undergrad, 2019-2020): Now a PhD student at the Jebsen Center for Genetic Epidemiology, Norway
  • Dr. Larbi Bedrani (bioinformatics intern, summer-fall 2015): Now a postdoc at the University of Toronto, Mount Sinai Hospital, Department of Gastroenterology
  • Dr. Coralie Deladrière (field & lab assistant, summer 2015): Now an analytical chemist at PCAS Canada.
  • Romane Marcoz (undergrad, summer 2015): Now doing a Masters in Public Health at UdeM
  • Yoann Santin (undergrad, winter 2015): Now doing a PhD in Microbiology at the Faculté des Sciences de Luminy (Marseille) Aix-Marseille Université
  • Simone Périnet (lab tech, winter-summer 2014): Now doing a Masters in Public Health at UdeM