Photo credit: Owen Egan
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Graduate students / Étudiants gradués
Naíla Barbosa da Costa
website: https://nailacosta.weebly.com/
Aquatic microbial communities are constantly exposed to a combination of different stressors, usually brought from agricultural lands within the watershed. In my PhD, I studied the impact of commonly-used agrochemicals on bacterioplankton. I worked in collaboration with researchers from McGill University in the LEAP project to gather experimental data on how freshwater bacteria respond to environmental disturbances at the community, genetic and population level. I also collaborated with the Lake Pulse microbiome research team producing sequencing data of bacterioplankton communities in lakes across Canada with different degrees of human impact.
website: https://nailacosta.weebly.com/
Aquatic microbial communities are constantly exposed to a combination of different stressors, usually brought from agricultural lands within the watershed. In my PhD, I studied the impact of commonly-used agrochemicals on bacterioplankton. I worked in collaboration with researchers from McGill University in the LEAP project to gather experimental data on how freshwater bacteria respond to environmental disturbances at the community, genetic and population level. I also collaborated with the Lake Pulse microbiome research team producing sequencing data of bacterioplankton communities in lakes across Canada with different degrees of human impact.
Emma Derrick
Research interests: Most of our current knowledge of bacterial evolution comes from experiments done in a laboratory environment. I am interested in studying how bacteria evolve in a semi-natural aquatic community, where bacteria can interact with each other and their environment. Using the McGill Gault Nature Reserve’s Large Experimental Array of Ponds, we can simulate a series of herbicide contaminated lakes to study 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 looking at susceptibility to cholera infection using metagenomes.
Research interests: Most of our current knowledge of bacterial evolution comes from experiments done in a laboratory environment. I am interested in studying how bacteria evolve in a semi-natural aquatic community, where bacteria can interact with each other and their environment. Using the McGill Gault Nature Reserve’s Large Experimental Array of Ponds, we can simulate a series of herbicide contaminated lakes to study 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 looking at 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 traits–such as color and wing morph–in aphids. I also conducted research 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.
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 traits–such as color and wing morph–in aphids. I also conducted research 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: Many bacterial species can transfer genetic contents between highly divergent genomes through mobile genetic elements or gene conversions. This might lead to convergence of initially different strains, as has been observed in Campylobacter. However, phylodynamics analysis has shown that many highly recombinogenic species can retain their strain structure over a long time. 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: I have been undertaking genomic studies on different microbial pathogens over the last few years. 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 on a project exploring the mechanisms that are controlling the multi-strain population structure of Streptococcus pneumoniae and Helicobacter pylori.
Research interests: Many bacterial species can transfer genetic contents between highly divergent genomes through mobile genetic elements or gene conversions. This might lead to convergence of initially different strains, as has been observed in Campylobacter. However, phylodynamics analysis has shown that many highly recombinogenic species can retain their strain structure over a long time. 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: I have been undertaking genomic studies on different microbial pathogens over the last few years. 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 on a project exploring the mechanisms that are controlling the multi-strain population structure of Streptococcus pneumoniae and Helicobacter pylori.
Postdocs & Research Associates
Nicolas Tromas
Website: https://nicolastromascyano.weebly.com
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.
Previous/current research: I did my PhD with Santiago F. Elena at the IBMCP (Instituto de Biologia Molecular y Celular de Plantas) of the Polytechnic University of Valencia, Spain where I used the plant virus TEV (Tobacco etch virus) 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 for few years with Angus Buckling and Jesse - worked (and still working on!!) one of the biggest Cyano genomics project (ATRAPP) - close to be an Academy fellow - currently working with Sam Chaffron (LS2N, Nantes) on Tara oceans data - currently reducing my stress by writing volume 2 of Fila&Bubbee (children's book).
Website: https://nicolastromascyano.weebly.com
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.
Previous/current research: I did my PhD with Santiago F. Elena at the IBMCP (Instituto de Biologia Molecular y Celular de Plantas) of the Polytechnic University of Valencia, Spain where I used the plant virus TEV (Tobacco etch virus) 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 for few years with Angus Buckling and Jesse - worked (and still working on!!) one of the biggest Cyano genomics project (ATRAPP) - close to be an Academy fellow - currently working with Sam Chaffron (LS2N, Nantes) on Tara oceans data - currently reducing my stress by writing volume 2 of Fila&Bubbee (children's book).
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Gavin Douglas
Website: www.gavindouglas.ca Research interests: 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. Previous research: 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. |
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Steven G. Sutcliffe
Research Interest: Wastewater based epidemiology (WBE) has long been used to track pathogens circulating in the community (e.g., Polio in the UK). WBE 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.
Previous research: 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!
Research Interest: Wastewater based epidemiology (WBE) has long been used to track pathogens circulating in the community (e.g., Polio in the UK). WBE 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.
Previous research: 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 have a strong background in microbiology, genomics, computational biology or evolutionary biology (or all of the above).
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
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
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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. 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 starting a PhD 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 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 |
