69th Annual Conference of the Canadian Society of Microbiologists, June 2019


Principal Investigator

Sébastien Rodrigue


Associate Professor

M. Sc. and Ph. D. Biologie, Université de Sherbrooke

Post-doctorate, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT)

Graduate students

Dominick Matteau, Ph.D. Student



By reprogramming cell functions, synthetic biology promises to tackle some of the most difficult challenges of the 21st century. However, current biological programming mostly relies on incomplete or inaccurate prediction-based cellular models, making gene circuit optimization efforts slow and expensive. By studying simple organisms such as Mesoplasma florum and Escherichia coli, we wish to replace these computational models by more accurate and complete experimental annotations generated using high-throughput technologies such as DNA-seq, RNA-seq, ChIP-exo, mass-spectrometry, etc. The integration of these multiple comprehensive datasets will help us to reach a deep, precise and global understanding of a simple bacterial cell, an important step towards the rational programming of biological systems and the development of synthetic biology.

Kevin Neil, Ph.D. Student


My project is to develop a new high-throughput genomic method that would allow sequencing of a multitude of organisms in parallel. To achieve this goal, I will use microfluidics to isolate microorganisms in agarose droplets, and I will use those as a support to lyse each microorganism, extract their genetic makeup and then amplify it, all in a single reaction.

Jean-Christophe Lachance, Ph.D. Student


As part of metabolic engineering and genome reduction of Mesoplasma florum L1, my project aims to develop a Cas9-based high-throughput genome modification method. This system will quickly generate a large number of modified Mesoplasma florum genomes, which can then be used to verify their viability in the broader goal of obtaining a minimal cell chassis.

Antoine Champie, Ph.D. Student


To create advanced new genetic circuits, we must fully understand the cell that will carry those constructions. Since even the most studied organisms like Escherichia coli are too complex to predict and model, my project is to simplify the genome of E. coli. Using information from multiple sources like HDTM, RNA-Seq, and Metabolic Models, I am trying to define what the essentials regions of the genome are. I will then reduce this genome through large genomic deletions to obtain a cell with a minimal genome, which would be able to grow in a rich medium at an acceptable growth rate. Once that minimal cell is obtained, I will characterize the remaining unknown elements to be able to finally model and predict this minimal E. coli.

Nancy Allard, Ph.D. Student

In the last decades, emergence of multidrug-resistant bacterial pathogens, both in clinical and environmental settings, have become an important issue to public healthcare systems. My project proposes an innovative approach to address the alarming problem of multidrug resistance.  I am working to engineer a modified probiotic bacterium that will be programmed to target and eliminate  pathogens. This innovative method could have a significative impact on medicine by eventually offering an alternative to antibiotics to prevent or treat many infectious diseases.

Jean-Christophe Berger-Dancause, Ph.D. Student (co-direction)

Romain Durand, Ph.D. Student (co-direction)

Cynthia Lemieux, M.Sc. Student

My project touches a key aspect of synthetic genomics, the development of an alternative to the current method of cloning and genome transplantation. In other words, my project aims to set up a genomic modification platform for our model organism Mesoplasma florum. To do this, Escherichia coli is used as a temporary host to make the desired modifications in M. florum genome, since it is highly characterized and a variety of molecular tools have been developed to manipulate it. The modified genome is then mobilized into the recipient cell by the conjugation process. We believe that this approach has great potential, as it would be significantly more efficient and faster than the genome transplantation and potentially applicable to a wider range of microorganisms.

Catherine Chamberland, M.Sc. Student

The study of minimal and near-minimal bacteria offers promising access to understanding many fundamental biological processes. Mesoplasma florum is one of those microorganisms that, by its simplicity, has the potential to be transformed into a prototyping platform for the programming of synthetic genomes. The lack of genetic engineering tools in this bacterium however remains a limiting factor in this approach. My project aims to develop new tools to build an easily modifiable strain to study and characterize genetic elements in M. florum. The development of such a strain is an important step towards the construction of a programmable cell chassis from this microorganism.

Olivier Trahan, M.Sc. Student

Patricia Roy, M.Sc. Student (summer 2019)

Marie-Eve Pepin, M.Sc. Student


The overall objective of my project is to develop inducible gene expression systems heavily regulated by the combination of regulatory motifs in Escherichia coli. Indeed, there is to date no 100% effective control system. Even when a system is suppressed, a basal level of expression, generally relatively high, is observed. Conversely, a strongly repressed system will be difficult to induce. The combination of regulatory motifs could significantly improve the level of regulation. Indeed, considering the fact that these mechanisms operate independently, their synergistic effect on the regulation therefore provide an extremely effective control of gene expression in artificial circuits.

Jean-François Rousseau, M.Sc. Student


My goal is to add the necessary genes for production of (2R, 3R) butanediol and optimize metabolic pathways involved in the bacterium Escherichia coli to bring a potentially economically viable level of production. This production will use whey generated by the Quebec dairy industry as a nutrient source, for revaluation purposes.

David Pivin, M.Sc. Student (co-direction)

Nicolas Allaire-Tanguay, M.Sc. Student (co-direction)

Undergraduate students

Anthony Duval

Günes-Hélène Isitan

Julien Faure-Lévesque

Research assistant

Joëlle Brodeur


Frédéric Grenier


Vincent Baby, Ph.D. Student


The objective of my project is to develop a plan to reduce the genome of the bacterium Mesoplasma florum . This project is divided into two parts. The first is to combine a comparative genomic analysis and the data of an experiment of transposon mutagenesis to identify essential genes and gene conserved in this bacterium. The second part is to clone the complete genome of the bacterium in yeast, and then develop a genome transplantation protocol. This method allows the use of many genome engineering tools already developed in yeast to modify and reduce the genome of M. florum.

Frédéric Grenier, M.Sc. Student


My master’s project is to experimentally acquire information on the essentiality of all different genomic elements in E. coli and to use that information to rationally reduce its genome. The resulting organization, with a reduced genome, can then serve as cellular chassis for synthetic biology.

David Jordan, undergraduate intern

Ariane Arsenault, Cégep de Sherbrooke intern

Alejandra Matsuri Rojano Nisimura, undergraduate intern (Mitacs Globalink)

Yogesh Lakhotia, undergraduate intern (Mitacs Globalink)

Jimmy Blouin, undergraduate intern

Samuel Jacques, undergraduate intern

Lucas Leclerc, undergraduate intern

Charles Coulombe, undergraduate intern

Mélissa Arango-Giraldo, undergraduate intern

Samuel Gauthier, undergraduate intern

Syed Fazle Rouf, post-doctoral student

April 2019

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