ARG-PASS v2.0 identifies previously unrecognized antibiotic resistance genes in environmental samples and links them to human gut microbiomes through dietary exposure.

bioRxiv · Oct 30, 2026 · PreprintMicrobiology

Insights Into The Early Diversification of blaNDM-1 Genetic Contexts Following its Emergence in Acinetobacter species and Spread to Enterobacterales

Nancy Allard, Dalila Touati, Nathan Faille, Frédéric Grenier, Emy Beauchemin-Lauzon, Simon Lévesque, Sébastien Rodrigue, Louis‐Patrick Haraoui

The paper analyzes early genetic contexts of blaNDM-1 in Acinetobacter and Enterobacterales isolates to understand its spread and resistance mechanisms.

bioRxiv · Oct 26, 2026 · PreprintMolecular Biology

Reducing growth-medium complexity reveals nutrient-responsive programs in a near-minimal bacterium

Anthony Duval, Jeremy Gagnon, Simon Jeanneau, Dominick Matteau, Pierre‐Étienne Jacques, Sébastien Rodrigue

The paper develops a serum-free medium for Mesoplasma florum that reveals nutrient-responsive gene expression programs and metabolic pathways.

bioRxiv · Sep 30, 2026 · PreprintSystems Biology

Optimization of DNA Transformation in Mesoplasma florum and Identification of a Candidate Recipient Strain for Genome Transplantation

Jeremy Gagnon, Dominick Matteau, Frédéric Grenier, Sébastien Rodrigue

This study optimizes DNA transformation in Mesoplasma florum and identifies a candidate recipient strain for genome transplantation, highlighting DNA topology as a key factor in transformation efficiency.

bioRxiv · Sep 30, 2026 · PreprintSynthetic Biology

Conserved protein sequence-structure signatures identify antibiotic resistance genes from the human microbiome

Lachlan Bartrop, Emy Beauchemin-Lauzon, Frédéric Grenier, Sébastien Rodrigue, Louis‐Patrick Haraoui

The paper introduces ARG-PASS, a method to identify antibiotic resistance genes from the human microbiome by analyzing conserved protein sequence-structure signatures, finding 80% of tested genes confer resistance at clinical breakpoints.

Microbiome · Aug 13, 2026Peer-reviewedMicrobiology

Comparative Analysis of Gene Importance in Escherichia coli Across Growth Conditions

Antoine Champie, Simon Jeanneau, Amélie De Grandmaison, Mathias Martin Silva, Jean‐Philippe Côté, Pierre‐Étienne Jacques, Sébastien Rodrigue

This study identifies growth medium-specific important genes in Escherichia coli using transposon mutagenesis and sequencing, revealing a core set of essential genes and medium-specific gene modules.

mSystems · Apr 14, 2026Peer-reviewedSystems Biology

De novo synthesis of a conjugative system from human gut metagenomic data for targeted delivery of Cas9 antimicrobials

Thomas A. Hamilton, Benjamin R. Joris, Arina Shrestha, Tyler S. Browne, Sébastien Rodrigue, Bogumil Jacek Karas, Gregory Brian Gloor, David R. Edgell

ACS Synthetic Biology · Dec 4, 2023Peer-reviewedSynthetic Biology

Crucial Role of Salmonella Genomic Island 1 Master Activator in Parasitism of IncC plasmids

Romain Durand, Kevin T. Huguet, Nicolas Rivard, Nicolas Carraro, Sébastien Rodrigue, Vincent Burrus

The paper investigates the role of SgaCD in SGI1 mobilization, showing it activates AcaCD-responsive promoters and is essential for SGI1 excision, replication, and destabilization of IncC plasmids.

Nucleic Acids Research · Mar 15, 2021Peer-reviewedMolecular Biology

BOFdat: generating biomass objective function stoichiometric coefficients from experimental data

Jean‐Christophe Lachance, Jonathan M. Monk, Colton J. Lloyd, Yara Seif, Bernhard Ørn Palsson, Sébastien Rodrigue, Adam M. Feist, Zachary A. King, Pierre‐Étienne Jacques

BOFdat generates biomass objective function stoichiometric coefficients from omic data and calculates maintenance costs.

bioRxiv · Jan 5, 2018 · PreprintSystems Biology