Biology subjects

Potvin-Trottier, L.

Publications and source records attributed to Potvin-Trottier, L..

4 recordsLinked to original sources

bioRxiv2025

Expanding the Bacteroides synthetic biology toolkit to develop an in vivo intestinal malabsorption biosensor.

The human gut is a highly dynamic physical environment where perturbations--including factors such as acidification, oxygenation, and particle concentration (osmolality)--can influence microbiota composition and contribute to disease states. Understanding gut environmental changes is essential for advancing diagnostic and therapeutic strategies for gut health. However, non-invasive methods for continuous monitoring remain limited. The bacterial gut microbiota represents a powerful platform for continuous, non-invasive biosensing technologies for the gut environment, with genetically tractable commensal species like Bacteroides thetaiotaomicron (B. theta) emerging as promising hosts for engineered biosensors. However, the availability of genetic tools for precise, modular environmental sensing and reporting control in B. theta remains limited. Here, we present an expanded genetic engineering toolkit for B. theta that enables precise, fluorescence-based environmental sensing of the gut environment. This toolkit includes i) three libraries of orthogonally inducible promoters capable of driving fluorescence expression, ii) a DNA-based system to tune repressor activity in B. theta, iii) a resulting modular transcriptional reporter circuit that integrates native promoter activation with fluorescent outputs, and iv) characterization of a novel plasmid integration mode in B. theta. To demonstrate its utility, we engineered biosensors for gut malabsorption, a condition characterized by increased luminal osmolality. Using identified osmolality-responsive native promoters from B. theta, we made biosensors capable of detecting changes in gut physiology through graded fluorescent outputs. These biosensors were validated both in vitro and in vivo using a murine model of laxative-induced malabsorption, where they enabled continuous, long-term, non-invasive monitoring of single-cell response from fecal samples with sensitivity to subclinical malabsorption levels. By expanding the genetic toolkit for Bacteroides and demonstrating its use in a physiologically relevant context, this approach highlights the potential of engineered gut bacteria as a monitoring platform for diverse gut health applications. This work advances strategies for microbial biosensing and positions gut commensals as key players in next-generation diagnostic methods.

synthetic biology↗

bioRxiv2023

Exploiting fluctuations in gene expression to detect causal interactions between genes

Characterizing and manipulating cellular behaviour requires a mechanistic understanding of the causal interactions between cellular components. We present an approach to detect causal interactions between genes without the need to perturb the physiological state of cells. This approach exploits naturally occurring cell-to-cell variability which is experimentally accessible from static population snapshots of genetically identical cells without the need to follow cells over time. Our main contribution is a simple mathematical relation that constrains the propagation of gene expression noise through biochemical reaction networks. This relation allows us to rigorously interpret fluctuation data even when only a small part of a complex gene regulatory process can be observed. We show how this relation can, in theory, be exploited to detect causal interactions by synthetically engineering a passive reporter of gene expression, akin to the established "dual reporter assay". While the focus of our contribution is theoretical, we also present an experimental proof-of-principle to demonstrate the real-world applicability of our approach in certain circumstances. Our experimental data suggest that the method can detect causal interactions in specific synthetic gene regulatory circuits in E. coli confirming our theoretical result in a narrow set of controlled experimental settings. Further work is needed to show that the approach is practical on a large scale, with naturally occurring gene regulatory networks, or in organisms other than E. coli.

systems biology↗

bioRxiv2023

Measuring prion propagation in single bacteria elucidates mechanism of loss

Prions are self-propagating protein aggregates formed by specific proteins that can adopt alternative folds. Prions were discovered as the cause of the fatal transmissible spongiform encephalopathies in mammals, but prions can also constitute non-toxic protein-based elements of inheritance in fungi and other species. Prion propagation has recently been shown to occur in bacteria for more than a hundred cell divisions, yet a fraction of cells in these lineages lost the prion through an unknown mechanism. Here, we investigate prion propagation in single bacterial cells as they divide using microfluidics and fluorescence microscopy. We show that the propagation occurs in two distinct modes with distinct stability and inheritance characteristics. We find that the prion is lost through random partitioning of aggregates to one of the two daughter cells at division. Extending our findings to prion domains from two orthologous proteins, we observe similar propagation and loss properties. Our findings also provide support for the suggestion that bacterial prions can form more than one self-propagating state. We implement a stochastic version of the molecular model of prion propagation from yeast and mammals that recapitulates all the observed single-cell properties. This model highlights challenges for prion propagation that are unique to prokaryotes and illustrates the conservation of fundamental characteristics of prion propagation across domains of life.

microbiology↗

bioRxiv2018

Variability of bacterial behavior in the mammalian gut captured using a growth-linked single-cell synthetic gene oscillator

The dynamics of the bacterial population that comprises the gut microbiota plays key roles in overall mammalian health. However, a detailed understanding of bacterial growth within the gut is limited by the inherent complexity and inaccessibility of the gut environment. Here, we deploy an improved synthetic genetic oscillator to investigate dynamics of bacterial colonization and growth in the mammalian gut under both healthy and disease conditions. The synthetic oscillator, when introduced into both Escherichia coli and Salmonella Typhimurium maintains regular oscillations with a constant period in generations across growth conditions. We determine the phase of oscillation from individual bacteria using image analysis of resultant colonies and thereby infer the number of cell divisions elapsed. In doing so, we demonstrate robust functionality and controllability of the oscillator circuits activity during bacterial growth in vitro, in a simulated murine gut microfluidic environment, and in vivo within the mouse gut. We determine different dynamics of bacterial colonization and growth in the gut under normal and inflammatory conditions. Our results show that a precise genetic oscillator can function in a complex environment and reveal single cell behavior under diverse conditions where disease may create otherwise impossible-to-quantify variability in growth across the population.

synthetic biology↗