Offre de thèse
ISITE - Mécanismes écologique et moléculaire de communautés microbiennes produisant des biomolécules présentant une activité anti-Listeria monocytogenes augmentée
Date limite de candidature
10-06-2026
Date de début de contrat
01-10-2026
Directeur de thèse
BORGES Frédéric
Encadrement
La co-directrice sera la Professeure Marie Filteau de l'Université Laval (Québec). Afin d'assurer une coordination efficace du projet, un comité de pilotage (Steering Committee, SC) sera mis en place. Il comprendra les directeurs de thèse, le doctorant, ainsi que 3 à 5 membres clés du laboratoire directement impliqués dans le projet. Le SC se réunira tous les deux mois afin de suivre l'avancement, évaluer les risques et prendre des décisions stratégiques, y compris d'éventuelles modifications du programme scientifique lorsque nécessaire. Des réunions de jalons auront lieu tous les 15 jours pour suivre les progrès à court terme et résoudre les problèmes opérationnels. Le projet respectera les principes FAIR (Facile à trouver, Accessible, Interopérable, Réutilisable) en matière de gestion des données, soutenus par un plan de gestion des données (Data Management Plan) détaillant les protocoles de collecte, de stockage et de partage des données. Un comité de suivi de thèse veillera à l'avancement académique, garantissant une finalisation dans les délais. Tous les résultats de recherche, y compris les versions post-publication (post-prints), seront déposés dans des archives en libre accès, tandis que les jeux de données et les codes seront archivés dans des répertoires dédiés afin d'assurer leur accessibilité à long terme. Cette approche structurée favorisera la transparence, la collaboration et la conformité aux standards de la science ouverte, contribuant ainsi à un processus de recherche solide et bien documenté.
Type de contrat
école doctorale
équipe
contexte
The consumption of food contaminated with pathogens is an important cause of morbidity and mortality worldwide. Every year, approximately 600 million people – 1 in 10 people – get sick from foodborne pathogens, 420,000 of whom die. Human damage caused by foodborne pathogens results in colossal economic losses amounting to USD 110 billion due to lost productivity and health expenses (Borges et al., 2022a; World Health Organization, 2015). Biopreservation refers to the use of beneficial microorganisms (such as lactic acid bacteria) producing antimicrobial substances to inhibit the growth of spoilage and pathogenic bacteria in food (Stiles, 1996). The primary antimicrobial agents used in biopreservation are bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by bacteria to inhibit or kill closely related strains (Cotter et al., 2005). Bacteriocins such as nisin (from Lactococcus lactis) and pediocin (from Pediococcus acidilactici) are widely studied for their food preservation properties due to their safety and efficacy (Cleveland et al., 2001). The efficacy of biopreservation systems has been repeatedly demonstrated under laboratory conditions. However, their activity can be bacteriostatic (Cherrat et al., 2024; Engstrom et al., 2021; García et al., 2020; Muñoz et al., 2019; Wiernasz et al., 2020) or bactericidal (Goranov et al., 2022; Mathieu et al., 1994). Additionally, end-users of these technologies report variable effectiveness (personal communication). The variable efficacy of biopreservation systems, particularly those based on bacteriocins, is due to multiple interacting factors. Microbial strain specificity is a key limitation, as bacteriocins exhibit narrow-spectrum activity and may fail against resistant pathogens (Cotter et al., 2005). In addition, the activity of biopreservation systems depends on the physicochemical parameters such as pH, salt, and temperature, which are highly variable at spatial and temporal levels in food products, particularly in fermented food (Leroy and de Vuyst, 1999). Matrix rheological properties can influence the diffusion of antimicrobial compounds (Carnet Ripoche et al., 2006), and biochemical components such as lipids can also block the activity by interacting with bacteriocins (Chollet et al., 2008). More importantly, interactions with indigenous microbiota can either enhance or inhibit bacteriocin activity (Borges et al., 2022b). These various effects can be attributed to the very high variability in the composition of microbial communities colonizing foods. For example, for the same cheesemaking technology, the species present can vary considerably from one cheese to another (Irlinger et al., 2024). This paves the way for improved control over food functionality, particularly antimicrobial activity, by regulating the composition of food-colonizing microbiomes. Microbiome engineering seeks to improve the function of an ecosystem by manipulating the composition of microbes (Albright et al., 2022). In microbiome engineering, top-down and bottom-up describe two opposite ways of controlling or constructing microbial communities. Bottom-up microbiome engineering assembles a subset of microorganisms with desired functions into a synthetic community (SynCom)(Henry and Bergelson, 2025). Lately, bottom-up microbiome engineering work conducted at LIBio has shown that it is possible to enhance anti-Listeria monocytogenes activity by assorting microorganisms with complementary antimicrobial effects (Mangavel et al., 2026). Top-down microbiome engineering starts from an existing, complex natural community and steering it toward a desired function by changing environmental or operating conditions such as pH, temperature, and nutrients. Top-down microbiome engineering has been successfully applied to screen microbial communities with improved function (Chang et al., 2021). A critical point in top-down strategy is the stabilization of the structure of microbial communities before being scored for function. This stabilization can be obtained by serially passaging communities (Chang et al., 2021). By applying this very simple strategy, a set of 88 communities originating from raw milk were stabilized at the laboratory, characterized by metabarcoding, and then phenotyped at the LIBio (Thèse Léa-Jehanne Robert). Some microbial communities exhibited greater anti-L. monocytogenes activity than a patented strain of Carnobacterium maltaromaticum (LIBio), which is currently used in industrial applications (BORGES and REVOL-JUNELLES, 2024; Cherrat et al., 2024). However, the robustness of antimicrobial activity in relation to the variability of abiotic parameters is was not investigated during the course of Léa-Jehanne's PhD. Furthermore, the biomolecules and ecological mechanisms underlying such activities remain unknown.spécialité
Génie biotechnologique et alimentairelaboratoire
LIBIO - Laboratoire d'Ingénierie des Biomolécules
Mots clés
Ingénierie, Microbiome, Ecologie, Biopréservation
Détail de l'offre
L'ingénierie de microbiomes est un domaine prometteur avec des applications dans de nombreux secteurs tels que l'environnement, l'agriculture, l'industrie agroalimentaire et la santé humaine. L'ingénierie de microbiomes consiste à concevoir et à manipuler des communautés microbiennes pour leur conférer une fonction souhaitée. Cette démarche s'appuie sur les propriétés écologiques de ces communautés, issues des interactions entre les micro-organismes, ainsi que leur structure, leur diversité fonctionnelle et leur stabilité. Dans ce projet de doctorat, des communautés microbiennes conçues par ingénierie de microbiomes seront étudiées pour leur capacité à produire des biomolécules antimicrobiennes innovantes. Des communautés disponibles au laboratoire seront décortiquées pour élucider les mécanismes écologiques et moléculaires à l'origine de leur activité antimicrobienne remarquable. Plus précisément, les interactions entre micro-organismes seront analysées afin de comprendre leur contribution au potentiel antimicrobien, tandis que des méthodes de caractérisation moléculaire seront employées pour identifier les molécules impliquées. Le projet mobilisera des approches de phénotypage à haut débit des interactions microbiennes, de microbiologie classique, de génomique et de spectrométrie de masse.
Keywords
Engineering, Microbiome, Ecology, BiopreservationMicrobiome engineering is a promising field with applications in the environment, agriculture, the agri-food industry
Subject details
Microbiome engineering is a promising field with applications in the environment, agriculture, the agri-food industry, and human health. It consists of designing and manipulating microbial communities to achieve specific functions or beneficial outcomes. This approach relies on the ecological properties of these communities, including interactions between microorganisms, community structure, functional diversity, and stability. In this PhD project, microbiome engineering will be considered for the production of innovative antimicrobial biomolecules. Microbiome engineering will be used to elucidate the ecological and molecular mechanisms of selected communities, already available in the laboratory, and exhibiting remarkable antimicrobial activities. The consortia will be studied in depth to better understand how microbial interactions contribute to their antimicrobial potential. The project will involve high-throughput phenotyping of microbial interactions, classical microbiological methods, genomics, and mass spectrometry.
Profil du candidat
Le candidat doit posséder de solides compétences en microbiologie et en écologie microbienne. Une expérience dans les domaines du criblage à haut débit, du metabarcoding et de l'analyse statistique de données sous R sera très appréciée. Le candidat devra démontrer une forte motivation pour la recherche scientifique, caractérisée par une forte curiosité intellectuelle, une pensée critique et un véritable intérêt pour la compréhension de systèmes biologiques complexes. Le candidat devra faire preuve d'initiative, d'autonomie et de persévérance lorsqu'il abordera des questions de recherche difficiles, et devra démontrer sa forte capacité de travail dans un environnement interdisciplinaire. Un engagement clair à faire progresser les connaissances, à contribuer à des projets de recherche novateurs et à communiquer efficacement les résultats – à la fois oralement et par écrit – sera très apprécié.
Candidate profile
The candidate must have a strong background in microbiology, particularly in microbial ecology. Experience in high-throughput screening methods, metabarcoding, and the statistical analysis of large datasets (R) would be an advantage. The candidate should demonstrate a strong motivation for scientific research, characterized by intellectual curiosity, critical thinking, and a genuine interest in understanding complex biological systems. The candidate is expected to show initiative, autonomy, and perseverance when addressing challenging research questions, as well as the ability to work collaboratively in an interdisciplinary environment. A clear commitment to advancing knowledge, contributing to innovative research projects, and communicating results effectively—both orally and in writing—will be highly valued.
Référence biblio
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