Ecological and molecular mechanisms of microbial communities producing biomolecules with enhanced anti-Listeria monocytogenes activity

Thesis topic

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.

Supervision of the thesis

The PhD thesis will be supervised by Professor Frédéric Borges (Laboratory of Biomolecular Engineering, LIBio, University of Lorraine, France) and Professor Marie Filteau (Laval University, Quebec). The thesis will be carried out mainly at LIBio; a stay of several months at Laval University (Quebec) will be undertaken during the course of the thesis. LIBio has been studying the mode of action of bacteriocins in model systems as well as in the food matrix. LIBio has expertise in the field of microbial competition in food systems. The research aims at understanding the role of interactions in the structuration of microbial communities in food in order to design microbiomes with enhanced functionality. These issues are studied using complementary approaches of biophysics and microbiology, including classical microbiology techniques, genomics, genetic engineering, metabarcoding, and high-throughput microbiological cultures. The final aim is to control food quality and safety. Professor Frédéric Borges has (co)authored 52 peer-reviewed research publications and review articles with overall more than 2000 citations an H index of 23.

Professor Marie Filteau’s laboratory at Laval University studies the role of microorganisms in food quality, typicity, and stability, with a particular focus on maple products and food microbial ecosystems. Her team combines metataxonomy, functional genomics, systems biology, and high-throughput culturing approaches to characterize microbial interactions and their effects on food matrices. Her research includes studying the microbial diversity of maple sap and its links to syrup complexity, as well as the impact of climate change on maple quality. The lab also works on valorizing downgraded maple syrups and participates in several major funded initiatives, including a Discovery Grant from NSERC (2025–2030). Professor Filteau has accumulated over 900 citations and an h-index of 17.

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.

Funding

ISITE-Lorraine, acquired

Salary

Approximately €27000 gross per year, €22000 net per year

Documents to be submitted with the application

CV, motivation letter, university transcripts, contact details of referees, and letters of recommendation.