Sibylle TABUTEAU

Link to join the defense remotely: https://inrae-fr.zoom.us/j/5815351591?omn=99630478068  

Composition of the jury:

• Mrs. Hélène FALENTIN , Senior Research Engineer, INRAE, Reviewer
• Mr. Frédéric BORGES, Professor, Université de Lorraine, Reviewer
• Mr. David VALLENET, Research Director, CEA, Examiner
• Mrs. Marie-Christine CHAMPOMIER-VERGÈS, Research Director, INRAE, Examiner 
• Mrs. Pavla DEBELJAK, Teacher-researcher, SupBiotech, Examiner

Mots clés : Cheese, microbial ecology, metagenomics, genomics, iron acquisition, siderophores

Résumé : Cheese is a fermented food whose characteristics are based on microbial communities composed of inoculated and environmental microorganisms. The structure and functioning of these communities are influenced by many factors, including iron, an essential nutrient that is highly limiting in cheeses. Microorganisms have various systems for acquiring iron, including direct iron import and siderophore import, molecules capable of chelating ferric iron. While several examples of iron-dependent interactions have been described in cheeses, no comprehensive analysis of iron acquisition systems has yet been conducted at the level of cheese microbial communities. The main objective of this work is to study iron acquisition systems in cheeses in order to better understand their diversity, taxonomic distribution and potential role in the structuring of microbial communities. First, the taxonomic and functional diversity of microbial communities in French PDO cheeses was characterised using a large metagenomic and genomic dataset (136 metagenomes, 1,263 MAGS and 280 isolates), highlighting the presence of a wide variety of bacterial, fungal and viral species. Based on these data, an investigation of iron acquisition systems was conducted at the community and species level. Genes involved in direct iron import, import of iron-siderophore complexes and siderophore biosynthesis were identified using a homology-based approach based on HMM profiles. This analysis revealed a wide diversity of iron acquisition systems, which were more abundant in surface communities than in core communities, and notably detected more than twenty siderophore biosynthesis pathways. Many microbial species have import systems without producing siderophores, suggesting interactions based on their sharing or exploitation. Finally, a comparative analysis of 461 genomes of the genus Vreelandella, from various environments, was carried out to study its adaptation to cheese, with a focus on its iron acquisition systems. The comparison revealed that cheese strains possess a significant number of siderophore import systems, sometimes acquired by horizontal transfer and similar to those of strains of other cheese genera, Pseudomonas and Pseudoalteromonas. These results show that horizontal gene transfer is a key mechanism in the adaptation of Vreelandella to cheese. This work thus provides new insights into iron acquisition systems in cheese-making microorganisms and highlights their potential role in structuring cheese microbial communities.