Microbial genomics

Annotation and analysis of microbial genomes are the core of our scientific activities, especially through collaborative projects using the MicroScope platform. They often involve comparative and phylogenetic analysis to understand dynamics and evolution of bacterial genomes, syntactic and functional annotation of new bacterial genomes or genomes from reference organisms (i.e., E. coli, B. subtilis, P. putida). To face the challenge of the analysis and visualisation of thousands microbial genomes, new methodological developments are addressed. Moreover, to answer to the needs of metagenomics data analysis, an instance of the MicroScope platform dedicated to the analysis of human (gut) microbiotes is developed together with a “standalone” platform allowing the detection pathogens in metagenomic data (PathoTRACK).


CarboMagnet : Contribution of magnetotactic bacteria forming intracellular carbonate mineral phases to the sequestration of organic carbon and alkaline earth elements

Abstract The project focuses on a poorly known carbon-sequestering environmental process by a group of diverse bacteria forming intracellular carbonates, occurring at oxic/anoxic boundaries (OAB) in aquatic environments. The molecular and geochemical processes of bacterial biomineralization will be studied by a combination of approaches in isotope and aqueous geochemistry, mineralogy, ...
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SymbioMAGNET : Deciphering the biodiversity, ecology and evolution of magnetotactic symbiosis

Abstract The project aims to decipher the biodiversity, ecology and evolution of a group of unicellular eukaryotes ubiquitous in marine anoxic sediments that sense the Earth’s magnetic field thanks to their symbiotic bacteria. This exploration will be done with a combination of approaches in microbiology, microscopy and genomics from the ...
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Background Today, thanks to the development of metagenomics, our knowledge of microbial diversity has greatly changed. Whereas previously cellular organisms were seen more as independent entities, today we know that they organize themselves into complex microbial communities made up of several species of bacteria, archaea and eukaryotes, and their mobilome ...
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PanGBank: exploring GenBank genomes through a resource of pangenome graphs

Many comparative genomic studies try to get a grasp on the overall gene content of a species. However, with the current explosion of available genomic data, it becomes more complex to use all-vs-all genome comparison approaches. Over the last years, the concept of pangenome emerged, whose goal is to capture ...
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