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).

 

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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panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of Genome Plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to Genomic Islands (GIs). The study of those regions at the species level has ...
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Discovery of the complete catabolic pathway for red algal carrageenans in marine bacteria

Discovery of the complete catabolic pathway for red algal carrageenans in marine bacteria An international consortium coordinated by the Marine Glycobiology team (UMR8227 – CNRS/UPMC) has just published the discovery of the complete system for the utilization of carrageenans, sulfated polysaccharides which are a major component of the cell walls ...
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Conceptualization and exploitation of a partitioned pangenome graph as a compact representation dedicated to the characterization of the diversity of the genomic repertoire of a bacterial species

Introduced in microbiology in 2005 by Medini et al. and Tettelin et al., pangenome approaches aim to compile the entire genomic diversity of a species. In these studies, we generally distinguish within the pangenome, the core genome: the set of gene families where gene representatives are present in all organisms; ...
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Large scale comparative genomics of Escherichia coli responsible for human bacteremia: clinical involvements and role of metabolic pathway.

E. coli is the first causative agent among community-acquired bacteraemia and it is also the most abundant species among facultative anaerobic bacteria in human gastro-intestinal tract (Tenaillon et al., Nat. Rev. Microbiol, 2010; Martin et al., N. Engl. J. Med., 2003). To understand the physiopathology of extra-intestinal infections, many traits ...
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Mining secondary metabolites in cyanobacterial genomes

Cyanobacteria are an ancient lineage of photosynthetic bacteria, which are prolific producers of secondary metabolites. Hundreds of bioactive compounds with diverse chemical structures , such as toxins and molecules of pharmaceutical interest, have been characterized from cyanobacteria ...
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