• Le 25 avril 2019
    De 11:00 à 12:00
    Campus Lombarderie
    Amphi du LS2N, bâtiment 34

Le Laboratoire des Sciences du Numérique de Nantes (LS2N - Université de Nantes - CNRS - Centrale Nantes - IMT Atlantique) accueille le Docteur Christopher Quince (University of Warwick, UK) lors d'un séminaire ouvert à tous, le jeudi 25 avril prochain.

Resolving de novo strain variation from metagenomes for high resolution analysis of microbiomes

Dr Christopher Quince (University of Warwick)

The importance of strain level variation in the human microbiome is well established. Short read metagenomics has the resolution to resolve strains but most current approaches require reference genomes. Methods for de novo resolving strains are still an area of active development. Strains cannot be simply assembled from metagenomes due to the complexity of the assembly graph when multiple closely related genomes are present. This results in fragmented assemblies of potentially millions of contigs. It is possible to cluster or bin contigs into metagenome assembled genomes (MAGs) using composition and co-occurrence across multiple samples. I will introduce our binning algorithm CONCOCT and illustrate its application to both environmental and human-associated microbial communities. However, the MAGs that result from metagenome binning are still composites of multiple strains. I will also demonstrate how co-occurrence across samples can also be used to resolve sub populations within MAGs, using our DESMAN (De novo extraction of strains from metagenomes) pipeline. This leads to a higher resolution picture of microbial community changes.