Florian TRIGODET Microbial genomic dynamism : rapid and unseen genomic alterations in microbial population
invité par Aude BATTISTELLA - Section Ecologie et Biologie de l’Evolution
12h
Le séminaire de Florian TRIGODET (Helmholtz Institute for Functional Marine Biodiversity) aura lieu dans la salle Favard, IBENS 46 rue d’Ulm 75005 Paris
Abstract : Microbial ecology relies on the simplification of the microbial diversity into discrete entities. Such entities, whether they are pangenomes, taxon names, amplicons sequence variants, or population genomes, enable quantitative and qualitative investigations as we seek to understand the interplay between microbes and their environments. Due to challenges associated with popular computational strategies and sequencing technologies, phenotypes of such discrete entities are de facto assumed to remain conserved across environments, despite decades of research that shows that heritable and non-heritable genetic alterations can rapidly change lifestyles of individual microbial populations in short evolutionary time scales. Here we used genome-resolved metagenomics, long-read sequencing and fecal microbiota transplantation to investigate rapid genomic alterations to donor microbial populations as they colonize distinct recipients. Our analyses reveal significant alterations to donor microbial population genomes in FMT recipients within weeks through multiple distinct mechanisms, such as inversions and diversity generating retroelements. Among our results, Bacteroides fragilis and Akkermansia muciniphila were the most dynamic populations with genomic inversions disrupting and re-organizing open-reading frames of a restriction modification system as well as promoter inversions regulating membrane related genes. Our findings show that characterizing genomic dynamism within complex ecosystems is quite underestimated at the moment, despite the massive functional implications of such events.