The microbiome, from a bioinformatics perspective

Submitted on 02/02/2021

At IRISA, researchers are working on the theme of microbiomes, notably within the GenScale and GenScale teams, in collaboration with several biology and health groups in the Brittany region. Several projects are in progress or start this year (industrial, collaborative, CIFRE, ANR...) including the ongoing projects SeqDigger, Idealg, Rapsodyn and Prolific to name a few, while waiting for the start of the Deep Impact and Seebioz projects this year.

During the Microbiomes Day, which took place in Rennes on October 01, various aspects concerning the place of microbiotes were discussed, notably on human health, for the development and resistance of plants and algae.  The understanding of this microbiota was also widely approached from a bioinformatics perspective, in particular through research and collaborative projects with IRISA :

  • Kevin DA SILVA, PhD student in the Genscale team: "Identification and quantification of strains in a strain mixture using variation graphs", as part of a project aimed at better characterizing intestinal microbiota data, in continuation of the work implemented by Genscale in the GATB software suite (
  • Arnaud BELCOUR, PhD student in the Dyliss research team: "Using metabolic complementarity in microbiome to understand interactions among organisms", who presented in particular the application of the metage2metabo tool ( in the framework of a collaboration with the Inrae center of Rheu.
  • The results presented by Elham KARIMI (LBI2M, Roscoff) "Expanding our understanding of the algal holobiont: potential keystone bacterial species of Ectocarpus singled out through metabolic complementarity", are the result of collaboration with the Dyliss research team, in particular the use of the AuReMe and miscoto tools.
  • And finally through the intervention of Christophe MOUGEL (IGEPP, Le Rheu): "The microbiota of plants, a scientific challenge". Presentation of a DeepImpact project (in the framework of "PPR Protecting and Cultivating differently") where the Dyliss and Genscale research teams are partners to identify synthetic communities to explain the response of plant bacterial environments.

To view or review the presentations from the Microbiomes Day, follow this link