Research – SymBioDiversity Associate Team

Visits, internships, collaborations, workshops

2023: Visit of Constanza Andreani (CMM, U. Chile) in Pleiade team (Inria Bordeaux) for a month and a half.
2023: Internships Chile of Rafael Kaempfer Danin (U. Pontifica Catolica) in Pleiade team (Inria Bordeaux). Spatio-temporal modelling of communities through the coupling of microbe-scale metabolic models with PDE models. Supported by Inria and Inria Chile.
2022: Visit of Alejandro Maass in Dyliss team (Inria Rennes).
2022: Internships Chile of Arie Wortsman Zurich (U. de Chile) in Pleiade team (Inria Bordeaux). Statistical learning of microbial metabolism: metamodelling of genome-scale metabolic models. Supported by Inria and Inria Chile.
2022: Workshop SymBioDiversity at the CMM (U. de Chile) with seminars of multiple members of the associated team.
2020: Internship of Adriana Concha Sepulveda supported by Inria Chile. Integration of metagenomic datasets of Atacama desert at the metabolic scale.

Metage2Metabo: Efficient computation of complementarity and redundancy in large-scale microbial communities and computation of minimal communities with desired functional traits.
Construction of metabolic networks for 200 strains and MAGs present in the Atacama desert. Structuration and consolidation of a sparql endpoint to explore and query the metabolic networks data and additional diversity metadata. Design of queries relevant for the application study (Internship of A. Concha, support by inria Chile).
Inference of metabolic networks from taxonomic affiliations
AuCoMe: inference and comparison of metabolic networks from heterogenous sets of annotated genomes. [more info]

Analysis of the impact of microbial interactions on Clostridium difficile infection thanks to evolutionary algorithm, used to explore and identify Boolean networks that agree with data about the infection of the bacterium Clostridium difficile in order to cluster Boolean networks which share similar dynamic behaviors.
Classification of mutualistic microbial interactions in large-scale ecosystems.
Enterosignatures as descriptors of the human gut microbiome diversity. [more info]

Multi–objective–based method to analyze metabolic relationships exhibited in microbial communities thanks to a space of all feasible metabolic steady states, identifying regions where metabolic fluxes present qualitative changes. Illustration on a microbial community composed by two bioleaching bacteria and on a community composed of four strains of Escherichia coli. [more info]