Community-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing
UGALDE-SALAS, Pablo
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
GHASSEMI NEDJAD, Chabname
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Laboratoire Bordelais de Recherche en Informatique [LaBRI]
Leer más >
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Laboratoire Bordelais de Recherche en Informatique [LaBRI]
UGALDE-SALAS, Pablo
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
GHASSEMI NEDJAD, Chabname
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Laboratoire Bordelais de Recherche en Informatique [LaBRI]
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Laboratoire Bordelais de Recherche en Informatique [LaBRI]
LECOMTE, Maxime
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
MULLER, Coralie
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
SHERMAN, David James
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
LABARTHE, Simon
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Biodiversité, Gènes & Communautés [BioGeCo]
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Biodiversité, Gènes & Communautés [BioGeCo]
FRIOUX, Clémence
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
< Leer menos
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
Idioma
en
Article de revue
Este ítem está publicado en
Microbial Biotechnology. 2024-01-20
Wiley
Resumen en inglés
Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genomescale metabolic network reconstructions (GENREs) are especially relevant as a means to ...Leer más >
Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genomescale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally-occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta-)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third generation sequencing, and we discuss the opportunities of long read sequencing, strain-level characterisation, and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.< Leer menos
Palabras clave en inglés
Metagenomics
Metabolic networks
Modelling
Microbial community
Third generation sequencing
Proyecto europeo
erc-stg-948219
Proyecto ANR
Computationel models of crop plant microbial biodiversity
Orígen
Importado de HalCentros de investigación