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Community-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing

hal.structure.identifierQuadram Institute
hal.structure.identifierEarlham Institute [Norwich]
dc.contributor.authorCERK, Klara
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorUGALDE-SALAS, Pablo
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
dc.contributor.authorGHASSEMI NEDJAD, Chabname
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorLECOMTE, Maxime
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorMULLER, Coralie
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorSHERMAN, David James
hal.structure.identifierQuadram Institute
hal.structure.identifierEarlham Institute [Norwich]
dc.contributor.authorHILDEBRAND, Falk
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLABARTHE, Simon
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorFRIOUX, Clémence
dc.date.created2023
dc.date.issued2024-01-20
dc.identifier.issn1751-7915
dc.description.abstractEnBuilding 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.
dc.description.sponsorshipComputationel models of crop plant microbial biodiversity - ANR-22-PEAE-0011
dc.language.isoen
dc.publisherWiley
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enMetagenomics
dc.subject.enMetabolic networks
dc.subject.enModelling
dc.subject.enMicrobial community
dc.subject.enThird generation sequencing
dc.title.enCommunity-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing
dc.typeArticle de revue
dc.identifier.doi10.1111/1751-7915.14396
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.description.sponsorshipEuropeerc-stg-948219
bordeaux.journalMicrobial Biotechnology
bordeaux.peerReviewedoui
hal.identifierhal-04409251
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-04409251v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Microbial%20Biotechnology&rft.date=2024-01-20&rft.eissn=1751-7915&rft.issn=1751-7915&rft.au=CERK,%20Klara&UGALDE-SALAS,%20Pablo&GHASSEMI%20NEDJAD,%20Chabname&LECOMTE,%20Maxime&MULLER,%20Coralie&rft.genre=article


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