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Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines

hal.structure.identifierLaboratoire de Biologie Intégrative des Modèles Marins [LBI2M]
dc.contributor.authorKARIMI, Elham
hal.structure.identifierLaboratoire de Biologie Intégrative des Modèles Marins [LBI2M]
hal.structure.identifierStation biologique de Roscoff = Roscoff Marine Station [SBR]
dc.contributor.authorGESLAIN, Enora
hal.structure.identifierDynamics, Logics and Inference for biological Systems and Sequences [Dyliss]
dc.contributor.authorBELCOUR, Arnaud
hal.structure.identifierQuadram Institute
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorFRIOUX, Clémence
hal.structure.identifierDynamics, Logics and Inference for biological Systems and Sequences [Dyliss]
dc.contributor.authorAITE, Méziane
hal.structure.identifierDynamics, Logics and Inference for biological Systems and Sequences [Dyliss]
dc.contributor.authorSIEGEL, Anne
hal.structure.identifierStation biologique de Roscoff = Roscoff Marine Station [SBR]
hal.structure.identifierFédération de recherche de Roscoff [FR2424]
dc.contributor.authorCORRE, Erwan
hal.structure.identifierLaboratoire de Biologie Intégrative des Modèles Marins [LBI2M]
dc.contributor.authorDITTAMI, Simon
dc.date.issued2021-05-06
dc.identifier.issn2167-8359
dc.description.abstractEnAnimals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases.
dc.description.sponsorshipBiotechnologies pour la valorisation des macroalgues - ANR-10-BTBR-0004
dc.language.isoen
dc.publisherPeerJ
dc.subject.enBioinformatics
dc.subject.enComputational Biology
dc.subject.enGenomics
dc.subject.enMicrobiology
dc.subject.enComputational Gene prediction
dc.subject.enFunctional annotation
dc.subject.enGenome-scale metabolic networks
dc.subject.enMetabolic complementary analyses
dc.subject.enMetabolic exchanges
dc.subject.enHolobionts
dc.title.enRobustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines
dc.typeArticle de revue
dc.identifier.doi10.7717/peerj.11344
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
bordeaux.journalPeerJ
bordeaux.page1-24
bordeaux.volume9
bordeaux.peerReviewedoui
hal.identifierhal-03223662
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03223662v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PeerJ&rft.date=2021-05-06&rft.volume=9&rft.spage=1-24&rft.epage=1-24&rft.eissn=2167-8359&rft.issn=2167-8359&rft.au=KARIMI,%20Elham&GESLAIN,%20Enora&BELCOUR,%20Arnaud&FRIOUX,%20Cl%C3%A9mence&AITE,%20M%C3%A9ziane&rft.genre=article


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