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9 results on '"Bordron, Philippe"'

1. Could the Microbiota Be a Predictive Factor for the Clinical Response to Probiotic Supplementation in IBS-D? A Cohort Study

Author

Marchix, Justine, primary, Quénéhervé, Lucille, additional, Bordron, Philippe, additional, Aubert, Philippe, additional, Durand, Tony, additional, Oullier, Thibauld, additional, Blondeau, Claude, additional, Ait Abdellah, Samira, additional, Bruley des Varannes, Stanislas, additional, Chaffron, Samuel, additional, Coron, Emmanuel, additional, and Neunlist, Michel, additional

Published
2023
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2. Maternal prebiotic supplementation impacts colitis development in offspring mice

Author

Lê, Amélie, primary, Selle, Amandine, additional, Aubert, Philippe, additional, Durand, Tony, additional, Brosseau, Carole, additional, Bordron, Philippe, additional, Delage, Erwan, additional, Chaffron, Samuel, additional, Petitfils, Camille, additional, Cenac, Nicolas, additional, Neunlist, Michel, additional, Bodinier, Marie, additional, and Rolli-Derkinderen, Malvyne, additional

Published
2023
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3. Fecal Supernatant from Adult with Autism Spectrum Disorder Alters Digestive Functions, Intestinal Epithelial Barrier, and Enteric Nervous System

Author

Gonzales, Jacques, Marchix, Justine, Aymeric, Laetitia, Le Berre-Scoul, Catherine, Zoppi, Johanna, Bordron, Philippe, Burel, Marie, Davidovic, Laetitia, Richard, Jean-Romain, Gaman, Alexandru, Lejuste, Florian, Brouillet, Julie, Le Vacon, Françoise, Chaffron, Samuel, Leboyer, Marion, Boudin, Hélène, Neunlist, Michel, The Enteric Nervous System in gut and brain disorders [U1235] (TENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Fondation FondaMental [Créteil], Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Hôpital Henri Mondor, Biofortis Mérieux NutriSciences [Saint-Herblain], Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), and NantesU M, Dépôt

Subjects
[SDV] Life Sciences [q-bio], enteric nervous system, QH301-705.5, intestinal permeability, [SDV]Life Sciences [q-bio], mental disorders, microbiota, autism, Biology (General), Article, bacterial metabolite
Abstract

International audience; Autism Spectrum Disorders (ASDs) are neurodevelopmental disorders defined by impaired social interactions and communication with repetitive behaviors, activities, or interests. Gastrointestinal (GI) disturbances and gut microbiota dysbiosis are frequently associated with ASD in childhood. However, it is not known whether microbiota dysbiosis in ASD patients also occurs in adulthood. Further, the consequences of altered gut microbiota on digestive functions and the enteric nervous system (ENS) remain unexplored. Therefore, we studied, in mice, the ability offecal supernatant (FS) from adult ASD patients to induce GI dysfunctions and ENS remodeling. First, the analyses of the fecal microbiota composition in adult ASD patients indicated a reduced α-diversity and increased abundance of three bacterial 16S rRNA gene amplicon sequence variants compared to healthy controls (HC). The transfer of FS from ASD patients (FS–ASD) to mice decreased colonic barrier permeability by 29% and 58% compared to FS–HC for paracellular and transcellular permeability, respectively. These effects are associated with the reduced expression of the tight junction proteins JAM-A, ZO-2, cingulin, and proinflammatory cytokines TNFα and IL1β. In addition, the expression of glial and neuronal molecules was reduced by FS–ASD as compared to FS-HC in particular for those involved in neuronal connectivity (βIII-tubulin and synapsin decreased by 31% and 67%, respectively). Our data suggest that changes in microbiota composition in ASD may contribute to GI alterations, and in part, via ENS remodeling.

Published
2021
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4. Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses

Author

Thomas, François, Bordron, Philippe, Eveillard, Damien, Michel, Gurvan, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Inria Chile, Universidad Diego Portales [Santiago] (UDP)-Universidad de la frontera [Chile]-Universidad de Concepción [Chile]-Pontificia Universidad Católica de Chile (UC)-Institut National de Recherche en Informatique et en Automatique (Inria)-Pontificia Universidad Católica de Valparaíso (PUCV)-Universidad Adolfo Ibáñez [Santiago]-Universidad de Valparaiso [Chile]-Universidad Tecnica Federico Santa Maria [Valparaiso] (UTFSM), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Mathomics, Universidad de Chile = University of Chile [Santiago] (UCHILE), Center for Genome Regulation [Santiago] (CGR), Laboratoire des Sciences du Numérique de Nantes (LS2N), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Combinatoire et Bioinformatique (COMBI), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), GIS Marine Genomics, Fondap 15090007, Basal program PFB-03 CMM, IntegrativeBioChile INRIAAssoc. Team, CIRIC-INRIA Chile (line Natural Resources), ANR-10-BTBR-0004,IDEALG,Biotechnologies pour la valorisation des macroalgues(2010), ANR-14-CE19-0020,BLUE ENZYMES,Découverte de nouvelles enzymes pour la valorisation de la biomasse algale(2014), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universidad Diego Portales [Santiago] (UDP)-Universidad de la frontera [Chile]-Pontificia Universidad Católica de Chile (UC)-Institut National de Recherche en Informatique et en Automatique (Inria)-Pontificia Universidad Católica de Valparaíso (PUCV)-Universidad Adolfo Ibáñez [Santiago]-Universidad de Valparaiso [Chile]-Universidad Tecnica Federico Santa Maria [Valparaiso] (UTFSM)-Universidad de Concepción - University of Concepcion [Chile], Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), and Combinatoire et Bioinformatique (LS2N - équipe COMBI)

Subjects
fungi, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], food and beverages, polysaccharide utilization locus, biochemical phenomena, metabolism, and nutrition, Microbiology, operon, flavobacteria-algae interactions, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], natural sciences, regulation of gene expression, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], microarray, geographic locations, Original Research, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Flavobacteriia are recognized as key players in the marine carbon cycle, due to their ability to efficiently degrade algal polysaccharides both in the open ocean and in coastal regions. The chemical complexity of algal polysaccharides, their differences between algal groups and variations through time and space, imply that marine flavobacteria have evolved dedicated degradation mechanisms and regulation of their metabolism during interactions with algae. In the present study, we report the first transcriptome-wide gene expression analysis for an alga-associated flavobacterium during polysaccharide degradation. Zobellia galactanivorans Dsij(T), originally isolated from a red alga, was grown in minimal medium with either glucose (used as a reference monosaccharide) or one selected algal polysaccharide from brown (alginate, laminarin) or red algae (agar, porphyran, ι- or κ-carrageenan) as sole carbon source. Expression profiles were determined using whole-genome microarrays. Integration of genomic knowledge with the automatic building of a co-expression network allowed the experimental validation of operon-like transcription units. Differential expression analysis revealed large transcriptomic shifts depending on the carbon source. Unexpectedly, transcriptomes shared common signatures when growing on chemically divergent polysaccharides from the same algal phylum. Together with the induction of numerous transcription factors, this hints at complex regulation events that fine-tune the cell behavior during interactions with algal biomass in the marine environment. The results further highlight genes and loci that may participate in polysaccharide utilization, notably encoding Carbohydrate Active enZymes (CAZymes) and glycan binding proteins together with a number of proteins of unknown function. This constitutes a set of candidate genes potentially representing new substrate specificities. By providing an unprecedented view of global transcriptomic responses during polysaccharide utilization in an alga-associated model flavobacterium, this study expands the current knowledge on the functional role of flavobacteria in the marine carbon cycle and on their interactions with algae.

Published
2017
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7. Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus.

Author

Nègre, Delphine, Aite, Méziane, Belcour, Arnaud, Frioux, Clémence, Brillet-Guéguen, Loraine, Liu, Xi, Bordron, Philippe, Godfroy, Olivier, Lipinska, Agnieszka P., Leblanc, Catherine, Siegel, Anne, Dittami, Simon M., Corre, Erwan, and Markov, Gabriel V.

Subjects
SACCHARINA, ABSCISIC acid, BIOSYNTHESIS, METABOLIC profile tests, ALGAE, METABOLIC models, BROWN algae, LAMINARIA
Abstract

Understanding growth mechanisms in brown algae is a current scientific and economic challenge that can benefit from the modeling of their metabolic networks. The sequencing of the genomes of Saccharina japonica and Cladosiphon okamuranus has provided the necessary data for the reconstruction of Genome–Scale Metabolic Networks (GSMNs). The same in silico method deployed for the GSMN reconstruction of Ectocarpus siliculosus to investigate the metabolic capabilities of these two algae, was used. Integrating metabolic profiling data from the literature, we provided functional GSMNs composed of an average of 2230 metabolites and 3370 reactions. Based on these GSMNs and previously published work, we propose a model for the biosynthetic pathways of the main carotenoids in these two algae. We highlight, on the one hand, the reactions and enzymes that have been preserved through evolution and, on the other hand, the specificities related to brown algae. Our data further indicate that, if abscisic acid is produced by Saccharina japonica, its biosynthesis pathway seems to be different in its final steps from that described in land plants. Thus, our work illustrates the potential of GSMNs reconstructions for formalizing hypotheses that can be further tested using targeted biochemical approaches. [ABSTRACT FROM AUTHOR]

Published
2019
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8. SIPPER: A flexible method to integrate heterogeneous data into a metabolic network

Author

Laboratoire d'Informatique de Nantes Atlantique (LINA) ; CNRS - Université de Nantes - École Nationale Supérieure des Mines - Nantes, Bordron, Philippe, Eveillard, Damien, Rusu, Irena, Laboratoire d'Informatique de Nantes Atlantique (LINA) ; CNRS - Université de Nantes - École Nationale Supérieure des Mines - Nantes, Bordron, Philippe, Eveillard, Damien, and Rusu, Irena

Abstract

6 pages, International audience, With the accumulation of available 'omics' data, developing automatic methods for integrating and analyzing them into a common context has become a key goal in bioinformatics. In this paper, we propose a general framework (called SIPPER) to integrate heterogeneous information from one or several external data sources into a metabolic network, and to perform an automatic, data-independent analysis. Our approach consists in including neighborhood/non-neighborhood information about proteins and genes into a metabolic network, via the admitted paradigm 'gene produces enzyme(s)'. The integration of this neighborhood information uses a distance involving data about genomic location, or gene expression, or connectivity in a PPI network. It may also use any freely chosen notion of distance between genes or proteins. The resulting model is a new (so-called integrated) network. Its low weight paths are the reaction chains of the metabolic network that are catalyzed by groups of closely related enzymes (according to the information the user chooses to integrate). Consequently, integrating heterogeneous knowledge using SIPPER allows us to find associations between genes, enzymes and metabolic reaction chains involved together in the system behavior.

9. Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses.

Author

Thomas F, Bordron P, Eveillard D, and Michel G

Abstract

Flavobacteriia are recognized as key players in the marine carbon cycle, due to their ability to efficiently degrade algal polysaccharides both in the open ocean and in coastal regions. The chemical complexity of algal polysaccharides, their differences between algal groups and variations through time and space, imply that marine flavobacteria have evolved dedicated degradation mechanisms and regulation of their metabolism during interactions with algae. In the present study, we report the first transcriptome-wide gene expression analysis for an alga-associated flavobacterium during polysaccharide degradation. Zobellia galactanivorans Dsij T , originally isolated from a red alga, was grown in minimal medium with either glucose (used as a reference monosaccharide) or one selected algal polysaccharide from brown (alginate, laminarin) or red algae (agar, porphyran, ι- or κ-carrageenan) as sole carbon source. Expression profiles were determined using whole-genome microarrays. Integration of genomic knowledge with the automatic building of a co-expression network allowed the experimental validation of operon-like transcription units. Differential expression analysis revealed large transcriptomic shifts depending on the carbon source. Unexpectedly, transcriptomes shared common signatures when growing on chemically divergent polysaccharides from the same algal phylum. Together with the induction of numerous transcription factors, this hints at complex regulation events that fine-tune the cell behavior during interactions with algal biomass in the marine environment. The results further highlight genes and loci that may participate in polysaccharide utilization, notably encoding Carbohydrate Active enZymes (CAZymes) and glycan binding proteins together with a number of proteins of unknown function. This constitutes a set of candidate genes potentially representing new substrate specificities. By providing an unprecedented view of global transcriptomic responses during polysaccharide utilization in an alga-associated model flavobacterium, this study expands the current knowledge on the functional role of flavobacteria in the marine carbon cycle and on their interactions with algae.

Published
2017
Full Text
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