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Community assembly Microbial communities Colonization Diversity Joint species distribution models Seed ARABIDOPSIS-THALIANA Environment TAKE-ALL FUNGUS Bacterial transmission Horizontal gene transfer Metabarcoding Phyllosphere Microbiome Spermosphere Seed microbiota Microbiota Endophyte Transmission BIOLOGICAL-CONTROL
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Matthieu Barret

I obtained my PhD in Microbiology in 2009 at Agrocampus Ouest (Rennes), studying bacterial-fungal interactions in the wheat rhizosphere. As a post-doctoral fellow with Fergal O’Gara at the University College Cork, I investigated the role of bacterial secretion systems in the rhizosphere competence of beneficial Pseudomonas strains. Since 2012, I worked as an INRAE scientist iat the IRHS (Angers). My research focuses on the the biological and ecological processes involved in the assembly of seed microbiota.

Article dans une revue50 documents

  • Clemence Canivet, Norma David, Helene Pailhoriès, Martial Briand, Cynthia Guy, et al.. Cross-linkage between bacterial taxonomy and gene functions: a study of metagenome-assembled genomes of Gut Microbiota in adult non-alcoholic fatty liver disease.. Alimentary Pharmacology & Therapeutics (Suppl), 2021, ⟨10.1111/apt.16262⟩. ⟨hal-03138752⟩
  • Tania Fort, Charlie Pauvert, Amy Zanne, Otso Ovaskainen, Thomas Caignard, et al.. Maternal effects shape the seed mycobiome in Quercus petraea. New Phytologist, Wiley, In press, pp.1-15. ⟨10.1111/nph.17153⟩. ⟨hal-03140262⟩
  • Guillaume Chesneau, Gloria Torres-Cortes, Martial Briand, Armelle Darrasse, Anne Preveaux, et al.. Temporal dynamics of bacterial communities during seed development and maturation. FEMS Microbiology Ecology, Wiley-Blackwell, 2020, 96 (12), pp.fiaa190. ⟨10.1093/femsec/fiaa190⟩. ⟨hal-02972234⟩
  • Alberto Prado Farias, Brice Marolleau, Bernard Vaissière, Matthieu Barret, Gloria Torres-Cortés. Insect pollination: an ecological process involved in the assembly of the seed microbiota. Scientific Reports, Nature Publishing Group, 2020, 10 (1), ⟨10.1038/s41598-020-60591-5⟩. ⟨hal-02623164⟩
  • Tania Fort, Charlie Pauvert, Amy Zanne, Otso Ovaskainen, Thomas Caignard, et al.. Maternal effects shape the seed mycobiome in Quercus petraea. New Phytologist, Wiley, In press, ⟨10.1111/nph.17153⟩. ⟨hal-03087294⟩
  • Alberto Prado Farias, Brice Marolleau, Bernard Vaissière, Matthieu Barret, Gloria Torres Cortes. Insect pollination is an ecological process involved in the assembly of the seed microbiota. BioRxiv, 2019, ⟨10.1101/626895⟩. ⟨hal-02624711⟩
  • Martial Briand, Mariam Bouzid, Gilles Hunault, Marc Legeay, Marion Le Saux, et al.. A rapid and simple method for assessing and representing genome sequences relatedness. BioRxiv, 2019, ⟨10.1101/569640⟩. ⟨hal-02171444⟩
  • Jean-Claude Ogier, Sylvie Pages, Maxime Galan, Matthieu Barret, Sophie Gaudriault. rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing. BMC Microbiology, BioMed Central, 2019, 19, ⟨10.1186/s12866-019-1546-z⟩. ⟨hal-02627663⟩
  • Lydie Kerdraon, Marie-Helene Balesdent, Matthieu Barret, Valerie Laval, Frederic Suffert. Crop Residues in Wheat-Oilseed Rape Rotation System: a Pivotal, Shifting Platform for Microbial Meetings. Microbial Ecology, Springer Verlag, 2019, 77 (4), pp.931 - 945. ⟨10.1007/s00248-019-01340-8⟩. ⟨hal-02620072⟩
  • Tania Fort, Charlie Pauvert, Amy E. Zanne, Otso Ovaskainen, Thomas Caignard, et al.. Maternal effects and environmental filtering shape seed fungal communities in oak trees. BioRxiv, 2019, ⟨10.1101/691121⟩. ⟨hal-02624819⟩
  • Gloria Torres-Cortés, B. J. Garcia, Stéphane Compant, Samir Rezki, P Jones, et al.. Differences in resource use lead to coexistence of seed-transmitted microbial populations. Scientific Reports, Nature Publishing Group, 2019, 9 (1), pp.6648. ⟨10.1038/s41598-019-42865-9⟩. ⟨hal-02557440⟩
  • Aude Rochefort, Martial Briand, Coralie Marais, Marie-Hélène Wagner, Anne Laperche, et al.. Influence of environment and host plant genotype on the structure and diversity of the Brassica napus seed microbiota. Phytobiomes Journal, APS Publications, 2019, 3 (4), pp.326-336. ⟨10.1094/PBIOMES-06-19-0031-R⟩. ⟨hal-02275205⟩
  • Lydie Kerdraon, Matthieu Barret, Valerie Laval, Frédéric Suffert. Differential dynamics of microbial community networks help identify microorganisms interacting with residue-borne pathogens: the case of Zymoseptoria tritici in wheat;. Microbiome, BioMed Central, 2019, 7 (1), pp.125 et suiv. ⟨10.1101/587667⟩. ⟨hal-02624822⟩
  • Matthieu Barret, P. Dufour, Mylène Durand-Tardif, Mahendra Mariadassou, Christophe Mougel, et al.. Optimize the plant microbiota to increase plant growth and health. Consortium Biocontrôle et GIS Biotechnologies Vertes , 2019, ⟨10.15454/1fve-e105⟩. ⟨hal-03297096⟩
  • Samir Rezki, Claire Campion, Philippe Simoneau, Marie-Agnès Jacques, Ashley Shade, et al.. Assembly of seed-associated microbial communities within and across successive plant generations. Plant and Soil, Springer Verlag, 2018, 422 (1-2), pp.67-79. ⟨10.1007/s11104-017-3451-2⟩. ⟨hal-02516590⟩
  • Armelle Darrasse, Matthieu Barret, Sophie Cesbron, Stéphane Compant, Marie-Agnès Jacques. Niches and routes of transmission of Xanthomonas citri pv. fuscans to bean seeds. Plant and Soil, Springer Verlag, 2018, 422 (1-2), pp.115-128. ⟨10.1007/s11104-017-3329-3⟩. ⟨hal-02516672⟩
  • Laurence Svanella-Dumas, Sébastien Theil, Matthieu Barret, Thierry Candresse. Complete genomic sequence of Raphanus sativus cryptic virus 4 (RsCV4), a novel alphapartitivirus from radish. Archives of Virology, Springer Verlag, 2018, 163 (4), pp.1097-1100. ⟨10.1007/s00705-017-3693-6⟩. ⟨hal-02516679⟩
  • Elodie Belmas, Martial Briand, Anthony Kwasiborski, Justine Colou, Guillaume Nguyen, et al.. Genome sequence of the necrotrophic plant pathogen Alternaria brassicicola Abra43. Genome Announcements, American Society for Microbiology, 2018, 6 (6), pp.e01559-17. ⟨10.1128/genomeA.01559-17⟩. ⟨hal-02516580⟩
  • Carolina Escobar Rodríguez, Birgit Mitter, Matthieu Barret, Angela Sessitsch, Stéphane Compant. Commentary: seed bacterial inhabitants and their routes of colonization. Plant and Soil, Springer Verlag, 2018, 422 (1-2), pp.129-134. ⟨10.1007/s11104-017-3368-9⟩. ⟨hal-02516685⟩
  • Eric Nelson, Philippe Simoneau, Matthieu Barret, Birgit Mitter, Stéphane Compant. Editorial special issue: the soil, the seed, the microbes and the plant. Plant and Soil, Springer Verlag, 2018, 422 (1-2), pp.1-5. ⟨10.1007/s11104-018-3576-y⟩. ⟨hal-02516579⟩
  • Claudia Bartoli, Léa Frachon, Matthieu Barret, Mylène Rigal, Carine Huard-Chauveau, et al.. In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana. ISME Journal, Nature Publishing Group, 2018, 12 (8), pp.2024-2038. ⟨10.1038/s41396-018-0152-7⟩. ⟨hal-02373577⟩
  • Gloria Torres-Cortés, Sophie Bonneau, Olivier Bouchez, Clémence Genthon, Martial Briand, et al.. Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence. Frontiers in Plant Science, Frontiers, 2018, 9, pp.902. ⟨10.3389/fpls.2018.00902⟩. ⟨hal-02516666⟩
  • Déborah Merda, Martial Briand, Eran Bosis, Céline Rousseau, Perrine Portier, et al.. Ancestral acquisitions, gene flow and multiple evolutionary trajectories of the type three secretion system and effectors in Xanthomonas plant pathogens. Molecular Ecology, Wiley, 2017, 26 (21), pp.1-14. ⟨10.1111/mec.14343⟩. ⟨hal-01904571⟩
  • Ashley Shade, Marie-Agnès Jacques, Matthieu Barret. Ecological patterns of seed microbiome diversity, transmission, and assembly. Current opinion in microbiology, 2017, 37, pp.15-22. ⟨10.1016/j.mib.2017.03.010⟩. ⟨hal-02516692⟩
  • Virginie Montagne, Hervé Capiaux, Matthieu Barret, Patrice Cannavo, Sylvain Charpentier, et al.. Bacterial and fungal communities vary with the type of organic substrate: implications for biocontrol of soilless crops. Environmental Chemistry Letters, Springer Verlag, 2017, 15 (3), pp.537-545. ⟨10.1007/s10311-017-0628-0⟩. ⟨hal-01524498⟩
  • Samir Rezki, Claire Campion, Béatrice Iacomi-Vasilescu, Anne Préveaux, Youness Toualbia, et al.. Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms. PeerJ, PeerJ, 2016, 4, pp.e1923. ⟨10.7717/peerj.1923⟩. ⟨hal-01392639⟩
  • Matthieu Barret, Jean-François Guimbaud, Armelle Darrasse, Marie Agnes Jacques. Plant microbiota affects seed transmission of phytopathogenic microorganisms. Molecular Plant Pathology, Wiley, 2016, 17 (6), pp.791-795. ⟨10.1111/mpp.12382⟩. ⟨hal-01353543⟩
  • Elisa Michel, Clarisse Monfort, Marion Deffrasnes, Stéphane Guezenec, Emilie Lhomme, et al.. Characterization of relative abundance of lactic acid bacteria species in French organic sourdough by cultural, qPCR and MiSeq high-throughput sequencing methods. International Journal of Food Microbiology, Elsevier, 2016, 239, pp.35-43. ⟨10.1016/j.ijfoodmicro.2016.07.034⟩. ⟨hal-01527569⟩
  • Matthieu Barret, Mariana Machado, Lionel Fizanne, Felix Araujo-Perez, Cynthia Guy, et al.. The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. Hepatology, Wiley-Blackwell, 2016, 63 (3), pp.764-75. ⟨10.1002/hep.28356⟩. ⟨hal-02516681⟩
  • Jérôme Boursier, Matthieu Barret, Anna Mae Diehl. Answer to Ling et al “Predictive roles of gut dysbiosis on the severity of NAFLD”. Hepatology, Wiley-Blackwell, 2016, 64 (3), pp.994-995. ⟨10.1002/hep.28562⟩. ⟨hal-02632028⟩
  • Stéphanie Klaedtke, Marie Agnes Jacques, Lorenzo Raggi, Anne Preveaux, Sophie Bonneau, et al.. Terroir is a key driver of seed-associated microbial assemblages. Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2016, 18 (6), pp.1792-1804. ⟨10.1111/1462-2920.12977⟩. ⟨hal-01455975⟩
  • Matthieu Barret, Martial Briand, Sophie Bonneau, Anne Préveaux, Sophie Valière, et al.. Emergence Shapes the Structure of the Seed Microbiota. Applied and Environmental Microbiology, American Society for Microbiology, 2015, 81 (4), pp.1257-1266. ⟨10.1128/AEM.03722-14⟩. ⟨hal-01153480⟩
  • Aurélie Deveau, Matthieu Barret, Abdala Gamby Diedhiou, Johan Leveau, Wietse de Boer, et al.. Pairwise transcriptomic analysis of the interactions between the ectomycorrhizal fungus laccaria bicolor S238N and three beneficial, neutral and antagonistic soil bacteria. Microbial Ecology, Springer Verlag, 2015, 69 (1), pp.146-159. ⟨10.1007/s00248-014-0445-y⟩. ⟨hal-01208788⟩
  • Hao Tan, Marlies J Mooij, Matthieu Barret, Pardraig M Hegarty, Catriona Harington, et al.. Identification of novel phytase genes from an agricultural soil-derived metagenome.. World Journal of Microbiology and Biotechnology, Springer Verlag, 2014, 24 (1), pp.113-8. ⟨10.4014/jmb.1307.07007⟩. ⟨hal-02639216⟩
  • Frank Egan, Matthieu Barret, Fergal O'Gara. The SPI-1-like Type III secretion system: more roles than you think. Frontiers in Plant Science, Frontiers, 2014, 5, ⟨10.3389/fpls.2014.00034⟩. ⟨hal-01210004⟩
  • Muriel Marchi, Morgane Boutin, Kévin Gazengel, Claude Rispe, Jean-Pierre Gauthier, et al.. Genomic analysis of the biocontrol strain Pseudomonas fluorescens Pf29Arp with evidence of T3SS and T6SS gene expression on plant roots. Environmental Microbiology Reports, Wiley, 2013, 5 (3), pp.393 - 403. ⟨10.1111/1758-2229.12048⟩. ⟨hal-01208629⟩
  • F. Jerry Reen, Matthieu Barret, Emilie Fargier, Marcus O’muinneacháin, Fergal O’gara. Molecular evolution of LysR-type transcriptional regulation in Pseudomonas aeruginosa. Molecular Phylogenetics and Evolution, Elsevier, 2013, 66 (3), pp.1041-1049. ⟨10.1016/j.ympev.2012.12.014⟩. ⟨hal-02649223⟩
  • Robert Phelan, Matthieu Barret, Paul Cotter, Paula O'Connor, Rui Chen, et al.. Subtilomycin: A New Lantibiotic from Bacillus subtilis Strain MMA7 Isolated from the Marine Sponge Haliclona simulans. Marine drugs, MDPI, 2013, 11 (6), pp.1878-1898. ⟨10.3390/md11061878⟩. ⟨hal-02651130⟩
  • Hao Tan, Matthieu Barret, Marlies J. Mooij, Olivia Rice, John P. Morrissey, et al.. Long-term phosphorus fertilisation increased the diversity of the total bacterial community and the phoD phosphorus mineraliser group in pasture soils. Biology and Fertility of Soils, Springer Verlag, 2013, 49 (6), pp.661-672. ⟨10.1007/s00374-012-0755-5⟩. ⟨hal-02653047⟩
  • Matthieu Barret, Frank Egan, Fergal O'Gara. Distribution and diversity of bacterial secretion systems across metagenomic datasets.. Environmental Microbiology Reports, Wiley, 2013, 5 (1), pp.117-26. ⟨10.1111/j.1758-2229.2012.00394.x⟩. ⟨hal-02653049⟩
  • Miguel Redondo-Nieto, Matthieu Barret, John Morrissey, Kieran Germaine, Francisco Martínez-Granero, et al.. Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction. BMC Genomics, BioMed Central, 2013, 14 (1), pp.1-17. ⟨10.1186/1471-2164-14-54⟩. ⟨hal-02650368⟩
  • Matthieu Barret, Frank Egan, Jennifer Moynihan, John P. Morrissey, Olivier Lesouhaitier, et al.. Characterization of the SPI-1 and Rsp type three secretion systems inPseudomonas fluorescens F113. Environmental Microbiology Reports, Wiley, 2013, 5 (3), pp.377-386. ⟨10.1111/1758-2229.12039⟩. ⟨hal-02644403⟩
  • M. Redondo-Nieto, Matthieu Barret, J. P. Morrisey, K. Germaine, F. Martinez-Granero, et al.. Genome Sequence of the Biocontrol Strain Pseudomonas fluorescens F113. Journal of Bacteriology, American Society for Microbiology, 2012, 194 (5), pp.1273-1274. ⟨10.1128/JB.06601-11⟩. ⟨hal-02652031⟩
  • Matthieu Barret, John P. Morrissey, Fergal O’gara. Functional genomics analysis of plant growth-promoting rhizobacterial traits involved in rhizosphere competence. Biology and Fertility of Soils, Springer Verlag, 2011, 47 (7), pp.729-743. ⟨10.1007/s00374-011-0605-x⟩. ⟨hal-02650050⟩
  • Matthieu Barret, F. Egan, E. Fargier, J. P. Morrissey, F. O'Gara. Genomic analysis of the type VI secretion systems in Pseudomonas spp.: novel clusters and putative effectors uncovered. Microbiology, Microbiology Society, 2011, 157 (6), pp.1726-1739. ⟨10.1099/mic.0.048645-0⟩. ⟨hal-02650365⟩
  • Pascale Frey-Klett, Peter Burlinson, Aurélie Deveau, Matthieu Barret, M. Tarkka, et al.. Bacterial-fungal Interactions: hyphens between agricultural, clinical, environmental, and food microbiologists. Microbiology and Molecular Biology Reviews, American Society for Microbiology, 2011, 75 (4), pp.583 - +. ⟨10.1128/MMBR.00020-11⟩. ⟨hal-02651157⟩
  • Thomas Browne, Matthieu Barret, Fergal O'Gara, John P Morrissey. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria. BMC Microbiology, BioMed Central, 2010, 10 (1), pp.1-12. ⟨10.1186/1471-2180-10-300⟩. ⟨hal-02656830⟩
  • Matthieu Barret, P. Frey-Klett, M. Boutin, Anne-Yvonne Guillerm-Erckelboudt, Frédérique Martin, et al.. The plant pathogenic fungus Gaeumannomyces graminis var. tritici improves bacterial growth and triggers early gene regulations in the biocontrol strain Pseudomonas fluorescens Pf29Arp. New Phytologist, Wiley, 2009, 181 (2), pp.435-447. ⟨10.1111/j.1469-8137.2008.02675.x⟩. ⟨inria-00359115⟩
  • Matthieu Barret, Pascale Frey-Klett, Anne-Yvonne Guillerm-Erckelboudt, Morgane Boutin, Grégory Guernec, et al.. Effect of wheat roots infected with the pathogenic fungus gaeumannomyces graminis var. tritici on gene expression of the biocontrol bacterium pseudomonas fluorescens Pf29Arp. Molecular Plant-Microbe Interactions, American Phytopathological Society, 2009, 22 (12), pp.1611-1623. ⟨10.1094/MPMI-22-12-1611⟩. ⟨hal-02663862⟩
  • Alain Sarniguet, Matthieu Barret, Lionel Lebreton, Stéphanie Daval. Bactéries et champignons interagissent pour la santé des plantes. Biofutur, Elsevier - Cachan : Lavoisier, 2008, 284, pp.30-33. ⟨hal-02664697⟩

Ouvrage (y compris édition critique et traduction)1 document

  • Xavier Fauvergue, Adrien Rusch, Matthieu Barret, Marc Bardin, Emmanuelle Jacquin-Joly, et al.. Biocontrôle : Éléments pour une protection agroécologique des cultures. Editions Quae, 376 p., 2020, Savoir Faire (Quae), 978-2-7592-3076-1. ⟨hal-02791036⟩

Chapitre d'ouvrage5 documents

  • Matthieu Barret, Marc Buée, Christophe Mougel, Corinne Vacher. Le microbiote des plantes : diversité, transmission et fonction. Biocontrôle. Éléments pour une protection agroécologique des cultures., Editions Quae, 376 p., 2020, Savoir Faire, 978-2-7592-3076-1. ⟨hal-03319624⟩
  • Philippe Lemanceau, Matthieu Barret, Manuel Blouin, Sylvie Mazurier, Barbara Pivato. Plant/micro-organism interactions in the rhizosphere. Chap 4. Soils as a Key Component of the Critical Zone vol 6 Geosciences Series – Soils Set, ISTE Ltd and John Wiley & Sons, 2018, 978-1-119-57311-1. ⟨hal-02786890⟩
  • Philippe Lemanceau, Matthieu Barret, Manuel Blouin, Sylvie Mazurier, Barbara Pivato. Interactions plantes/micro-organismes dans la rhizosphère. Les sols au coeur de la zone critique 6, écologie, ISTE, 2018, ISBN : 9781784053840 (papier) ISBN : 9781784063849 (ebook). ⟨hal-02786073⟩
  • Philippe Lemanceau, Matthieu Barret, Sylvie Mazurier, Samuel Mondy, Barbara Pivato, et al.. Plant communication with associated microbiota in the spermosphere, rhizosphere and phyllosphere. How plants communicate with their biotic environment, 82, Academic Press - Elsevier, 2017, Advances in Botanical Research, 978-0-12-801431-8. ⟨10.1016/bs.abr.2016.10.007⟩. ⟨hal-01608302⟩
  • Matthieu Barret, Pascale Frey-Klett, Anne-Yvonne Guillerm-Erckelboudt, Morgane Boutin, Grégory Guernec, et al.. Combined effects of wheat roots and pathogenic fungus Gaeumannomyces graminis var tritici on Gene Expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp. Molecular Microbial Ecology of the Rhizosphere: Volume 1 & 2, Wiley, 2013, 978-1-118-29617-2. ⟨10.1002/9781118297674.ch61⟩. ⟨hal-02803298⟩

Thèse1 document

  • Matthieu Barret. Analyse différentielle du transcriptome de la rhizobactérie Pseudomonas fluorescens Pf29Arp lors d'intercations avec le champignon pathogène du blé Gaeumannomyces graminis var. tritici. Sciences du Vivant [q-bio]. AGROCAMPUS OUEST, 2009. Français. ⟨tel-02818996⟩