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African army ants at the forefront of virome surveillance in a remote tropical forest. Fritz Matthieu, Reggiardo Bérénice, Filloux Denis, Claude Lisa, Fernandez Emmanuel, Mahe Frédéric, Kraberger Simona, Custer Joy M., Becquart Pierre, Mebaley Telsta Ndong, Kombila Linda Bohou, Lenguiya Léadisaelle H., Boundenga Larson, Mombo Illich M., Maganga Gaël Darren, Niama Fabien R., Koumba Jean-Sylvain, Ogliastro Mylène, Yvon Michel, Martin Darren Patrick, Blanc Stéphane, Varsani Arvind, Leroy Eric M., Roumagnac Philippe. 2023. Peer Community Journal, 3:e24, 21 p.

Interpreting phylogenetic placements for taxonomic assignment of environmental DNA. Ewers Isabelle, Rajter Lubomir, Czech Lucas, Mahe Frédéric, Stamatakis Alexandros, Dunthorn Micah. 2023. Journal of Eukaryotic Microbiology, 70 (5):12990, 10 p.

Pan-Arctic plankton community structure and its global connectivity. Ibarbalz Federico M., Henry Nicolas, Mahe Frédéric, Ardyna Mathieu, Zingone Adriana, Scalco Eleonora, Lovejoy Thomas E., Lombard Fabien, Jaillon Olivier, Iudicone Daniele, Malviya Shruti, Sullivan Matthew B., Chaffron Samuel, Karsenti Eric, Babin Marcel, Boss Emmanuel, Wincker Patrick, Zinger Lucie, de Vargas Colomban, Bowler Chris, Karp-Boss Lee. 2023. Elementa, 11 (1):00060, 17 p.

Fruit fly phylogeny imprints bacterial gut microbiota. Ravigné Virginie, Becker Nathalie, Massol François, Guichoux Erwan, Boury Christophe, Mahe Frédéric, Facon Benoît. 2022. Evolutionary Applications, 15 (10), n.spéc. Evolution in Agricultural Systems : 1621-1638.

Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale. de Vargas Colomban, Le Bescot Noan, Pollina Thibault, Henry Nicolas, Romac Sarah, Colin Sébastien, Haëntjens Nils, Carmichael Margaux, Berger Calixte, Le Guen David, Decelle Johan, Mahe Frédéric, Poulain Julie, Malpot Emmanuel, Beaumont Carole, Hardy Michel, Guiffant Damien, Probert Ian, Gruber David F., Allen Andrew E., Gorsky Gabriel, Follows Michael J., Pochon Xavier, Troublé Romain, Cael B.B., Lombard Fabien, Boss Emmanuel, Prakash Manu. 2022. Frontiers in Marine Science, 9:936972, 17 p.

Seasonal dynamics of marine protist communities in tidally mixed coastal waters. Caracciolo Mariarita, Rigaut-Jalabert Fabienne, Romac Sarah, Mahé Frédéric, Forsans Samuel, Gac Jean-Philippe, Arsenieff Laure, Manno Maxime, Chaffron Samuel, Cariou Thierry, Hoebeke Mark, Bozec Yann, Goberville Eric, Le Gall Florence, Guilloux Loïc, Baudoux Anne-Claire, de Vargas Colomban, Not Fabrice, Thiébaut Eric, Henry Nicolas, Simon Nathalie. 2022. Molecular Ecology, 31 (14) : 3761-3783.

Swarm v3: Towards tera-scale amplicon clustering. Mahe Frédéric, Czech Lucas, Stamatakis Alexandros, Quince Christopher, de Vargas Colomban, Dunthorn Micah, Rognes Torbjørn. 2022. Bioinformatics, 38 (1) : 267-269.

Towards a microbiota-based understanding of sugarcane health. Sanguin Hervé, Sood Sushma, Tournier Estelle, Julian Charlotte, Fernandez Emmanuel, Mahe Frédéric, Filloux Denis, Daugrois Jean-Heinrich, Roumagnac Philippe, Rott Philippe. 2022. Sugar Journal (June), Résumé : 28-29. ASSCT 2022 Annual Meeting, Bonita Springs, États-Unis, 21 Juin 2022/23 Juin 2022.

pr2-primers: An 18S rRNA primer database for protists. Vaulot Daniel, Geisen Stefan, Mahe Frédéric, Bass David. 2022. Molecular Ecology Resources, 22 (1) : 168-179.

Genetic variation in host-specific competitiveness of the symbiont Rhizobium leguminosarum symbiovar viciae. Boivin Stéphane, Mahé Frédéric, Debellé Frédéric, Pervent Marjorie, Tancelin Mathilde, Tauzin Marc, Wielbo Jerzy, Mazurier Sylvie, Young Peter, Lepetit Marc. 2021. Frontiers in Plant Science, 12:719987, 17 p.

High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans. Schoenle Alexandra, Hohlfeld Manon, Hermanns Karoline, Mahé Frédéric, de Vargas Colomban, Nitsche Frank, Arndt Hartmut. 2021. Communications Biology, 4:501, 10 p.

Identifying potential hosts of short-branch microsporidia. Doliwa Annemie, Dunthorn Micah, Rassoshanska Erika, Mahé Frédéric, Bass David, Duarte Ritter Camila. 2021. Microbial Ecology, 82 : 549-553.

Periodontitis associates with species-specific gene expression of the oral microbiota. Belstrom Daniel, Constancias Florentin, Drautz-Moses Daniela I., Schuster Stephan C., Veleba Mark, Mahé Frédéric, Givskov Michael. 2021. npj Biofilms and Microbiomes, 7:76, 10 p.

Temporal recovery of soil biological activity and diversity after 915-MHz microwave treatments. Maynaud Géraldine, Baudoin Ezékiel, Mahé Frédéric, Villenave Cécile, Cleyet-Marel Jean-Claude, Brunel Béatrice. 2021. Biology and Fertility of Soils, 57 (5) : 603-616.

The Windblown: Possible explanations for dinophyte DNA in forest soils. Gottschling Marc, Czech Lucas, Mahé Frédéric, Adl Sina, Dunthorn Micah. 2021. Journal of Eukaryotic Microbiology, 68 (1):e12833, 6 p.

metaXplor: An interactive viral and microbial metagenomic data manager. Sempere Guilhem, Petel Adrien, Abbé Magsen, Lefeuvre Pierre, Roumagnac Philippe, Mahé Frédéric, Baurens Gaël, Filloux Denis. 2021. GigaScience, 10 (2):giab001 : 1-8.

Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink. Rodríguez-Martínez Raquel, Leonard Guy, Milner David S., Sudek Sebastian, Conway Mike, Moore Karen, Hudson Theresa, Mahé Frédéric, Keeling Patrick J., Santoro Alyson E., Worden Alexandra Z., Richards Thomas A.. 2020. ISME Journal, 14 (4) : 984-998.

Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. Arsenieff Laure, Le Gall Florence, Rigaut-Jalabert Fabienne, Mahé Frédéric, Sarno Diana, Gouhier Léna, Baudoux Anne-Claire, Simon Nathalie. 2020. ISME Journal, 14 (8) : 1966-1981.

Heterogeneity of the rice microbial community of the Chinese centuries-old Honghe Hani rice terraces system. Alonso Pascal, Blondin Laurence, Gladieux Pierre, Mahé Frédéric, Sanguin Hervé, Ferdinand Romain, Filloux Denis, Desmarais Eric, Cerqueira Frédérique, Jin Baihui, Huang Huichuan, He Xiahong, Morel Jean-Benoit, Martin Darren Patrick, Roumagnac Philippe, Vernière Christian. 2020. Environmental Microbiology, 22 (8) : 3429-3445.

South Green bioinformatic resources for tropical and Mediterranean crops. Rouard Mathieu, Bocs Stéphanie, Breton Catherine, Comte Aurore, De Lamotte Frédéric, Dereeper Alexis, Droc Gaëtan, Dufayard Jean François, Guignon Valentin, Hamelin Chantal, Larmande Pierre, Lopez David, Mahé Frédéric, Martin Guillaume, Orjuela-Bouniol Julie, Pitollat Bertrand, Ravel Sébastien, Ruiz Manuel, Sabot François, Sarah Gautier, Sempere Guilhem, Summo Marilyne, Tando Ndomassi, Tranchant-Dubreuil Christine. 2020. . SFBI, IFB, GDR-BIM. Montpellier : SFBI, 1 p. Journées ouvertes de biologie, informatique et mathématique (JOBIM 2020). 20, Montpellier, France, 30 Juin 2020/3 Juillet 2020.

The belowground bacterial and fungal communities differed in their significance as microbial indicator of Moroccan carob habitats. Khassali Hamza, Baumel Alex, Mahé Frédéric, Tournier Estelle, Tisseyre Pierre, Prin Yves, Ouahmane Lahcen, Sanguin Hervé. 2020. Ecological Indicators, 114:106341, 9 p.

The repetitive content in lupin genomes. Ainouche Abdelkader, Paris Aurore, Giraud Delphine, Keller Jean, Raimondeau Pauline, Mahé Frédéric, Neuman Pavel, Novak Petr, Macas Jiri, Ainouche Malika Lily, Salmon Armel, Martin Guillaume. 2020. In : The lupin genome. Singh Karam B. (ed.), Kamphuis Lars G. (ed.), Nelson Matthew N. (ed.). Cham : Springer, 161-186. (Compendium of Plant Genomes) ISBN 978-3-030-21269-8

Global trends in marine plankton diversity across kingdoms of life. Ibarbalz Federico M., Henry Nicolas, Martini Séverine, Busseni Greta, Byme Hannah, Coelho Luis Pedro, Endo Hisashi, Gasol Josep M., Gregory Ann C., Mahé Frédéric, Rigonato Janaina, Royo-Llonch Marta, Salazar Guillem, Sanz-Sáez Isabel, Scalco Eleonora, Soviadan Dodji, Zayed Ahmed A., Zingone Adriana, Labadie Karine, Ferland Joannie, et al.. 2019. Cell, 179 (5) : 1084-1097.

How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation. Robin Agnès, Pradier Céline, Sanguin Hervé, Mahé Frédéric, Lambais George Rodrigues, de Araujo Pereira Arthur Prudêncio, Germon Amandine, Cintra Santana Maiele, Tisseyre Pierre, Pablo Anne-laure, Heuillard Pauline, Sauvadet Marie, Bouillet Jean-Pierre, Dini Andreote Fernando, Plassard Claude, De Moraes Gonçalves Jose Leonardo, Bran Nogueira Cardoso Elke Jurandy, Laclau Jean-Paul, Hinsinger Philippe, Jourdan Christophe. 2019. Mycorrhiza, 29 (6) : 637-648.

In the intimacy of an old Mediterranean affair between a fruit tree and a microbiota: perspectives in conservation and agroecology. Sanguin Hervé, Mahé Frédéric, Ouahmane Lahcen, Khassali Hamza, Tournier Estelle, Tisseyre Pierre, Geoffroy Alexandre, Le Roux Christine, Prin Yves, Hafidi Mohamed, Hugot Laetitia, Diadema Katia, Mirleau Fatma, Nieto-Feliner Gonzalo, Bou Dagher Kharrat Magda, La Malfa Stefano, Médail Frédéric, Viruel Juan, Baumel Alex. 2019. In : Dedicated to the origins of agriculture and the domestication, evolution and utilization of genetic resources. Abstracts book. IRD, Bioversity International, Agropolis International, CIRAD, Montpellier SupAgro, Université de Montpellier, INRA. Montpellier : IRD, Résumé, p. 133. Jack R. Harlan International Symposium. 3, Montpellier, France, 3 Juin 2019/7 Juin 2019.

The rhizosphere microbiome: A key component of sustainable cork oak forests in trouble. Maghnia Fatima Zahra, Abbas Younes, Mahe Frédéric, Prin Yves, El Ghachtouli Naima, Duponnois Robin, Sanguin Hervé. 2019. Forest Ecology and Management, 434 : 29-39.

Clarifying the relationships between microsporidia and cryptomycota. Bass David, Czech Lucas, Williams Bryony A. P., Berney Cédric, Dunthorn Micah, Mahe Frédéric, Torruella Guifré, Stentiford Grant D., Williams Tom A.. 2018. Journal of Eukaryotic Microbiology, 65 (6) : 773-782.

Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists. Lentendu Guillaume, Mahé Frédéric, Bass David, Rueckert Sonja, Stoeck Thorsten, Dunthorn Micah. 2018. Molecular Ecology, 27 (13) : 2846-2857.

Development of MetaXplor: a viral metagenomics database. P29. Filloux Denis, Petel Adrien, Sempere Guilhem, Claverie Sohini, Lefeuvre Pierre, Mahe Frédéric, Roumagnac Philippe. 2018. In : Book of abstract Pathobiome 2018. INRA. Ajaccio : INRA, Résumé, 50. Pathobiome, Ajaccio, France, 18 Mars 2018/20 Mars 2018.

Development of a multigenic metabarcoding protocol for deciphering the diversity of plant-associated Archaea. [144]. Pieretti Isabelle, Mahé Frédéric, Alonso Pascal, Blondin Laurence, Roumagnac Philippe, Vernière Christian. 2018. In : Book of abstract of the International Phytobiomes Conference 2018. International Phytobiomes Alliance, INRA, IRD. Montpellier : International Phytobiomes Alliance-INRA, 68. International phytobiomes conference. 2, Montpellier, France, 4 Décembre 2018/6 Décembre 2018.

How deep can ectomycorrhizae go? A case study down to 4 meter depth in a Brazilian Eucalyptus plantation under rainfall reduction. Robin Agnès, Pradier Céline, Sanguin Hervé, Mahe Frédéric, Lambais George Rodrigues, de Araujo Pereira Arthur Prudêncio, Germon Amandine, Cintra Maiele, Tisseyre Pierre, Pablo Anne-laure, Heuillard Pauline, Saudavet Marie, Bouillet Jean-Pierre, Androte Fernando Dini, Plassard Claude, Bran Nogueira Cardoso Elke Jurandy, Laclau Jean-Paul, Hinsinger Philippe, Jourdan Christophe. 2018. In : Eucalyptus 2018: Managing Eucalyptus plantation under global changes. Abstracts book. CIRAD, IUFRO, MUSE. Montpellier : CIRAD, Résumé, 38-39. ISBN 978-2-87614-743-0 Eucalyptus 2018, Montpellier, France, 17 Septembre 2018/21 Septembre 2018.

Rice genetic diversity and microbiome characterization of a centuries-old Chinese rice agro-system. Alonso Pascal, Filloux Denis, Blondin Laurence, Mahé Frédéric, Fournier Elisabeth, Gladieux Pierre, Ducasse Aurélie, Morel Jean-Benoit, Mournet Pierre, Huang Huichuan, Jin Baihui, He Xiahong, Ferdinand Romain, Fernandez Emmanuel, Vernière Christian, Roumagnac Philippe. 2018. In : Book of abstract of the International Phytobiomes Conference 2018. International Phytobiomes Alliance, INRA, IRD. Montpellier : International Phytobiomes Alliance-INRA, 48. International phytobiomes conference. 2, Montpellier, France, 4 Décembre 2018/6 Décembre 2018.

South Green, une plateforme de bioinformatique tournée vers l'agriculture dans les pays du sud. Ravel Sébastien, Bocs Stéphanie, Brousseau Louise, De Lamotte Frédéric, Dereeper Alexis, Droc Gaëtan, Dufayard Jean François, Guignon Valentin, Hamelin Chantal, Larmande Pierre, Mahé Frédéric, Martin Guillaume, Orjuela-Bouniol Julie, Pitollat Bertrand, Rouard Mathieu, Ruiz Manuel, Sabot François, Sarah Gautier, Sempere Guilhem, Summo Marilyne, Tando Ndomassi, Tranchant-Dubreuil Christine. 2018. In : JOBIM 2018 Abstracts. SFBI, GdR BiM, IFB, AMU, INSERM, CNRS. Marseille : SFBI, 418-420. Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2018), Marseille, 3 Juillet 2018/6 Juillet 2018.

Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages. Morard Raphaël, Garet-Delmas Marie-José, Mahé Frédéric, Romac Sarah, Poulain Julie, Kucera Michal, de Vargas Colomban. 2018. Scientific Reports, 8:2539, 10 p.

Transcriptome profiles of nod factor-independent symbiosis in the tropical legume Aeschynomene evenia. Gully Djamel, Czernic Pierre, Cruveiller Stéphane, Mahé Frédéric, Longin Cyrille, Vallenet David, François Philippe, Nidelet Sabine, Rialle Stéphanie, Giraud Eric, Arrighi Jean-François, DasGupta Maitrayee, Cartieaux Fabienne. 2018. Scientific Reports, 8:10934, 12 p.

What are the ecological drivers of symbiotic microbiome assemblages? The case of an antic affair between an iconic Mediterranean fruit tree and its symbiotic microbiome. Mahé Frédéric, Tisseyre Pierre, Tournier Estelle, Khassali Hamza, Le Roux Christine, Geoffroy Alexandre, Mirleau Pascal, Miché L., Arrighi Jean-François, Duponnois Robin, Hafidi Mohamed, Ouhammou A., Vincentelli Bruno, Anziani Carole, Hugot Laetitia, Diadema Katia, Feliner Gonzalo Nieto, Viruel Juan, Médail Frédéric, Bou Dagher Kharrat Magda, La Malfa Stefano, Prin Yves, Ouahmane Lahcen, Baumel Alex, Sanguin Hervé. 2018. In : Booklet of Sfécologie 2018. Société Française d'Écologie et d'Évolution. Rennes : Société Française d'Écologie et d'Évolution, Résumé, 300-301. International Conference on Ecological Sciences : Sfécologie 2018, Rennes, France, 22 Octobre 2018/25 Octobre 2018.

Worldwide occurrence and activity of the reef-building coral symbiont Symbiodinium in the open ocean. Decelle Johan, Carradec Quentin, Pochon Xavier, Henry Nicolas, Romac Sarah, Mahé Frédéric, Dunthorn Micah, Kourlaiev Artem, Voolstra Christian R., Wincker Patrick, de Vargas Colomban. 2018. Current Biology, 28 (22):e3 : 3625-3633.

The human-driven impacts on a long-term affair between an iconic Mediterranean fruit tree and its microbiome. Sanguin Hervé, Mahé Frédéric, Ouahmane Lahcen, Tisseyre Pierre, Tournier Estelle, Khassali Hamza, Le Roux Christine, Prin Yves, Miche Lucie, Mirleau Pascal, Duponnois Robin, Arrighi Jean-François, Hafidi Mohamed, Ouhammou A., Vincentelli Bruno, Anziani Carole, Hugo Laetitia, Diadema Katia, Feliner Gonzalo Nieto, Mirleau Fatma, Bou Dagher Kharrat Magda, La Malfa Stefano, Médail Frédéric, Viruel Juan, Baumel Alex. 2018. In : Book of abstract of the International Phytobiomes Conference 2018. International Phytobiomes Alliance, INRA, IRD. Montpellier : International Phytobiomes Alliance-INRA, 71. International phytobiomes conference. 2, Montpellier, France, 4 Décembre 2018/6 Décembre 2018.

Development of bioinformatics tools for sequence data mining and virus discovery. [P40]. Filloux Denis, Petel Adrien, Sempere Guilhem, Claverie Sohini, Lefeuvre Pierre, Mahe Frédéric, Roumagnac Philippe. 2017. In : Livre des résumés des 16 ème Rencontres de virologie végétale. CIRAD, CNRS, INRA, IRD, SFP. Aussois : CIRAD-CNRS, 101. Rencontres de virologie végétale, Aussois, France, 15 Janvier 2017/19 Janvier 2017.

Habitat- and soil-related drivers of the root-associated fungal community of Quercus suber in the Northern Moroccan forest. Maghnia Fatima Zahra, Abbas Younes, Mahé Frédéric, Kerdouh Benaissa, Tournier Estelle, Ouadji Mohamed, Tisseyre Pierre, Prin Yves, El Ghachtouli Naima, Bakkali-Yakhlef Salahedine, Duponnois Robin, Sanguin Hervé. 2017. PloS One, 12 (11):e0187758, 17 p.

Meiotic genes in colpodean ciliates support secretive sexuality. Dunthorn Micah, Zufall Rebecca A., Chi Jingyun, Paszkiewicz Konrad, Moore Karen, Mahé Frédéric. 2017. Genome Biology and Evolution, 9 (6) : 1781-1787.

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests. Mahé Frédéric, de Vargas Colomban, Bass David, Czech Lucas, Stamatakis Alexandros, Lara Enrique, Singer David, Mayor Jordan, Bunge John, Sernaker Sarah, Siemensmeyer Tobias, Trautmann Isabelle, Romac Sarah, Berney Cédric, Kozlov Alexey, Mitchell Edward A. D., Seppey Christophe V. W., Egge Elianne, Lentendu Guillaume, Wirth Rainer, Trueba Gabriel, Dunthorn Micah. 2017. Nature Ecology and Evolution, 1 (4):0091, 8 p.

UniEuk: Time to speak a common language in protistology! Berney Cédric, Ciuprina Andreea, Bender Sara, Brodie Juliet, Edgcomb Virginia, Kim Eunsoo, Rajan Jeena, Wegener Parfrey Laura, Adl Sina, Audic Stéphane, Bass David, Caron David, Cochrane Guy, Czech Lucas, Dunthorn Micah, Geisen Stefan, Glöckner Franck Olivier, Mahé Frédéric, Quast Christian, Kaye Jonathan Z., Simpson Alastair G.B., Stamatakis Alexandros, del Campo Javier, Yilmaz Pelin, de Vargas Colomban. 2017. Journal of Eukaryotic Microbiology, 64 (3) : 407-411.

Yeasts dominate soil fungal communities in three lowland Neotropical rainforests. Dunthorn Micah, Kauserud Håvard, Bass David, Mayor Jordan, Mahé Frédéric. 2017. Environmental Microbiology Reports, 9 (5) : 668-675.

Are mycorrhizal-bacterial community networks impacted by the sexual type of their host tree? Sanguin Hervé, Mahe Frédéric, Tisseyre Pierre, Tournier Estelle, Ouahmane Lahcen, Le Roux Christine, Duponnois Robin, Médail Frédéric, Dagher-Kharrat Magda Bou, La Malfa Stefano, Baumel Alex, Prin Yves. 2016. In : Sfécologie 2016. Marseille : Sfé, Résumé, 1 p. International Conference on Ecological Sciences, Marseille, France, 24 Octobre 2016/28 Octobre 2016.

VSEARCH: a versatile open source tool for metagenomics. Rognes Torbjørn, Flouri Tomás, Nichols Ben, Quince Christopher, Mahe Frédéric. 2016. PeerJ, 4 (e2584), 22 p.

A fungal community-based high throughput approach to determine ecological bio-indicators of Moroccan cork oak decline. Maghnia Fatima Zahra, Mahe Frédéric, Bakkali-Yakhlef Salahedine, Kerdouh Benaissa, Ouajdi M., Prin Yves, El Ghachtouli Naima, Duponnois Robin, Abbas Younes, Sanguin Hervé. 2016. In : EcoSummit 2016 - Ecological Sustainability: Engineering Change. Montpellier : INRA-IRD, 1 poster International EcoSummit Congress 2016. 5, Montpellier, France, 29 Août 2016/1 Septembre 2016.

Phylogénie, éléments transposables et évolution de la taille des génomes chez les lupins. Mahé Frédéric. 2009. Rennes : Université de Rennes 1, 252 p. Thèse de doctorat : Biologie : Université de Rennes 1