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Journal Article

  • Aigle, A., Colin, Y., Bouchali, R., Bourgeois, E., Marti, R., Ribun, S., Marjolet, L., Pozzi, A.C.M., Misery, B., Colinon, C., Bernardin-Souibgui, C., Wiest, L., Blaha, D., Galia, W., Cournoyer, B., 2021. Spatio-temporal variations in chemical pollutants found among urban deposits match changes in thiopurine S-methyltransferase-harboring bacteria tracked by the tpm metabarcoding approach. Science of The Total Environment 767, 145425.

  • Barbi, F., Vallon, L., Guerrero-Galán, C., Zimmermann, S.D., Melayah, D., Abrouk, D., Doré, J., Lemaire, M., Fraissinet-Tachet, L., Luis, P., Marmeisse, R., 2021. Datamining and functional environmental genomics reassess the phylogenetics and functional diversity of fungal monosaccharide transporters. Applied Microbiology and Biotechnology 105, 647-660.

  • Guesmi, S., Nouioui, I., Pujic, P., Dubost, A., Najjari, A., Ghedira, K., Igual, J.M., Cherif, A., Klenk, H.-peter, Sghaier, H., Normand, P., 2021. Draft genome sequence of Promicromonospora panici sp. nov., a novel ionizing-radiation-resistant actinobacterium isolated from roots of the desert plant Panicum turgidum. Extremophiles 25, 25-38.

  • Guesmi, S., Pujic, P., Nouioui, I., Dubost, A., Najjari, A., Ghedira, K., Igual, J.M., Miotello, G., Cherif, A., Armengaud, J., Klenk, H.-peter, Normand, P., Sghaier, H., 2021. Ionizing-radiation-resistant Kocuria rhizophila PT10 isolated from the Tunisian Sahara xerophyte Panicum turgidum: Polyphasic characterization and proteogenomic arsenal. Genomics 113, 317-330.

  • Hugoni, M., Nunan, N., Thioulouse, J., Dubost, A., Abrouk, D., Martins, J.M.F., Goffner, D., Prigent-Combaret, C., Grundmann, G., 2021. Small-Scale Variability in Bacterial Community Structure in Different Soil Types. Microbial Ecology.

  • Lebon, Y., Navel, S., Moro, M., Voisin, J., Cournoyer, B., François, C., Volatier, L., Mermillod-Blondin, F., 2021. Influence of stormwater infiltration systems on the structure and the activities of groundwater biofilms: Are the effects restricted to rainy periods? Science of The Total Environment 755, 142451.

  • Lecomte, S., Nesme, X., Franzino, T., Villard, C., Pivard, M., Vial, L., Doré, J., Hommais, F., Haichar, F.H., 2021. Agrobacterium fabrum C58 involved nitrate reductase NapA and antisense RNA NorR to denitrify. FEMS Microbiology Ecology 97.

  • Moyne, O., Castelli, F., Bicout, D.J., Boccard, J., Camara, B., Cournoyer, B., Faudry, E., Terrier, S., Hannani, D., Huot-Marchand, S., Léger, C., Maurin, M., Ngo, T.-D., Plazy, C., Quinn, R.A., Attree, I., Fenaille, F., Toussaint, B., Le Gouëllec, A., 2021. Metabotypes of Pseudomonas aeruginosa Correlate with Antibiotic Resistance, Virulence and Clinical Outcome in Cystic Fibrosis Chronic Infections. Metabolites 11, 63.

  • Padilla, R., Gaillard, V., Le, T.N., Bellvert, F., Chapulliot, D., Nesme, X., Dessaux, Y., Vial, L., Lavire, C., Kerzaon, I., 2021. Development and validation of a UHPLC-ESI-QTOF mass spectrometry method to analyze opines, plant biomarkers of crown gall or hairy root diseases. Journal of Chromatography B 1162, 122458.

  • Sarazin, G., Jezequel, D., Leboulanger, C., Fouilland, E., Le Floc'h, E., Bouvy, M., Gérard, E., Agogué, H., Bernard, C., Hugoni, M., Grossi, V., Troussellier, M., Ader, M., 2021. Geochemistry of an endorheic thalassohaline ecosystem: the Dziani Dzaha crater lake (Mayotte Archipelago, Indian Ocean). Comptes Rendus Géoscience.

  • Vautrin, F., Pujic, P., Paquet, C., Bergeron, E., Mouniée, D., Marchal, T., Salord, H., Bonnet, J.-M., Cournoyer, B., Winiarski, T., Louzier, V., Rodriguez-Nava, V., 2021. Microbial risk assessment of Nocardia cyriacigeorgica in polluted environments, case of urban rainfall water. Computational and Structural Biotechnology Journal 19, 384-400.

  • Vigouroux, A., Meyer, T., Naretto, A., Legrand, P., Aumont-Nicaise, M., Di Cicco, A., Renoud, S., Doré, J., Lévy, D., Vial, L., Lavire, C., Moréra, S., 2021. Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum. Nucleic Acids Research 49, 529-546.
Book Section

  • Haichar, F.Z., Achouak, W., 2021. Newly Introduced or Modified Genes in Plants Potentially Modulate the Host Microbiome, in: Gupta, V.V.S.R., Sharma, A.K. (Eds.), Rhizosphere Biology: Interactions Between Microbes And Plants, Rhizosphere Biology. Springer, Singapore, p. 185-193.


Newspaper Article

  • Cournoyer, B., Moulin, L., 2020. Coronavirus / M comme « microbiologie urbaine ». Tribune. Le Monde (France).

  • Cournoyer, B., Moulin, L., Bouchali, R., Mandon, C., Toussaint, J.-Y., 2020. La microbiologie urbaine : un champ d’investigation en émergence. Edition « Ecole de l'Anthropocène » (Lyon, France).
Journal Article

  • Adamo, M., Voyron, S., Chialva, M., Marmeisse, R., Girlanda, M., 2020. Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats. PLOS ONE 15, e0244682.

  • Akanny, E., Bonhommé, A., Commun, C., Doleans‐Jordheim, A., Farre, C., Bessueille, F., Bourgeois, S., Bordes, C., 2020. Surface‐enhanced Raman spectroscopy using uncoated gold nanoparticles for bacteria discrimination. Journal of Raman Spectroscopy jrs.5827.

  • Barberis, L., Chevalier, W., Toussaint, M.-L., Binet, P., Piola, F., Michalet, S., 2020. Responses of the species complex Fallopia × bohemica to single-metal contaminations to Cd, Cr or Zn: growth traits, metal accumulation and secondary metabolism. Environmental Monitoring and Assessment 192, 673.

  • Betzabeth Espina-Benitez, M., Denet, E., Bolzinger, M.-A., Rodriguez-Nava, V., Pollet, T., Pitault, I., Blaha, D., Briancon, S., 2020. Décontamination sèche de simulants chimiques et biologiques. Medecine de Catastrophe Urgences Collectives.

  • Camus, L., Briaud, P., Bastien, S., Elsen, S., Doléans-Jordheim, A., Vandenesch, F., Moreau, K., 2020. Trophic cooperation promotes bacterial survival of Staphylococcus aureus and Pseudomonas aeruginosa. The ISME Journal 14, 3093-3105.

  • Cantarel, A.A.M., Allard, V., Andrieu, B., Barot, S., Enjalbert, J., Gervaix, J., Goldringer, I., Pommier, T., Saint-Jean, S., Le Roux, X., 2020. Plant functional trait variability and trait syndromes among wheat varieties: the footprint of artificial selection. Journal of Experimental Botany.

  • Cantarel, A.A.M., Rouifed, S., Simon, L., Bourg, J., Gervaix, J., Blazère, L., Poussineau, S., Creuzé des Châtelliers, C., Piola, F., 2020. In Nitrate-Rich Soil, Fallopia x bohemica Modifies Functioning of N Cycle Compared to Native Monocultures. Diversity 12, 156.

  • Colin, Y., Bouchali, R., Marjolet, L., Marti, R., Vautrin, F., Voisin, J., Bourgeois, E., Rodriguez-Nava, V., Blaha, D., Winiarski, T., Mermillod-Blondin, F., Cournoyer, B., 2020. Coalescence of bacterial groups originating from urban runoffs and artificial infiltration systems among aquifer microbiomes. Hydrology and Earth System Sciences 24, 4257-4273.

  • Courtois, P., Rorat, A., Lemiere, S., Guyoneaud, R., Attard, E., Longepierre, M., Rigal, F., Levard, C., Chaurand, P., Grosser, A., Grobelak, A., Kacprzak, M., Lors, C., Richaume, A., Vandenbulcke, F., 2020. Medium-term effects of Ag supplied directly or via sewage sludge to an agricultural soil on Eisenia fetida earthworm and soil microbial communities. Chemosphere 128761.

  • Czarnes, S., Mercier, P.-E., Lemoine, D.G., Hamzaoui, J., Legendre, L., 2020. Impact of soil water content on maize responses to the plant growth-promoting rhizobacterium Azospirillum lipoferum CRT1. Journal of Agronomy and Crop Science n/a.

  • de Oliveira, A.B., Cantarel, A.A.M., Seiller, M., Florio, A., Bérard, A., Hinsinger, P., Le Cadre, E., 2020. Short-term plant legacy alters the resistance and resilience of soil microbial communities exposed to heat disturbance in a Mediterranean calcareous soil. Ecological Indicators 108, 105740.

  • Denet, E., Espina-Benitez, M.B., Pitault, I., Pollet, T., Blaha, D., Bolzinger, M.-A., Rodriguez-Nava, V., Briançon, S., 2020. Metal oxide nanoparticles for the decontamination of toxic chemical and biological compounds. International Journal of Pharmaceutics 583, 119373.

  • Denet, E., Triadou, S., Michalet, S., Nazaret, S., Favre‐Bonté, S., 2020. Growth of Stenotrophomonas maltophilia and expression of Sme efflux pumps encoding genes in the presence of supernatants from amoebal and bacterial co-cultures: towards the role of amoebal secondary metabolites. Environmental Microbiology Reports 12, 702-711.

  • Duangsodsri, T., Villain, L., Vestalys, I.R., Michalet, S., Abdallah, C., Breitler, J.-C., Bordeaux, M., Villegas, A.M., Raherimandimby, M., Legendre, L., Etienne, H., Bertrand, B., Campa, C., 2020. 5-CQA and Mangiferin, Two Leaf Biomarkers of Adaptation to Full Sun or Shade Conditions in Coffea arabica L. Metabolites 10, 383.

  • Duplouy, A., Minard, G., Saastamoinen, M., 2020. The gut bacterial community affects immunity but not metabolism in a specialist herbivorous butterfly. Ecology and Evolution 10, 8755-8769.

  • Fouret, J., Brunet, F.G., Binet, M., Aurine, N., Enchéry, F., Croze, S., Guinier, M., Goumaidi, A., Preininger, D., Volff, J.-N., Bailly-Bechet, M., Lachuer, J., Horvat, B., Legras-Lachuer, C., 2020. Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding. Frontiers in Microbiology 11.

  • Galland, W., Piola, F., Mathieu, C., Bouladra, L., Simon, L., Haichar, F.Z., 2020. Does Biological Denitrification Inhibition (BDI) in the Field Induce an Increase in Plant Growth and Nutrition in Apium graveolens L. Grown for a Long Period? Microorganisms 8, 1204.

  • Gaudino, M., Aurine, N., Dumont, C., Fouret, J., Ferren, M., Mathieu, C., Reynard, O., Volchkov, V.E., Legras-Lachuer, C., Georges-Courbot, M.-C., Horvat, B., 2020. High Pathogenicity of Nipah Virus from <i>Pteropus lylei</i> Fruit Bats, Cambodia. Emerging Infectious Diseases 26, 104-113.

  • Goulas, A., Belhadi, D., Descamps, A., Andremont, A., Benoit, P., Courtois, S., Dagot, C., Grall, N., Makowski, D., Nazaret, S., Nélieu, S., Patureau, D., Petit, F., Roose-Amsaleg, C., Vittecoq, M., Livoreil, B., Laouénan, C., 2020. How effective are strategies to control the dissemination of antibiotic resistance in the environment? A systematic review. Environmental Evidence 9, 4.

  • Guégan, M., Martin, E., Valiente Moro, C., 2020. Comparative Analysis of the Bacterial and Fungal Communities in the Gut and the Crop of Aedes albopictus Mosquitoes: A Preliminary Study. Pathogens 9, 628.

  • Guégan, M., Tran Van, V., Martin, E., Minard, G., Tran, F.H., Fel, B., Hay, A.-E., Simon, L., Barakat, M., Potier, P., Haichar, F.Z., Valiente Moro, C., 2020. Who is eating fructose within the <i>Aedes albopictus</i> gut microbiota? Environmental Microbiology 1462-2920.14915.

  • Gueneau, R., Blanchet, D., Rodriguez-Nava, V., Bergeron, E., Soulier, M., Bestandji, N., Demar, M., Couppie, P., Blaizot, R., 2020. Actinomycetoma caused by Gordonia westfalica: first reported case of human infection. New Microbes and New Infections 100658.

  • Habbadi, K., Duplay, Q., Chapulliot, D., Kerzaon, I., Benkirane, R., Benbouazza, A., Wisniewski-Dyé, F., Lavire, C., Achbani, E.H., Vial, L., 2020. Characterization and phylogenetic diversity of Allorhizobium vitis isolated from grapevine in Morocco. Journal of Applied Microbiology 128, 828-839.

  • Hay, A.E., Herrera-Belaroussi, A., Rey, M., Fournier, P., Normand, P., Boubakri, H., 2020. Feedback Regulation of N Fixation in <i>Frankia-Alnus</i> Symbiosis Through Amino Acids Profiling in Field and Greenhouse Nodules. Molecular Plant-Microbe Interactions® 33, 499-508.

  • Herrera-Belaroussi, A., Normand, P., Pawlowski, K., Fernandez, M.P., Wibberg, D., Kalinowski, J., Brachmann, A., Berckx, F., Lee, N., Blom, J., Pozzi, A.C., Fournier, P., Bethencourt, L., Dubost, A., Abrouk, D., Sellstedt, A., 2020. Candidatus Frankia nodulisporulans sp. nov., an Alnus glutinosa-infective Frankia species unable to grow in pure culture and able to sporulate in-planta. Systematic and Applied Microbiology 43, 126134.

  • Jurburg, S.D., Assemien, F.L., Beaumelle, L., Salles, J.F., Van Elsas, J.D., Le Roux, X., 2020. A history of extreme disturbance affects the relationship between the abundances of nitrifiers in soil. Biology and Fertility of Soils 56, 1177-1187.

  • Laffite, A., Florio, A., Andrianarisoa, K.S., Creuze des Chatelliers, C., Schloter‐Hai, B., Ndaw, S.M., Periot, C., Schloter, M., Zeller, B., Poly, F., Le Roux, X., 2020. Biological inhibition of soil nitrification by forest tree species affects <i>Nitrobacter</i> populations. Environmental Microbiology 1462-2920.14905.

  • Lafont, E., Conan, P.-L., Rodriguez-Nava, V., Lebeaux, D., 2020. Invasive Nocardiosis: Disease Presentation, Diagnosis and Treatment – Old Questions, New Answers? Infection and Drug Resistance Volume 13, 4601-4613.

  • Lafont, E., Marciano, B.E., Mahlaoui, N., Neven, B., Bustamante, J., Rodriguez-Nava, V., Rawat, A., Unzaga, M.J., Fischer, A., Blanche, S., Lortholary, O., Holland, S.M., Lebeaux, D., 2020. Nocardiosis Associated with Primary Immunodeficiencies (Nocar-DIP): an International Retrospective Study and Literature Review. Journal of Clinical Immunology.

  • Le, H.T., Rochelle‐Newall, E., Ribolzi, O., Janeau, J.L., Huon, S., Latsachack, K., Pommier, T., 2020. Land use strongly influences soil organic carbon and bacterial community export in runoff in tropical uplands‐. Land Degradation & Development 31, 118-132.

  • Lebot, V., Kaoh, J., Legendre, L., 2020. High-Throughput Analysis of Flavokawains in Kava (Piper methysticum Forst. f.) Roots, Chips and Powders and Correlations with Their Acetonic Extracts Absorbance. Food Analytical Methods 13, 1583-1593.

  • Lotte, R., Chevalier, A., Dantas, S., Degand, N., Gaudart, A., Rörhlich, P.-S., Boyer, L., Rodriguez-Nava, V., Del Giudice, P., Ruimy, R., 2020. Nocardia takedensis: a newly recognized pathogen responsible for skin and soft tissue infections. Annals of Clinical Microbiology and Antimicrobials 19, 38.

  • Malassigné, S., Valiente Moro, C., Luis, P., 2020. Mosquito Mycobiota: An Overview of Non-Entomopathogenic Fungal Interactions. Pathogens 9, 564.

  • Mani, K., Taib, N., Hugoni, M., Bronner, G., Bragança, J.M., Debroas, D., 2020. Transient Dynamics of Archaea and Bacteria in Sediments and Brine Across a Salinity Gradient in a Solar Saltern of Goa, India. Frontiers in Microbiology 11.

  • Massip, C., Coullaud-Gamel, M., Gaudru, C., Amoureux, L., Doleans-Jordheim, A., Hery-Arnaud, G., Marchandin, H., Oswald, E., Segonds, C., Guet-Revillet, H., 2020. In vitro activity of 20 antibiotics against Cupriavidus clinical strains. Journal of Antimicrobial Chemotherapy 75, 1654-1658.

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