Toutes les publications


Renaudie M., Dumas C., Vuilleumier S. & Ernst B. (2024). Spontaneous dark fermentation in a pre-seeded liquid-gas membrane bioreactor : Impact of wine and coffee biowaste microflora on continuous biohydrogen production. J Cleaner Prod 437, art. 140759.

Pilatowski-Herzing, E., Samson, R., Takemata, N., Badel, C., Bohall P. & Bell, S. (2024) Capturing chromosome conformation in Crenarchaea. Molecular Microbiology

Delogu, F., Kunath, B.J., Queirós, P.M., Halder, R., Lebrun, L.A., Pope P.B., May P., Widder, S., Muller E.E.L. & Wilmes P. (2024) Forecasting the dynamics of a complex microbial community using integrated meta-omics. Nature Ecology and Evolution, 8, 32-44.


Hellal, J., Barthelmebs, L., Bérard, A., Cébron, A., Cheloni, G., Colas, S., Cravo-Laureau, C., De Clerck, C., Gallois, N., Hery, M., Martin-Laurent, F., Martins, J., Morin, S., Palacios, C., Pesce, S., Richaume-Jolion, A. & Vuilleumier, S. (2023) Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges. FEMS Microbiol Ecol, 99, 1-21.

Prieto-Espinoza, M., Di Chiara Roupert, R., Muller, EEL., Vuilleumier, S., Imfeld, G. & Weill, S. (2023) Combining multi-phase flow and pathway-specific reactive transport modeling to investigate the impact of water table fluctuations on dichloromethane biodegradation. Adv Water Res, in press.

Wasmund, K., Trueba-Santiso , A., Vicent, T., Adrian, L., Vuilleumier, S. & Marco-Urrea S (2023) Proteogenomics of the novel Dehalobacterium formicoaceticum strain EZ94 highlights a key role of methyltransferases during anaerobic dichloromethane degradation. Environ Sci Pollut Res 30, 80602-80612.

Muller, E.E.L. (2023) The social dimension of microbial niches. Nature Ecology & Evolution 7, 649-650.

Husser, C., Vuilleumier, S. & Ryckelynk, M. (2023) FluorMango, an RNA-based fluorogenic biosensor for the direct and specific detection of fluoride. Small, 19, 2205232.


Chaignaud, P., Gruffaz, C., Borreca, A., Fouteau, S., Kuhn, L., Masbou, J., Rouy, Z., Hammann, P., Imfeld, G., Roche, D. & Vuilleumier, S. (2023) A methylotrophic bacterium growing with the antidiabetic drug Metformin as its sole carbon, nitrogen and energy source. Microorganisms. 10(11):2302.

Renaudie, M., Dumas, C., Vuilleumier, S., & Ernst, B (2022) New way of valorization of raw coffee silverskin: Biohydrogen and acetate production by dark fermentation without exogenous inoculum. Bioresource Technology Reports. 17, 100918.

Delogu, F., Kunath, B., Queiros,P., Halder, R., Lebrun, L., Pope, P., May, P., Widder, S., Muller,E.E.L. & Wilmes, P. (2022) Forecasting of a complex microbial community using meta-omics. bioRxiv, 2022-10.

Jarrige, D., Haridas, S., Bleykasten-Grosshans, C., Joly, M., Nadalig, T., Sancelme, M., Vuilleumier, S., Grigoriev, I., Amato, P. & Bringel, F. (2022) High-quality genome of the basidiomycete yeast Dioszegia hungarica PDD-24b-2 isolated from cloud water. Genes Genomes Genetics, 12, jkac282.

Jarrige, D., Nadalig, T., Joly, M., Sancelme, M., Vuilleumier, S., Amato, P. & Bringel, F. (2022) Complete genome of Sphingomonas aerolata PDD-32b-11, isolated from cloud water at the summit of puy de Dôme, France. Microbiology Resource Announcements, 11 (10) e00684-22.

Maucourt, B., Roche, D., Chaignaud, P., Vuilleumier, S. & Bringel, F. (2022) Genome-wide transcription start sites mapping in Methylorubrum grown with dichloromethane and methanol. Microorganisms, 10, 1301.

Kröber, E., Kanukollu, S., Wende, S., Bringel, F., & Kolb, S. (2022) A putatively new family of alphaproteobacterial chloromethane degraders from a deciduous forest soil revealed by stable isotope probing and metagenomics. Environ Microbiome17(1):24.

Geersens, É., Vuilleumier, S., & Ryckelynck, M. (2022) Growth-associated droplet shrinkage for bacterial quantification, growth monitoring, and separation by ultrahigh-throughput microfluidics. ACS Omega 7(14):12039-12047.


Prieto-Espinoza, M., Weill, S., Belfort, B., Muller, EEL., Masbou, J., Lehmann, F., Vuilleumier, S., & Imfeld, G. (2022) Water table fluctuations affect dichloromethane biodegradation in lab-scale aquifers contaminated with organohalides. Water Res. 203:117530.

Martinez Arbas, S., Narayanasami, S., Herold, M., Lebrun, L., Hoopmann, M., Li, S., Lam, T., Kunath, B.,  Hicks, N., Liu, C., Price, L., Laczny, C., Gillece, J., Schupp, J., Keim, P., Moritz, R.,  Faust, K., Tang, H;, Ye, Y., Skupin, A., May, A., Muller, E.E.L. & Wilmes, P. (2021) Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nat. Microb.6, 123-135.

François, E., Dumas, C., Gougeon, R., Alexandre, H., Vuilleumier, S. & Ernst, B. (2021) Unexpected high production of biohydrogen from the endogenous fermentation of grape must deposits.Bioresource Technol, 320, art. 124334.

Kröber, E., Wende, S., Kanukollu, S., Buchen-Tschiskale, C., Besaury, L., Keppler, F., Vuilleumier, S., Kolb, S. & Bringel, F. (2021)             13C-chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern. Environ. Microbiol. 23, 8, 4450-4465.

Hellal, J., , Joulian, C., Urien, C., Ferreira, S., Denonfoux, J., Hermon, L., Vuilleumier, S., & Imfeld, G. (2021) Chlorinated ethene biodegradation and associated bacterial taxa in multi-polluted groundwater: Insights from biomolecular markers and stable isotope analysis. Sci Total Environ. 319, art. 142950.

Renaudie, M., Dumas, C., Vuilleumier, S., & Ernst, B. (2021) Biohydrogen production in a continuous liquid/gas hollow fiber membrane bioreactor: Efficient retention of hydrogen producing bacteria via granule and biofilm formation. Bioresource Technol. 319, art. 124203.


Hayoun, K., Geersens, E., Laczny, C.C., Halder, R., Lázaro Sánchez, C., Manna, A., Bringel, F., Ryckelynck, M., Wilmes, P., Muller, E.E.L., Alpha-Bazin, B., Armengaud, J. & Vuilleumier, S. (2020)Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics. Microorganisms , 8, 1876.

Herold, M., Martinez Arbas, S., Narayanasami, S., Sheik, A., Kleine-Borgmann, L., Lebrun, L., Kunath, B., Roume, H., Bessarab, I., Williams, R., Gillece, J., Schupp, J., Keim, P., Jäger, C., Hoopmann, M., Moritz, R., Ye, Y., Li, S., Tang, H., Heintz-Buschart, A., May, P., Muller, E.E.L., Laczny, C. & Wilmes, P. (2020) Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance. Nat Commun11, 5281.

Maucourt, B., Vuilleumier, S., & Bringel, F. (2020) Transcriptional regulation of organohalide pollutant utilisation in bacteria, FEMS Microbiology Reviews44, 189-207.

Keppler, F., Barnes, J.D., Horst, A., Bahlmann, E., Luo, J., Nadalig, T., Greule, M., Hartmann, S.C.,  & Vuilleumier, S. (2020) Chlorine isotope fractionation of the major chloromethane degradation processes in the environment. Environ. Sci. Technol.54, 3, 1634-1645.


Boachon, B., Burdloff, Y., Ruan, J.-X., Rojo, R.,  Bruno, V., Robert, J., Bringel, F., Lesot, A., Henry, L., Bassard,  J.E., Matthieu, S., Lionel, A., Kaplan, I., Dudareva, N., Vuilleumier, S., Laurence, M. André, F., Navrot, N., Chen, X.-Y. & Werck D. (2019) A promiscuous cyp706a3 reduces terpene volatile emission from Arabidopsis flowers, with impacts on florivores and floral microbiome. Plant Cell. 31, 2947-2972.

Muller, E.E.L. (2019) Determining microbial niche breadth in the environment for better ecosystem fate predictions. mSystems4:e00080-19.

Chevallier, M.L., Della-Negra, O., Chaussonnerie, S., Barbance, A., Muselet, D., Lagarde, F., Darii, E., Ugarte, E.,  Lescop, E., Fonknechten, N., Weissenbach, J., Woignier, T., Gallard, J-F., Vuilleumier, S.,  Imfeld, G., Le Paslier, D. &  Saaidi, P-L. (2019) Natural chlordecone degradation revealed by numerous transformation products characterized in key French West Indies environmental compartments. Environ. Sci. Technol.53, 6133-6143.

Elahi, A., Ajaz, M., Rehman, A., Vuilleumier, S., Khan, Z. & Hussain, S.Z. (2019). Isolation, characterization, and multiple heavy metal-resistant and hexavalent chromium-reducing Microbacterium testaceum B-HS2 from tannery effluent. J King Saud University, 31, 1437-144.

Bringel, F., Besaury, L., Amato, P., Kröber, E., Kolb, S., Keppler, F., Vuilleumier, S. & Nadalig, T. (2019) Methylotrophs and Methylotroph Populations for Chloromethane Degradation. In Methylotrophs and Methylotroph Communities, Ed : L. Chistoserdova, Caister Academic Press, Chap. 8, 149-171.

Hermon, L., Hellal, J., Denonfoux, J., Vuilleumier, S., Imfeld, G., Ferreira, S. & Joulian, C. (2019). Functional genes and bacterial communities during organohalide respiration of chloroethenes in microcosms of multi-contaminated groundwater. Front. Microbiol.10, art. 89.

Loyaux-Lawniczak, S., Vuilleumier, S. & Geoffroy, V. (2019). Efficient reduction of iron oxides by
Paenibacillus spp. strains isolated from tropical soils. Geomicrobiol. J.36, 423-432.

Torgonskaya, M.T., Zyakun, A.M., Trotsenko, Y.A., Laurinavichius, K.S., Kümmel, S., Vuilleumier, S. & Richnow, H.H. (2019). Individual stages of bacterial dichloromethane degradation mapped by stable carbon and chlorine isotope abundance ratios. J. Environ. Sci.78, 147-160.


Imfeld, G., Besaury, L., Maucourt, B., Donadello,S., Baran, N. & Vuilleumier, S. (2018) Toward Integrative Bacterial Monitoring of Metolachlor Toxicity in Groundwater. Front. Microbiol. 9:2053.  

Shah, P., Muller, E.E.L., Lebrun, L.A., Wampach, L., Wilmes, P. (2018) Sequential isolation of DNA, RNA, protein, and metabolite fractions from murine organs and intestinal contents for integrated omics of host–microbiota interactions. Special issue: Microbial Proteomics: Methods and Protocols.Methods in Molecular Biology, 1841:279-291.

Chaignaud P., Morawe M., Besaury L., Kröber E., Vuilleumier S., Bringel F. & Kolb S. (2018). Methanol consumption drives the bacterial chloromethane sink in a forest soil. ISME J.12, 2681-2693.

Hermon, L., Denonfoux, J., Hellal, J., Joulian, C., Ferreira, S., Vuilleumier, S. & Imfeld, G. (2018). Dichloromethane biodegradation in multi-contaminated groundwater: insights from biomolecular and compound-specific isotope analyses. Water Res. 142, 217-226.

Bibi-Triki, S., Husson, G., Maucourt, B., Vuilleumier, S., Carapito, C. & Bringel,F.  (2018) N-terminome and proteogenomic analysis of the Methylobacteriumextorquens DM4 reference strain for dichloromethane utilization.J. Proteomics. 179, 131-139.

Jaeger, N., Besaury, L., Röhling, A.N., Koch, F., Delort, A.-M., Gasc, C., Greule, M.,  Kolb, S., Nadalig, T., Peyret, P., Vuilleumier, S., Amato, P., Bringel, F. &  Keppler, F. (2018) Chloromethane formation and degradation in the fern phyllosphere. Sci. Total Environ. 634, 1278-1287.

Jaeger, N., , Besaury, L., Kröber, E., Delort, A-M, Greule, M., Lenhart, K., Nadalig, T., Vuilleumier, S., Amato, P., Kolb, S., Bringel, F. & Keppler, F. (2018) Chloromethane degradation in soils - a combined microbial and two-dimensional stable isotope approach.J. Environ.Qual.47, 254-262.

Bringel, F. & Couée, I. (2018) Plant-pesticide interactions and the global chloromethane budget.Trends Plant Sci.23(2), 95-99.

Muller, E.E.L., Faust, K., Widder, S., Herold, M., Martinez Arbas, S. & Wilmes, P. (2018) Using metabolic networks to resolve ecological properties of microbiomes. Curr. Opin. Sys. Biol. 8, 73-80.


Farhan Ul Haque, M., Besaury, L., Nadalig, T., Bringel, F., Mutterer, J., Schaller, H. & Vuilleumier, S. (2017) Correlated production and consumption of chloromethane in the Arabidopsis thaliana phyllosphere. Scientific Reports7, 17589.

Svartström, O., Alneberg, J., Terrapon, N., Lombard, V., de Bruijn, I., Malmsten, J., Dalin, A-M., Muller E.E.L., Shah, P., Wilmes, P., Henrissat, B., Aspeborg, H. & Andersson, A.F. (2017) Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. ISME J.11, 2538-2551.

Bringel, F. & Vuilleumier, S. (2017). Metabolic regulation: A master role for ribulose-1,5-bisphosphate in one-carbon assimilation. Curr. Biol. 27, R1127-R1129.

Chaignaud, P.,Maucourt, B., Weiman, M., Alberti, A., Kolb, S., Cruveiller, S., Vuilleumier, S. & Bringel, F. (2017). Genomic and transcriptomic analysis of growth-supporting dehalogenation of chlorinated methanes in Methylobacterium. Front. Microbiol. 8:1600.

Bringel, F., Postema, C.P., Mangenot, S., Bibi-Triki, S., Chaignaud, P.,Farhan Ul Haque, M., Gruffaz, C., Hermon, L., Louhichi, Y., Maucourt, B., Muller, E.E.L., Nadalig, T., Lajus, A., Rouy, Z., Médigue, C., Barbe, V., Janssen, D.B. & Vuilleumier, S. (2017) Genome sequence of the dichloromethane-degrading bacterium Hyphomicrobium sp. strain GJ21. Genome Announc. 5, art. 00622-17.

Kaysen, A., Heintz-Buschart, A., Muller, E.E.L., Narayanasamy, S., Wampach, L., Laczny, C.C., Graf, N., Simon, A., Franke, K., Bittenbring, J., Wilmes, P. & Schneider, J.G. (2017) Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic stem cell transplantation. Transl. Res. 186;79:94.

 Wampach, L., Heintz-Buschart, A., Hogan, A., Muller, E.E.L., Narayanasamy, S., Laczny, C.C., Hugerth, L.W., Bindl, L., Bottu, J., Andersson, A.F., de Beaufort, C. & Wilmes, P. (2017) Colonization and succession within the human gut microbiome by archaea, bacteria and microeukaryotes during the first year of life. Front. Microbiol. 2;8:738.

Bradley, A. S., Swanson, P.K., Muller, E. E. L., Bringel, F., Carroll, S. M., Pearson, A., Vuilleumier, S., Marx, C. J. (2017). Hopanoid-free Methylobacterium extorquens DM4 overproduces carotenoids and has widespread growth impairment. PLoS ONE12 (3):e0173323. 

Frindte, K., Kalyuzhnaya, M., Bringel, F., Dunfield, P., Jetten, M., Khmelenina, V., Klotz, M., Murrell, C., Op Den Camp, H., Sakai, Y., Semrau, J., Shapiro, N., Dispirito, A., Stein, L., Svenning, M., Trotsenko, Y., Vuilleumier, S., Woyke, T. & Knief, C. (2017) Draft genome sequences of two gammaproteobacterial methanotrophs isolated from rice ecosystems. Genome Announc.5, art. 00526-17.


Michener, J.K., Vuilleumier, S., Bringel, F. & Marx, C.J (2016). Transfer of a catabolic pathway for chloromethane in Methylobacterium strains highlights different limitations for growth with chloromethane or with dichloromethane. Front. Microbiol. 7:1116.

Narayanasamy, S., Jarosz, Y., Muller, E.E.L., Laczny, C.C., Herold, M., Kaysen, A., Heintz-Buschart, A., May, P., Pinel, N. & Wilmes, P. (2016) IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses. GenomeBiol.17:260.

Dispirito, A.A., Semrau, J.D., Murrell, J.C., Gallagher, W.H., Dennison, C. & Vuilleumier, S. (2016). Methanobactin and the link between copper and bacterial methane oxidation.Microbiol Mol Biol Rev. 80, 387-409.

Flynn, J., Hirayama, H., Sakai, Y., Dunfield, PF., Klotz, MG., Knief, C., Op den Camp, HJ., Jetten, MJM., Khmelenina, VN., Trotsenko, YA., Murrell, JC., Semrau, JD., Svenning, MM., Stein, LY., Kyrpides, N., Shapiro, N., Woyke, T., Bringel, F., Vuilleumier, S., DiSpirito, AA. & Kalyuzhnaya, MG. (2016). Draft genomes of gammproteobacterial methanotrophs isolated from marine ecosystems. Genome Announc. 4(1):e01629-15.

Alioua, S., Abdi, A., Fhoula, I., Bringel, F., Boudabous, A., Ouzari, I. H. (2016) Diversity of vaginal lactic acid bacterial microbiota in 15 Algerian pregnant women with and without bacterial vaginosis by using culture independent method. J. Clin. Diagn. Res. 10(9):DC23-DC27.


Al Dine, EJ., Mokbel, H., Elmoll, A., Massemin, S., Vuilleumier, S., Toufaily, J., Hanieh, T. & Millet, M. (2015) Concomitant evaluation of atmospheric levels of polychlorinated biphenyls, organochlorine pesticides, and polycyclic aromatic hydrocarbons in Strasbourg (France) using pine needle passive samplers. Environ. Sci. Pollut. Res.22, 17850-17859.

Penny, C., Gruffaz, C., Nadalig, T., Cauchie, H.-M., Vuilleumier, S. & Bringel, F. (2015) Tetrachloromethane-degrading bacterial enrichment cultures and isolates from a contaminated aquifer. Microorganisms 3, 327-343.

Sharp, C., Smirnova, A., Kalyuzhnaya, M., Bringel, F., Hirayama, H., Jetten, M., Khmelenina, V., Klotz, M., Knief, C., Kyrpides, N., Op den Camp, H., Reshetnikov, A., Sakai, Y., Shapiro, N., Trotsenko, Y., Vuilleumier, S., Woyke, T. & Dunfield, P. (2015) Draft genome sequence of the moderately halophilic methanotroph, Methylohalobius crimeensis strain 10Ki.Genome Announc.3(3):e00644-15

Hamilton, R., Kits, J., Ramonovskay, V., Rozova, ON., Yurimoto, H., Iguchi, H., Khmelenina, VN., Sakai, Y., Dunfield, PF., Klotz, MG., Knief, C., Op den Camp, HJM., Jetten, MSM., Bringel, F., Vuilleumier, S., Svenning, MM., Shapiro, N., Woyke, T., Trotsenko, YA., Stein, LY. & Kalyuzhnaya, MG. (2015) Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. Genome Announc.3(3):e00515-15

Bringel, F. & Couée I (2015). Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics. Front. Microbiol.6:486.

Elsayed, O.F., Maillard, E., Vuilleumier, S., Millet, M. & Imfeld, G. (2015) Degradation of chloroacetanilide herbicides and bacterial community composition in lab-scale wetlands. Sci. Tot. Environ.520, 222-231.

Bringel, F. & Couée, I. (2015) Les microbiomes de la phyllosphère. In La métagénomique : Développements actuels et futures applications, Editors Champomier-Vergès, M.F. & Zagorec, M., Editions Quae, Collection Savoir faire, Chapitre 8, 97-108. ISBN 9782759222933.


Michener, J.K., Camargo Neves, A.A., Vuilleumier, S., Bringel, F. & Marx, C.J. (2014). Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement. eLife 2014; 3:04279.

Nadalig, T., Greule, M., Bringel, F., Keppler, F. & Vuilleumier, S. (2014) Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation. Front. Microbiol.5: 523.

Elsayed, O., Maillard, E., Vuilleumier, S. & Imfeld, G. (2014) Bacterial communities in batch and continuous-flow wetlands treating the herbicide S-metolachlor. Sci. Tot. Environ. 499, 327-335.

Ghiglione, J.F., Martin-Laurent, F., Stachowski-Haberkorn, S., Pesce, S. & Vuilleumier, S. (2014) The coming of age of Microbial Ecotoxicology: report on the first two meetings in France. Environ. Sci. Pollut. Rep. 21, 14241-14245.

Boguta, A.M., Bringel, F., Martinussen, J. & Jensen P.R. (2014) Screening of Lactic Acid Bacteria for their potential as microbial cell factories for bioconversion of lignocellulosic feedstocks. Microb. Cell Fact. 13, 97.

Lundquist Parker, D., Lee, S-W., Geszvain, K., Davis, R., Gruffaz, C., Meyer, J-M., Torpey, J. & Tebo, B. (2014) Pyoverdine synthesis by the Mn(II)-oxidizing bacterium Pseudomonas putida GB-1. Front. Microbiol.5: 202.

Gruffaz, C., Muller, E.E.L., Louhichi-Jelail, Y., Nelli, Y.R., Guichard, G. & Bringel, F. (2014) Genes of the N-methylglutamate pathway are essential for growth of Methylobacterium extorquens DM4 with monomethylamine. Appl. Environ. Microbiol.80, 3541-3550.

Michener, J., Vuilleumier, S., Bringel, F. & Marx, C. (2014) Phylogeny poorly predicts the utility of a challenging horizontally-transferred gene in Methylobacterium strains. J. Bacteriol.196, 2101-2107.

Vorobev, A., Jagadevan, S., Jain, S., Anantharaman, K., Dick, G., Vuilleumier, S. & Semrau, J.D. (2014) Genomic and transcriptomic analysis of Methylocystis strain SB2 grown on methane and on ethanol. Appl. Environ. Microbiol.80, 3044-3052.

Elsayed, O., Maillard, E., Vuilleumier, S., Nijenhuis, I., Richnow, H.H. & Imfeld, G. (2014) Using compound specific isotope analysis to assess the degradation of chloroacetanilide herbicides in lab-scale wetlands. Chemosphere99, 89-95.


Kalyuzhnaya, M.G., Yang, S., Rozova, O.N., Smalley, N.E., Clubb, J., Lamb, A., Nagana Gowda, G.A., Raftery, D., Fu, Y., Bringel, F., Vuilleumier, S., Trotsenko, Y.A., Beck, D., Khmelenina, V.N. & Lidstrom, M.E. (2013) Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nature Communications4, 2785.

Nadalig, T., Greule, M., Bringel, F., Vuilleumier, S. & Keppler, F. (2013) Hydrogen and carbon isotope fractionation during degradation of chloromethane by methylotrophic bacteria. MicrobiologyOpen2 (6), 893-900.

Farhan Ul Haque, M., Nadalig, T., Bringel, F., Schaller, H. & Vuilleumier, S. (2013) A fluorescence-based bacterial bioreporter for the specific detection of methyl halide emissions in the environment. Appl. Environ. Microbiol.79, 6561-6567.

Khmelenina, V.N., Beck, D., Munk, C., Davenport, K., Daligault, H., Erkkila, T., Goodwin, L., Gu, W., Lo, C-C., Scholz, M., Teshima, H., Xu, Y., Chain, P., Bringel, F., Vuilleumier, S., DiSpirito, A., Dunfield, P., Jetten, M.S.M., Klotz, M.G., Knief, C., Murrell, J.C., Op den Camp, H.J.M., Sakai, Y., Semrau, S., Svenning, M., Stein, L.Y., Trotsenko, Y.A. & Kalyuzhnaya, M.G. (2013) Draft genome sequence of Methylomicrobium buryatense 5G, a haloalkaline-tolerant methanotrophic bacterium. Genome Announc.1(4):e00053-13.

Semrau, J.D., Jagadevan, S., DiSpirito, A.A., Khalifa, A., Scanlan, J., Bergman, B.H., Freemeier, B.C., Baral, B.S., Bandow, N.L., Vorobev, A., Haft, D.H., Vuilleumier, S. & Murrell, J.C. (2013) Methanobactin and MmoD work in concert to act as the “copper-switch” in methanotrophs. Environ. Microbiol.15 (11), 3077-3086.

Kits, K., Kalyuzhnaya, M., Klotz, M., Jetten, M., Op den Camp, H., Vuilleumier, S., Bringel, F., DiSpirito, A., Murrell, C., Bruce, D., Cheng, J-F., Copeland, A., Goodwin, L., Hauser, L., Lajus, A., Land, M., Lapidus, A., Lucas, S., Médigue, C., Pitluck, S., Woyke, T., Zeytun, A. & Stein, L. (2013) Genome sequence of the obligate Gammaproteobacterial methanotroph Methylomicrobium album strain BG8. Genome Announc.1(2):e00170-13.

Roselli, S., Nadalig, T., Vuilleumier, S. & Bringel, F. (2013) The 380 kb pCMU01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin B12- and tetrahydrofolate-dependent chloromethane metabolism in Methylobacterium extorquens CM4: A proteomic and bioinformatics study. PLoS ONE8(4), e56598.


Marx, C.J., Bringel, F., Chistoserdova, L., Moulin, L., Farhan Ul Haque, M., Fleischman, D.E., Gruffaz, C., Jourand, P., Knief, C., Lee, M-C., Muller, E.E.L., Nadalig, T., Peyraud, R., Roselli, S., Russ, L., Goodwin, L.A., Ivanova, N., Kyrpides, N., Lajus, A., Land, M.L., Médigue, C., Mikhailova, N., Nolan, M., Woyke, T., Stolyar, S., Vorholt, J.A. & Vuilleumier, S. (2012). Complete genome sequences of six strains of the genus Methylobacterium. J. Bacteriol. 194, 4746-4748.

Khadem, F.A., Wieczorek, A.S., Pol, A., Vuilleumier, S., Harhangi, H.R., Dunfield, P.F., Kalyuzhnaya, M.G., Murrell, J.C., Francoijs, K-J., Stunnenberg, H.G., Stein, L.Y., DiSpirito, A.A., Semrau, J.D., Lajus, A., Médigue, C., Klotz, M.G., Jetten, M.S.M. & Op den Camp, H.J.M. (2012). Draft genome sequence of the volcano-inhabiting thermoacidophilic methanotroph Methylacidiphilum fumariolicum strain SolV. J. Bacteriol.194, 3729-3730.

Imfeld, G. & Vuilleumier, S. (2012). Measuring the effects of pesticides on bacterial communities in soil: a critical review. Eur. J. Soil Biol.49, 22-30.

Hamon, E., Horvatovitch, P., Bisch, M., Bringel, F., Marchioni, E., Aoude-Werner, D. &  Ennahar, S. (2012). Investigation of biomarkers of bile tolerance in Lactobacillus casei using comparative proteomics. J Proteome Res. 111, 109-118.

Vuilleumier, S., Khmelenina, V.N., Bringel, F., Reshetnikov, A.S., Lajus, A., Mangenot, S., Rouy, Z., Op den Camp, H.J.M., Jetten, M.S.M., DiSpirito, A.A., Dunfield, P., Klotz, M.G., Semrau, J.D., Stein, L.Y., Barbe, V., Médigue, C., Trotsenko Y.A. & Kalyuzhnaya, M.G. (2012). Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z. J. Bacteriol. 194, 551-552.



Boden, R., Cunliffe, M., Scanlan, J., Moussard, H., Kitz, K., Klotz, M.G., Jetten, M.S.M., Vuilleumier, S., Han, J., Peters, L., Mikhailova, N., Teshima, N., Tapia, R., Kyrpides, N., Ivanova, N., Pagani, I., Cheng, J-F., Goodwin, L., Han, C., Hauser, L., Land, M., Lapidus, A., Lucas, S., Pitluck, S., Woyke, T., Stein, L.Y. & Murrell, J.C. (2011). Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J. Bacteriol.193, 7001-7002.

Svenning, M.M., Hestnes, A.G., Wartiainen, I., Stein, L.Y., Klotz, M.G., Kalyuzhnaya, M.G., Spang, A., Bringel, F., Vuilleumier, S., Lajus, A., Médigue, C., Bruce, D.C., Cheng, J.F., Goodwin, L., Ivanova, N., Han, J., Han, C.S., Hauser, L., Held, B., Land, M.L., Lapidus, A., Lucas, S., Nolan, M., Pitluck, S. & Woyke, T. (2011). Genome sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96. J.Bacteriol.193, 6418-6419.

Muller, E., Bringel, F. & Vuilleumier, S. (2011) Dichloromethane-degrading bacteria in the genomic age. Res Microbiol.162, 869-876.

Vuilleumier, S., Nadalig, T., Farhan Ul Haque, M., Magdelenat, G., Lajus, A., Roselli, S., Muller, E.E.L., Gruffaz, C., Barbe, V., Médigue, C. & Bringel, F. (2011) Complete genome sequence of the chloromethane-degrading strain Hyphomicrobium sp. strain MC1. J. Bacteriol.193, 5035-5036.

Kittichotirat, W., Good, N., Hall, R., Bringel, F., Lajus, A., Médigue, C., Smalley, N., Beck, D., Bumgarner, R., Vuilleumier, S. & Kalyuzhnaya, M.G. (2011). Genome sequence of Methyloversatilis universalis FAM5T, a methylotrophic representative of the order Rhodocyclales. J. Bacteriol.193, 4541-4542.

Muller, E., Hourcade, E., Louhichi-Jelail, Y., Hammann, P., Vuilleumier, S. & Bringel, F. (2011) Functional genomics of dichloromethane utilisation in Methylobacterium extorquens DM4. Environ. Microbiol.13, 2518-2535.

Semrau, J.D., DiSpirito, A.A. & Vuilleumier, S. (2011) Facultative methanotrophy: False leads, true results, and suggestions for future research. FEMS Microbiol. Lett.323, 1-12.

Nadalig, T., Farhan Ul Haque, M., Roselli, S., Schaller, H., Bringel, F. & Vuilleumier, S. (2011) Detection and isolation of chloromethane-degrading bacteria from the Arabidopsis thaliana phyllosphere, and characterization of chloromethane utilisation genes. FEMS Microbiol. Ecol.77, 438-448.

Bois, P., Huguenot, D., Norini, M.P., Farhan Ul Haque, M., Vuilleumier, S. & Lebeau, T. (2011). Herbicide degradation and copper complexation by bacterial mixed cultures from a vineyard stormwater basin. J. Soils Sedim.11, 860-873.

Torgonskaya, M.L., Doronina, N.V., Hourcade, E., Trotsenko, Y. & Vuilleumier, S. (2011) Chloride-specific adaptive response in aerobic methylotrophic dichloromethane-utilising bacteria. J. Basic Microbiol. 51, 296-303.

Stein, L.Y., Bringel, F., DiSpirito, A.A., Han, S., Jetten, M.S.M., Kalyuzhnaya, M.G., Kits, K.D., Klotz, M.G., Op den Camp, H.J.M., Semrau, J.D., Vuilleumier, S., Bruce, F., Cheng, J.F., Copeland, A., Davenport, K.W., Goodwin, L., Han, S., Hauser, L., Lajus, A., Land, M.L., Lapidus, A., Lucas, S., Médigue, C., Pitluck, S. & Woyke, T. (2011). Genome sequence of the methanotrophic Alphaproteobacterium, Methylocystis sp. Rockwell (ATCC 49242). J. Bacteriol.193, 2668-2669.

Hamon, E., Horvatovich P., Izquierdo E., Bringel, F., Marchioni, E., Aoude-Werner, D. & Ennahar, S. (2011) Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance. BMC Microbiology. 11, 63.

Imfeld, G., Bringel, F. & Vuilleumier, S. (2011) Bacterial tolerance in contaminated soils: potential of the PICT approach in microbial ecology. In: Tolerance to Environmental Contaminants (Amiard-Triquet C, Rainbow PS, Roméo M), CRC Press, Boca Raton, Chapitre 14, 335-364.

Ramette, A., Frapolli, M., Fischer-Le Saux, M., Gruffaz, C., Meyer, J-M., Defago, G., Sutra, L., Moenne-Loccoz, Y. (2011) Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin. Syst. Appl. Microbiol.34, 180-188.


Rozova, O.N., Khmelenina, V.N., Vuilleumier, S. & Trotsenko, Y.A. (2010) Characterization of recombinant pyrophosphate-dependent 6-phosphofructokinase from halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. Res. Microbiol. 160, 861-868

Stein, L.Y., Semrau, J.D., DiSpirito, A.A., Crombie, A., Murrell, J.C., Vuilleumier, S., Kalyuzhnaya, M.G., Op den Camp, H.J.M., Bringel, F., Bruce, F., Cheng, J.F., Copeland, A.,  Goodwin, L., Han, S., Hauser, L., Jetten, M.S.M., Lajus, A., Land, M.L., Lapidus, A., Lucas, S., Médigue, C., Pitluck, S., Woyke, T., Yoon, S., Zeytun, A. & Klotz, M.G. (2010) Genome sequence of the obligate methanotroph, Methylosinus trichosporium strain OB3b. J. Bacteriol. 192, 6497-6498

Krentz, B.D., Mulheron, H.J., Semrau, J.D., DiSpirito, A.A., Bandow, N.L., Haft, D.H., Vuilleumier, S., Murrell, J.C., McEllistrem, M.T., Hartsel, S.C. & Gallagher, W.H. (2010) A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain SB2 predicts methanobactins are synthesized from diverse ribosomally produced peptide precursors modified to create a common core for binding and reducing copper ions. Biochemistry 49, 10117-10130

Todorova, T.T., Kujumdzieva, A.V. & Vuilleumier, S. (2010). Non-enzymatic roles for the URE2 glutathione S-transferase in the response of Saccharomyces cerevisiae to arsenic. Arch Microbiol. 192, 909-918

Couée, I & Bringel, F. (2010) Expanding importance of mRNA expression in understanding stress and stress responses. J. Theor. Biol. 266, 479-482

Penny, C., Vuilleumier, S. & Bringel, F. (2010) Microbial degradation of tetrachloromethane : mechanisms and perspectives for bioremediation. FEMS Microbiol.Ecol. 74, 257-275

Penny, C., Nadalig, T., Alioua, M., Gruffaz, C., Vuilleumier, S. & Bringel, F. (2010). Coupling of denaturing high-performance liquid chromatography and terminal restriction fragment length polymorphism with precise fragment size calling for microbial community profiling and characterization. Appl. Environ. Microbiol.76, 648-651


Cambon-Bonavita, M.A., Nadalig, T., Roussel, E., Delage, E., Duperron, S., Caprais, J.-C., Boetius, A. & Sibuet, M. (2009). Diversity and distribution of methane oxidizing microbial communities associated with different faunal assemblages in a giant pockmark of the Gabon continental margin. Deep-Sea ResearchII, 53, 2248-2258

Firsova, J., Doronina, N., Lang, E., Spröer, C., Vuilleumier, S. & Trotsenko, Y.A. (2009). Ancylobacter dichloromethanicus sp. nov. - a new aerobic facultatively methylotrophic bacterium utilizing dichloromethane. Syst. Appl. Microbiol.32, 227-232.

Greenwald, J., Nader, M., Celia, H., Gruffaz, C., Geoffroy, V., Meyer, J.-M., Schalk, I.J. & Pattus, F. (2009). FpvA bound to non-cognate pyoverdines: molecular basis of siderophore recognition by an iron transporter. Mol. Microbiol.72, 1246-1259.

Mainguet, S.E., Gakiere, B., Majira, A., Pelletier, S., Bringel, F., Guerard, F., Caboche, M., Berthome, R. & Renou, J. P. (2009). Uracil salvage is necessary for early Arabidopsis development. Plant J.60, 280-291.

Todorova, T.T., Petrova, V.Y., Vuilleumier, S. & Kujumdzieva, A.V. (2009). Response to different oxidants of Saccharomyces cerevisiae ure2Δmutant. Arch. Microbiol. 191, 837-845.

Vuilleumier, S., Chistoserdova, L., Lee, M.-C., Bringel, F., Lajus, A., Zhou, Y., Gourion, B., Barbe, V., Chang, J., Cruveiller, S., Dossat, C., Gillett, W., Gruffaz, C., Haugen, E., Hourcade, E., Levy, R., Mangenot, S., Muller, E., Nadalig, T., Pagni, M., Penny, C., Peyraud, R., Robinson, D.G., Roche, D., Rouy, Z., Saenampechek, C., Salvignol, G., Vallenet, D., Wu, Z., Marx, C.J., Vorholt, J.A., Olson, M. V., Kaul, R., Weissenbach, J., Médigue, C. & Lidstrom, M.E. (2009). Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. PLoS ONE4, e5584.


Bringel, F., Hammann, P., Kugler, V. & Arsene-Ploetze, F. (2008). Lactobacillus plantarum response to inorganic carbon concentrations: PyrR2-dependent and -independent transcription regulation of genes involved in arginine and nucleotide metabolism. Microbiology154, 2629-2640.

Bringel, F., Vuilleumier, S. & Arsene-Ploetze, F. (2008). Low carbamoyl phosphate pools may drive Lactobacillus plantarum CO2-dependent growth phenotype. J. Molec. Microbiol. Biotechnol.14, 22-30.

Chapalain, A., Rossignol, G., Lesouhaitier, O., Merieau, A., Gruffaz, C., Guerillon, J., Meyer, J.-M., Orange, N. & Feuilloley, M.G.J. (2008). Comparative study of 7 fluorescent pseudomonad clinical isolates. Can. J. Microbiol.54, 19-27.

David, M., Bringel, F., Pagni, M., Gilmartin, N., Boubakri, H., Nadalig, T., Simonet, P., Vogel, T. & Vuilleumier, S. (2008). Diversité et évolution des déshalogénases bactériennes : détection bioinformatique et perspectives de recherche. Les Actes du BRG7, 83-94.

Meyer, J.-M., Gruffaz, C., Raharinosy, V., Bezverbnaya, I., Schäfer, M. & Budzikiewicz, H. (2008). Siderotyping of fluorescent Pseudomonas: molecular mass determination by mass spectrometry as a powerful pyoverdine siderotyping method. Biometals. 21, 259-271.

Mulet, M., Gomila, M., Gruffaz, C., Meyer, J.-M., Palleroni, N.J., Lalucat, J. & Garcia-Valdes, E. (2008). Phylogenetic analysis and siderotyping as useful tools in the taxonomy of Pseudomonas stutzeri: description of a novel genomovar. Int. J. Syst. Evol. Microbiol.58, 2309-2315.


Losekann, T., Knittel, K., Nadalig, T., Fuchs, B., Niemann, H., Boetius, A. & Amann, R. (2007). Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby mud volcano, Barents sea. Appl. Environ. Microbiol.73, 3348-3362.

Meyer, J.-M., Gruffaz, C., Tulkki, T. & Izard, D. (2007). Taxonomic heterogeneity, as shown by siderotyping, of strains primarily identified as Pseudomonas putida. Int. J. Syst. Evol. Microbiol.57, 2543-2556.

Schröder, P., Navarro-Aviñó, J., Azaizeh, H., Goldhirsh, A.G., DiGregorio, S., Komives, T., Langergraber, G., Lenz, A., Maestri, E., Memon, A. R., Ranalli, A., Sebastiani, L., Smrcek, S., Vanek, T., Vuilleumier, S. & Wissing, F. (2007). Using phytoremediation technologies to upgrade waste water treatment in Europe. Environ.Sci. Pollution Rep.14, 440-447.

Todorova, T.T., Vuilleumier, S. & Kujumdzieva, A. (2007). Role of glutathione S-transferases and glutathione in arsenic and peroxide resistance in Saccharomyces cerevisiae: a reverse genetic analysis approach. Biotech. Biotech. Equip.21, 348-352.

Tralau, T., Vuilleumier, S., Thibault, C., Campbell, B. J., Hart, A. & Kertesz, M. A. (2007). Transcriptomic analysis of the sulfate starvation response of Pseudomonas aeruginosa. J. Bacteriol.189, 6743-6750.


Arsène-Ploetze, F., Kugler, V., Martinussen, J. & Bringel, F. (2006). Expression of the pyr operon of Lactobacillus plantarum is regulated by inorganic carbon availability through a second regulator, PyrR(2), homologous to the pyrimidine-dependent regulator PyrR(1). J. Bacteriol.188, 8607-8616.

Arsène-Ploetze, F., Nicoloff, H., Kammerer, B., Martinussen, J. & Bringel, F. (2006). Uracil salvage pathway in Lactobacillus plantarum : Transcription and genetic studies. J. Bacteriol.188, 4777-4786.

Hauser, F., Lindemann, A., Vuilleumier, S., Patrignani, A., Schlapbach, R., Fischer, H.-M. & Hennecke, H. (2006). Design and validation of a partial-genome microarray for transcriptional profiling of the Bradyrhizobium japonicum symbiotic gene region. Mol. Genet. Genom.275, 55-67.

Niemann, H., Losekann, T., de Beer, D., Elvert, M., Nadalig, T., Knittel, K., Amann, R., Sauter, E. J., Schluter, M., Klages, M., Foucher, J. P. & Boetius, A. (2006). Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature443, 854-858.

Ondréas, H., Olu, K., Fouquet, Y., Charlou, J.-L., Gay, A., Dennielou, B., Donval, J.-P., Fifis, A., Nadalig, T., Cochonat, P., Cauquil, E. & Sibuet, M. (2006). ROV study of a giant pockmark on the Gabon continental margin. Geo-Marine Lett. 25, 281-292.

Petrovic, T., Niksic, M. & Bringel, F. (2006). Strain typing with ISLpl1 in lactobacilli. FEMS Microbiol Lett. 255, 1-10.


Arsène-Ploetze, F., Nicoloff, H. & Bringel, F. (2005). Lactobacillus plantarum ccl gene is non-essential, arginine-repressed and codes for a member conserved protein in Firmicutes. Arch. Microbiol.183, 307-316.

Bringel, F., Castioni, A., Olukoya, D. K., Felis, G. E., Torriani, S. & Dellaglio, F. (2005). Lactobacillus plantarum subsp. argentoratensis subsp. nov., isolated from vegetable matrices. Int. J. Syst. Environ. Bacteriol.55, 1629-1634.

Duperron, S., Nadalig, T., Caprais, J. C., Sibuet, M., Fiala-Medioni, A., Amann, R. & Dubilier, N. (2005). Dual symbiosis in a Bathymodiolus sp. mussel from a methane seep on the gabon continental margin (southeast Atlantic): 16S rRNA phylogeny and distribution of the symbionts in gills. Appl. Environ. Microbiol.71, 1694-1700.

Molenaar, D., Bringel, F., Schuren, F. H., de Vos, W. M., Siezen, R. J. & Klerebezeem, M. (2005). Exploring Lactobacillus plantarum genome diversity using microarrays. J. Bacteriol.187, 6119-6127.

Nicoloff, H., Elagöz, A., Arsène-Ploetze, F., Kammerer, B., Martinussen, J. & Bringel, F. (2005). Repression of the pyr operon in Lactobacillus plantarum prevents its ability to grow at low carbon dioxide levels. J. Bacteriol.187, 2093-2104.