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Accueil > Français > Équipes > Génomique de l’environnement et bioinformatique (MEB) > Publications


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Lepère C, Domaizon I, Humbert JF, Jardillier L, Hugoni M, Debroas D (2019). Diversity, spatial distribution and activity of fungi in freshwater ecosystems. PeerJ, 7 : e6247., I.F. : 2.11835.
Carles L, Gardon H, Joseph L, Sanchís J, Farré M, Artigas J (2019). Meta-analysis of glyphosate contamination in surface waters and dissipation by biofilms. Environ Int, 124 : 284-93. doi : 10.1016/j.envint.2018.12.064, I.F. : 7.721

Bazin A, Debroas D, Mephu Nguifo E (2018). A de novo robust clustering approach for amplicon-based sequence data. J Comput Biol. doi : 10.1089/cmb.2018.0170,
Biderre-Petit C, Taib N, Gardon H, Hochart C, Debroas D (2018). New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics. FEMS Microbiol Ecol, 95(3). doi : 10.1093/femsec/fiy183.
Bisseux M, Colombet J, Mirand A, Roque-Afonso AM, Abravanel F, Izopet J, Archimbaud C, Peigue-Lafeuille H, Debroas D, Bailly JL, Henquell C (2018). Monitoring human enteric viruses in wastewater and relevance to infections encountered in the clinical setting : a one-year experiment in Central France, 2014 to 2015. Euro Surveill,23(7 doi 10.2807/1560-7917.Es.2018.23.7.17-00237.
Galand PE, Pereira O, Hochart C, Auguet JC, Debroas D (2018). A strong link between marine microbial community composition and function challenges the idea of functional redundancy. ISME J, 12 : 2470-78. doi : 10.1038/s41396-018-0158-1, I.F. : 9.520
Batut B, Gravouil K, Defois C, Hiltemann S, Brugère JF, Peyretaillade E, Peyret P (2018). ASaiM : a Galaxy-based framework to analyze microbiota data. Gigascience, 7(6). doi : 10.1093/gigascience/giy057, I.F. : 7.267
Frouin E, Bes M, Olliver B, Quemeneur M, Postec A, Debroas D, Armoungom F, Erauso G (2018). Diversity of rare and abundant prokaryotic phylotypes in the prony hydrothermal field and comparison with other serpentinite-hosted ecosystems. Front Microbiol, 9 : 102. doi : 10.3389/Fmicb.2018.00102, I.F. : 4.019
Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J, The Bioconda Team (Gravouil K) (2018). Bioconda : sustainable and comprehensive software distribution for the life sciences. Nat Methods, 15 : 475-76. doi:10.1038/s41592-018-0046-7, I.F. : 26.919
Hennequin C, Chlilek A, Beyrouthy R, Bonnet R, Robin F (2018). Diversity of Dha-1-encoding plasmids in Klebsiella pneumoniae isolates from 16 French hospitals. J Antimicrob Chemother, 73 : 2981-89. doi : 10.1093/Jac/Dky285, I.F. : 5.217
Lavergne C, Hugoni M, Hubas C, Debroas D, Dupuy C, Agogue H (2018). Diel rhythm does not shape the vertical distribution of bacterial and archaeal 16S rRNA transcript diversity in intertidal sediments : a mesocosm study. Microb Ecol, 75 : 364-74. doi : 10.1007/S00248-017-1048-1, I.F. : 3.614


Debroas D, Mone A, Ter Halle A. Plastics in the North Atlantic garbage patch : A boat-microbe for hitchhikers and plastic degraders. Sci Total Environ. 2017 Dec 1 ;599-600:1222-1232. doi : 10.1016/j.scitotenv.2017.05.059.

Amato P, Joly M, Besaury L, Oudart A, Taib N, Moné AI, Deguillaume L, Delort AM, Debroas D. Active microorganisms thrive among extremely diverse communities in cloud water. PLoS One. 2017 Aug 8 ;12(8):e0182869. doi : 10.1371/journal.pone.0182869.

Lavergne C, Hugoni M, Hubas C, Debroas D, Dupuy C, Agogué H. Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments : a Mesocosm Study. Microb Ecol. 2017 Aug 4. doi : 10.1007/s00248-017-1048-1.

Capo E, Debroas D, Arnaud F, Perga ME, Chardon C, Domaizon I. Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming. Environ Microbiol. 2017 Jul ;19(7):2873-2892. doi : 10.1111/1462-2920.13815.

Zancarini A, Echenique-Subiabre I, Debroas D, Taïb N, Quiblier C, Humbert JF. Deciphering biodiversity and interactions between bacteria and microeukaryotes within epilithic biofilms from the Loue River, France. Sci Rep. 2017 Jun 28 ;7(1):4344. doi : 10.1038/s41598-017-04016-w.

Briand JF, Barani A, Garnier C, Réhel K, Urvois F, LePoupon C, Bouchez A, Debroas D, Bressy C. Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments. Microb Ecol. 2017 Apr 3. doi : 10.1007/s00248-017-0966-2.

Debroas D, Domaizon I, Humbert JF, Jardillier L, Lepère C, Oudart A, Taïb N. Overview of freshwater microbial eukaryotes diversity : a first analysis of publicly available metabarcoding data. FEMS Microbiol Ecol. 2017 Apr 1 ;93(4). doi : 10.1093/femsec/fix023.

Li S, Bronner G, Lepère C, Kong F, Shi X. Temporal and spatial variations in the composition of freshwater photosynthetic picoeukaryotes revealed by MiSeq sequencing from flow cytometry sorted samples. Environ Microbiol. 2017 Jun ;19(6):2286-2300. doi : 10.1111/1462-2920.13724.


Li S., Shi X., Lepère C., Liu M., Wang X., Kong F. (2016). Unexpected predominance of photosynthetic picoeukaryotes in shallow eutrophic lakes. Journal of Plankton Research 38 : 830–842

Capo E, Debroas D, Arnaud F, Guillemot T, Bichet V, Millet L, Gauthier E, Massa C, Develle AL, Pignol C, Lejzerowicz F, Domaizon I. Long-term dynamics in microbial eukaryotes communities : a palaeolimnological view based on sedimentary DNA. Mol Ecol. 2016 Dec ;25(23):5925-5943. doi : 10.1111/mec.13893.

Hennequin C, Robin F. Correlation between antimicrobial resistance and virulence in Klebsiella pneumoniae. Eur J Clin Microbiol Infect Dis. 2016 Mar ;35(3):333-41. doi : 10.1007/s10096-015-2559-7.

Zhu L, Zancarini A, Louati I, De Cesare S, Duval C, Tambosco K, Bernard C, Debroas D, Song L, Leloup J, Humbert JF. Bacterial Communities Associated with Four Cyanobacterial Genera Display Structural and Functional Differences : Evidence from an Experimental Approach. Front Microbiol. 2016 Oct 24 ;7:1662.

Pardo CA, Tan RN, Hennequin C, Beyrouthy R, Bonnet R, Robin F. Rapid detection of AAC(6’)-Ib-cr production using a MALDI-TOF MS strategy. Eur J Clin Microbiol Infect Dis. 2016 Dec ;35(12):2047-2051.

West NJ, Lepère C, Manes CL, Catala P, Scanlan DJ, Lebaron P. Distinct Spatial Patterns of SAR11, SAR86, and Actinobacteria Diversity along a Transect in the Ultra-oligotrophic South Pacific Ocean. Front Microbiol. 2016 Mar 8 ;7:234. doi : 10.3389/fmicb.2016.00234.

Jeanbille M, Gury J, Duran R, Tronczynski J, Ghiglione JF, Agogué H, Saïd OB, Taïb N, Debroas D, Garnier C, Auguet JC. Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments. Front Microbiol. 2016 Aug 19 ;7:1303. doi : 10.3389/fmicb.2016.01303.

Roux S, Enault F, Ravet V, Colombet J, Bettarel Y, Auguet JC, Bouvier T, Lucas-Staat S, Vellet A, Prangishvili D, Forterre P, Debroas D, Sime-Ngando T. Analysis of metagenomic data reveals common features of halophilic viral communities across continents. Environ Microbiol. 2016 Mar ;18(3):889-903. doi : 10.1111/1462-2920.13084.

Lepère C, Domaizon I, Hugoni M, Vellet A, Debroas D. Diversity and Dynamics of Active Small Microbial Eukaryotes in the Anoxic Zone of a Freshwater Meromictic Lake (Pavin, France). Front Microbiol. 2016 Feb 10 ;7:130. doi : 10.3389/fmicb.2016.00130.

Louati I, Pascault N, Debroas D, Bernard C, Humbert JF, Leloup J. Correction : Structural Diversity of Bacterial Communities Associated with Bloom-Forming Freshwater Cyanobacteria Differs According to the Cyanobacterial Genus. PLoS One. 2016 Jan 7 ;11(1):e0146866. doi : 10.1371/journal.pone.0146866.

Biderre-Petit C, Dugat-Bony E, Mege M, Parisot N, Adrian L, Moné A, Denonfoux J, Peyretaillade E, Debroas D, Boucher D, Peyret P. Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes. PLoS One. 2016 Jan 6 ;11(1):e0145558. doi : 10.1371/journal.pone.0145558. PubMed


Mylène Hugoni, Hélène Agogué, Najwa Taib, Isabelle Domaizon, Anne Moné, Pierre E. Galand, Gisèle Bronner, Didier Debroas, Isabelle Mary (2015). Temporal dynamics of active prokaryotic nitrifiers and archaeal communities from river to sea. Microbial Ecology (In press).

Hugoni M, Domaizon I, Taib N, Biderre-Petit C, Agogué H, Galand PE, Debroas D, Mary I. (2015) Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes. Environ Microbiol Rep. 7(2):321-9. doi : 10.1111/1758-2229.12251.

Debroas D, Hugoni M, Domaizon I. (2015) Evidence for an active rare biosphere within freshwater protists community. Mol Ecol. 17. doi : 10.1111/mec.13116.

Roux Simon, Enault Francois, Ravet Viviane, Pereira Olivier, Sullivan Matthew B (2015). Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages. Frontiers in Microbiology. 6 (199).

Olga Savichtcheva, Didier Debroas, Marie Elodie Perga, Fabien Arnaud, Clément Villar, Emilie Lyautey, Amy Kirkham, Cécile Chardon, Benjamin Alric, Isabelle Domaizon (2015). Effects of nutrients and warming on Planktothrix dynamics and diversity : a palaeolimnological view based on sedimentary DNA and RNA. Freshwater biology 60, 31-49.

Sabart M, Misson B, Jobard M, Bronner G, Donnadieu-Bernard F, Duffaud E,Latour D. (2015). Genetic diversity along the life cycle of the cyanobacterium Microcystis : highlight on the complexity of benthic and planktonic interactions. Environmental Microbiology 17, 901-911


Tocquard K, Lafon-Placette C, Auguin D, Muries B, Bronner G, Lopez D,
Venisse JS. (2014). In silico study of wall-associated kinase family
reveals large-scale genomic expansion potentially connected with
functional diversification in Populus. Tree Genetics & Genomes, 10(5),

Peyretaillade E, Boucher D, *Parisot N*, Gasc C, Butler R, Pombert JF,
Lerat E, Peyret P : Exploiting the architecture and the features of the
microsporidian genomes to investigate diversity and impact of these
parasites on ecosystems. Heredity (Edinb) 2014.

Parisot N, Pelin A, Gasc C, Polonais V, Belkorchia A, Panek J, Alaoui HE, Biron DG, Brasset E, Vaury C, Peyret P, Corradi N, Peyretaillade E, Lerat E : Microsporidian genomes harbour a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoans. Genome Biol Evol 2014.

Girault G, *Parisot N*, Peyretaillade E, Peyret P, Derzelle S : Draft
Genomes of Three Strains Representative of the Bacillus anthracis Diversity Found in France. Genome Announc 2014, 2:e00736–14.

Borrel G*, *Parisot N**, Harris HM, Peyretaillade E, Gaci N, Tottey W,
Bardot O, Raymann K, Gribaldo S, Peyret P, O Toole PW, Brugère J-F :
Comparative genomics highlights the unique biology of
Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics 2014, 15:679

Panek J, Alaoui El H, Mone A, Urbach S, Demettre E, Texier C, Brun C,
Zanzoni A, Peyretaillade E, *Parisot N*, Lerat E, Peyret P, Delbac F, Biron DG : Hijacking of Host Cellular Functions by an Intracellular Parasite, the Microsporidian Anncaliia algerae. PLoS One 2014, 9:e100791.

Jaziri F*, *Parisot N**, Abid A, Denonfoux J, Ribière C, Gasc C, Boucher
D, Brugère J-F, Mahul A, Hill DRC, Peyretaillade E, Peyret P : PhylOPDb : a
16S rRNA oligonucleotide probe database for prokaryotic identification.
Database 2014, 2014:bau036–bau036.

Jaziri F, Peyretaillade E, Missaoui M, Parisot N, Cipière S, Denonfoux
J, Mahul A, Peyret P, Hill DRC : Large Scale Explorative Oligonucleotide
Probe Selection for Thousands of Genetic Groups on a Computing Grid :
Application to Phylogenetic Probe Design Using a Curated Small Subunit
Ribosomal RNA Gene Database. The Scientific World Journal 2014, 2014:9–9.

Noémie Pascault, Valentin Loux, Sandra Derozier, Véronique Martin, Didier Debroas, Selma Maloufi, Jean-François Humbert, Julie Leloup (2014). Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems. Genetica

Pascault N, Roux S, Artigas J, Pesce S, Leloup J, Tadonleke RD, Debroas D,
Bouchez A, Humbert JF. (2014). A high-throughput sequencing ecotoxicology study offreshwater bacterial communities and their responses to tebuconazole. FEMS Microbiol Ecol. doi : 10.1111/1574-6941.12416

Artigas J, Pascault N, Bouchez A, Chastain J, Debroas D, Humbert JF, Leloup J, Tadonleke RD, ter Halle A, Pesce S. (2014 ) Comparative sensitivity to the fungicide tebuconazole of biofilm and plankton microbial communities in freshwater ecosystems. Sci Total Environ 15 :326-36. doi : 10.1016/j.scitotenv.2013.08.074.

Roux S, Tournayre J, Mahul A, Debroas D, Enault F. (2014) Metavir 2 : new tools for viral metagenome comparison and assembled virome analysis. BMC Bioinformatics. 19 ;15:76. doi : 10.1186/1471-2105-15-76


Simon Roux, Mart Krupovic, Didier Debroas, Patrick Forterre and François Enault (2013). Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences. Open Biology 3(12):130160. doi : 10.1098/rsob.130160.

S Roux, F Enault, G Bronner, D Vaulot, P Forterre, M Krupovic Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses. Nature communications 4

Borrel G, Harris HMB, *Parisot N*, Gaci N, Tottey W, Mihajlovski A, Deane J, Gribaldo S, Bardot O, Peyretaillade E, Peyret P, O’Toole PW, Brugère J-F : Genome Sequence of “Candidatus Methanomassiliicoccus intestinalis” Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces. Genome Announc 2013, 1.

Tottey W, Denonfoux J, Jaziri F, *Parisot N*, Missaoui M, Hill DRC,
Borrel G, Peyretaillade E, Alric M, Harris HMB, Jeffery IB, Claesson MJ,
O’Toole PW, Peyret P, Brugère J-F : The Human Gut Chip “HuGChip,” an
Explorative Phylogenetic Microarray for Determining Gut Microbiome
Diversity at Family Level. PLoS One 2013, 8:e62544.

Denonfoux J*, *Parisot N**, Dugat-Bony E, Biderre-Petit C, Boucher D,
Morgavi DP, Le Paslier D, Peyretaillade E, Peyret P : Gene capture coupledto high-throughput sequencing as a strategy for targeted metagenome exploration. DNA Res 2013, 20:185–196.

Parveen B, Ravet V, Djediat C, Mary I, Quiblier C, Debroas D, Humbert JF. (2013) Bacterial communities associated with Microcystis colonies differ from free-living communities living in the same ecosystem. Environ Microbiol Rep. 5(5):716-24. doi : 10.1111/1758-2229.12071.

Podmirseg S.M., Seewald M.S.A., Knapp B.A., Bouzid O., Biderre-Petit C., Peyret P., Insam H. (2013). Wood ash amendment to biogas reactors as an alternative to landfilling ? A preliminary study on changes in process chemistry and biology, Waste Management and Research, 2013, 31, 829-842

Domaizon, I., Savichtcheva, O., Debroas, D., Arnaud, F., Villar, C., Pignol, C., Alric, B., and Perga, M. E. (2013) DNA from lake sediments reveals the long-term dynamics and diversity of Synechococcus assemblages, Biogeosciences, 10, 3817-3838, doi:10.5194/bg-10-3817-2013.

Borrel G, Harris HM, Parisot N, Gaci N, Tottey W, Mihajlovski A, Deane J, Gribaldo S, Bardot O, Peyretaillade E, Peyret P, O’Toole PW, Brugère JF (2013). Genome Sequence of "Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces. Genome Announc, 11, 1(4). pii : e00453-13. doi : 10.1128/genomeA.00453-13.

Tottey W, Denonfoux J, Jaziri F, Parisot N, Missaoui M, Hill D, Borrel G, Peyretaillade E, Alric M, Harris HM, Jeffery IB, Claesson MJ, O’Toole PW, Peyret P, Brugère JF (2013). The human gut chip "HuGChip", an explorative phylogenetic microarray for determining gut microbiome diversity at family level. PlosOne, 17, 8(5):e62544. doi : 10.1371/journal.pone.0062544.

S Roux, D Debroas, F Enault. Application des approches métagénomiques à l’étude de la diversité virale environnementale Virologie 2013 17 (4), 229-242

Parveen B, Mary I, Vellet A, Ravet V, Debroas D. Temporal dynamics and
phylogenetic diversity of free-living and particle-associated Verrucomicrobia communities in relation to environmental variables in a mesotrophic lake. FEMS Microbiol Ecol. 2013 Jan ;83(1):189-201. doi : 10.1111/j.1574-6941.2012.01469.x.

Hugoni M, Taib N, Debroas D, Domaizon I, Jouan Dufournel I, Bronner G, Salter I, Agogué H, Mary I, Galand PE. (2013). Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. Proc Natl Acad Sci U S A. 110(15):6004-9. doi : 10.1073/pnas.1216863110.

Taib N, Mangot JF, Domaizon I, Bronner G, Debroas D. (2013). Phylogenetic Affiliation of SSU rRNA Genes Generated by Massively Parallel Sequencing : New Insights into the Freshwater Protist Diversity.
PLoS One. 8(3):e58950. doi : 10.1371/journal.pone.0058950. Epub 2013 Mar 14.

Lepère C, Domaizon I, Taïb N, Mangot JF, Bronner G, Boucher D, Debroas D. (2013). Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems. FEMS Microbiol Ecol.. doi : 10.1111/1574-6941.12100.

Hugoni M, Etien S, Bourges A, Lepère C, Domaizon I, Mallet C, Bronner G, Debroas D, Mary I. (2013). Dynamics of ammonia-oxidizing Archaea and Bacteria in contrasted freshwater ecosystems. Res Microbiol. 164(4):360-70. doi : 10.1016/j.resmic.2013.01.004.

Denonfoux J., Parisot N., Dugat-Bony E., Biderre-Petit C., Boucher D., Morgavi D., Le Paslier D., Peyretaillade E., Peyret P. (2013). Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration. DNA Research, 20, 185–196

Parveen B, Mary I, Vellet A, Ravet V, Debroas D. (2013). Temporal dynamics and phylogenetic diversity of free-living and particle-associated Verrucomicrobia communities in relation to environmental variables in a mesotrophic lake. FEMS Microbiol Ecol. 83(1):189-201. doi : 10.1111/j.1574-6941.2012.01469.x.

Mangot JF, Domaizon I, Taib N, Marouni N, Duffaud E, Bronner G, Debroas D. Short-term dynamics of diversity patterns : evidence of continual reassembly within lacustrine small eukaryotes. Environ Microbiol. 2013 Jun ;15(6):1745-58. doi : 10.1111/1462-2920.12065.


Peyretaillade E, Parisot N, Polonais V, Terrat S, Denonfoux J, Dugat-Bony E, Wawrzyniak I, Biderre-Petit C, Mahul A, Rimour S, Gonçalves O, Bornes S, Delbac F, Chebance B, Duprat S, Samson G, Katinka M, Weissenbach J, Wincker P, Peyret P. (2012). Annotation of microsporidian genomes using transcriptional signals. Nature Communications, 3:1137

Domaizon I, Lepère C, Debroas D, Bouvy M, Ghiglione JF, Jacquet S, Bettarel Y, Bouvier C, Torréton JP, Vidussi F, Mostajir B, Kirkham A, Lefloc’h E, Fouilland E, Montanié H, Bouvier T. Short-term responses of unicellular planktonic eukaryotes to increases in temperature and UVB radiation. BMC Microbiol. 2012 Sep 11 ;12:202. doi : 10.1186/1471-2180-12-202.

Roux S, Krupovic M, Poulet A, Debroas D, Enault F (2012) Evolution and Diversity of the Microviridae Viral Family through a Collection of 81 New Complete Genomes Assembled from Virome Reads. PLoS ONE 7(7) : e40418. doi:10.1371/journal.pone.0040418

Roux S, Enault F, Robin A, Ravet V, Personnic S, Theil S, Colombet J, Sime-Ngando T, Debroas D (2012) Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics. PLoS ONE 7(3) : e33641. doi:10.1371/journal.pone.0033641

Dugat-Bony E., Biderre-Petit C., Jaziri F., David M.M., Denonfoux J., Lyon D.Y., Richard J.Y., Curvers C., Boucher D., Vogel T.M., Peyretaillade E., Peyret P. (2012) In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes. Microbial Biotechnology, doi : 10.1111/j.1751-7915.2012.00339.x.

Borrel G, Harris HM, Tottey W, Mihajlovski A, Parisot N, Peyretaillade E, Peyret P, Gribaldo S, O’Toole PW, Brugère JF (2012). Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. J Bacteriol, 194(24):6944-5. doi : 10.1128/JB.01867-12.

Parisot N, Denonfoux J, Dugat-Bony E, Peyret P, Peyretaillade E (2012). KASpOD—a web service for highly specific and explorative oligonucleotide design. Bioinformatics, 28, 3161-3162.

Lorieux M., Blein M., Lozano J., Bouniol M., Droc G., Diévart A., Périn C., Mieulet D., Lanau N, Martine Bès M., Rouvière C., Gay C., Piffanelli P., Larmande P., Michel C., Barnola I., Biderre-Petit C., Sallaud C., Perez P., Bourgis F., Ghesquière A., Gantet P., Tohme J., Morel J.B., Guiderdoni E. (2012) In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches. Plant Biotechnology Journal, doi : 10.1111/j.1467-7652.2012.00689.x, pp 1–14.

Dugat-Bony E., Peyretaillade E., Parisot N., Biderre-Petit C., Jaziri F., Hill D., Rimour S., Peyret P. (2012) Detecting unknown sequences with DNA microarrays : explorative probe design strategies. Environmental Microbiology, 14, 356-371.

Franchel J, Bouzidi MF, Bronner G, Vear F, Nicolas P, Mouzeyar S. (2012) Positional cloning of a candidate gene for resistance to the sunflower downy mildew, Plasmopara halstedii race 300. Theor Appl Genet. 2012 Sep 29.

Lopez D, Bronner G, Brunel N, Auguin D, Bourgerie S, Brignolas F, Carpin S, Tournaire-Roux C, Maurel C, Fumanal B, Martin F, Sakr S, Label P, Julien JL, Gousset-Dupont A, Venisse JS. (2012) - Insights into Populus XIP aquaporins : evolutionary expansion, protein functionality, and environmental regulation. J Exp Bot. 2012 Jan 5.


Simon Roux, Michaël Faubladier, Antoine Mahul, Nils Paulhe, Aurélien Bernard, Didier Debroas and François Enault (2011). METAVIR : a web server dedicated to virome analysis. Bioinformatics 27(21):3074-5

Olga Savichtcheva, Didier Debroas, Rainer Kurmayer, Clement Villar, Jean Philippe Jenny, Fabien Arnaud, Marie Elodie Perga, and Isabelle Domaizon (2011). Quantitative PCR enumeration of total and toxic Planktothrix rubescens/agardhii and other cyanobacteria in preserved DNA isolated from lake sediments.Appl. Environ. Microbiol. 77(24):8744-53

Peyretaillade E, El Alaoui H, Diogon M, Polonais V, Parisot N, Biron DG, Peyret P, Delbac F (2011). Extreme reduction and compaction of microsporidian genomes. Res Microbiol, 162, 598-606.

Simon Roux , François Enault, Gisèle Bronner and Didier Debroas (2011). Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing the microbial diversity (Bacteria and Archaea) in ecosystems. FEMS Microb. Ecol. 78(3):617-28

Bushra Parveen, Jean-Philippe Reveilliez, Isabelle Mary, Viviane Ravet, Gisèle Bronner, Jean-François Mangot, Isabelle Domaizon, Didier Debroas (2011). Diversity and dynamics of free-living and particle-associated Betaproteobacteria and Actinobacteria in relation to phytoplankton and zooplankton communities. FEMS Microb. Ecol. 77(3):461-76

Polly G. Hill, Isabelle Mary, Duncan A. Purdie, Mikhail V. Zubkov (2011). Similarity in microbial amino acid uptake in surface waters of the
North and South Atlantic (sub-)tropical gyres. Progress in Oceanography DOI : 10.1016/j.pocean.2011.05.006

Mangot J-F., Debroas D., Domaizon I (2011). Review of the Perkinsozoa, a well-known marine protozoan flagellate parasite group, newly discovered in lacustrine systems. Hydrobiologia 659, Number 1, 37-48

Gourcilleau D., Lenne C., Armenise C., Moulia B., Julien JL, Bronner G. and Leblanc-Fournier (2011). Phylogenetic Study of Plant Q-type C2H2 Zinc Finger Proteins and Expression Analysis of Poplar Genes in Response to Osmotic, Cold and Mechanical Stresses. DNA Research 18, 77–92. La minute de la recherche

Borrel G ., Jézéquel D., Biderre-Petit C., Morel-Desrosiers N., Morel J.P., Peyret P., Fonty G., Lehours A.C. (2011) Production and consumption of methane in freshwater lake ecosystems. Research in Microbiology, 162, 832-847.

Boucher D., Laffaire J.B., Jaziri F., David C., Biderre-Petit C., Duquenne P., Peyretaillade E. and Peyret P. (2011) Bacterial community composition of biological degreasing systems and health risk assessment for workers. Microbial Ecology, 62, 868-881.

Biderre-Petit C., Jézéquel D., Dugat-Bony E., Lopes F., Kuever J., Borrel G.,Viollier E., Fonty G. and Peyret P. (2011) Identification of microbial communities involved in the methane cycle in a freshwater meromictic lake (Lake Pavin). FEMS Microbiol Ecol, 77, 533-535.

Dugat-Bony E., Missaoui M., Peyretaillade E., Biderre-Petit C., Bouzid O., Gouinaud C., Hill D. and Peyret P. (2011) HiSpOD : probe design for functional DNA microarrays. Bioinformatics, 27, 641-648.

Biderre-Petit C., Boucher D., Kuever J., Alberic P., Jézéquel D., Chebance B., Borrel G., Fonty G. and Peyret P. (2011) Identification of sulfur-cycle prokaryotes in a low-sulfate lake (Lake Pavin) using aprA and 16S rRNA gene markers. Microbial Ecology, 61, 313-327.

Hill PG, Mary I, Purdie DA, Zubkov MV. (2011) Similarity in microbial amino acid uptake in surface waters of the North and South Atlantic (sub-)tropical gyres. Progress in Oceanography. 2011 ; 91 : 437-446.


Cecile Lepère, Sylvie Masquelier, Jean-François Mangot, Didier Debroas and Isabelle Domaizon (2010). Vertical structure of small eukaryotes in 3 lakes differing by their trophic status : a quantitative approach.ISME J. 4, 1509–1519.

Mary I., Oliver A., Skipp P., Holland R., ToAppl. Environ. Microbiol. pping J., Tarran G., Scanlan, D.J., O’Connor D., Whiteley A.S., Burkill P.H. & Zubkov M.V. (2010). Metaproteomic and metagenomic analyses of defined oceanic microbial populations using microwave cell fixation and flow cytometric sorting. FEMS Microbiol Ecol. 74, 10–18

Didier Debroas , François Enault, Isabelle Jouan-Dufournel, Gisèle Bronner and Jean-François Humbert. Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a lacustrine ecosystem. Handbook of Molecular Microbial Ecology II : Metagenomics in Different Habitats , edited by Frans J. de Bruijn (John Wiley & Sons, Inc) (In press).

Terrat S., Peyretaillade E., Gonçalves O., Dugat-Bony E., Gravelat F., Mone A., Biderre-Petit C., Boucher D., Troquet J. and Peyret P. (2010) Studying the ‘unknown’ with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development. BMC Bioinformatics, 11, 478-494.


Anne Roué-Le Gall, Michel Poulin, Didier Debroas, Nicolas Flipo (2009). A physical-microbial food web coupled model to study the evolution of the ecological functioning of a new reservoir after its flooding (Sep, Puy de Dôme). Ecol. Model. 220, 841-856

Mangot Jean-François, Lepère Cécile, Bouvier Christophe, Debroas Didier, Domaizon Isabelle (2009). Community structure and dynamics of small eukaryotes (< 5 µm) targeted by new oligonucleotide probes : a new insight into the lacustrine microbial food web. Appl. Environ. Microbiol. 75 : 6373 - 6381

Boucher D. and Debroas D. (2009) Impact of environmental factors on couplings between bacterial community composition and ectoenzymatic activities in a lacustrine ecosystem. FEMS Microbiol. Ecol. 70, 66-48

Didier Debroas, Jean-François Humbert, François Enault, Gisèle Bronner, Michael Faubladier, Emmanuel Cornillot (2009). Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a mesotrophic lake (Lac du Bourget - France) Environ. Microbiol. 11(9), 2412–2424

Jean-F. Humbert, Ursula Dorigo, Philippe Cecchi, Brigitte Le Berre, D. Debroas and Marc Bouvy (2009). Comparison of the structure and composition of bacterial communities from temperate and tropical freshwater ecosystems. Environ. Microbiol. 11(9), 2339–2350

Lepère C, Domaizon I, Debroas D. (2008) Composition of freshwater small eukaryotes community : unexpected importance of potential parasites. Appl. Environ. Microbiol. 74 : 2940-2949

Biderre C, Belkorchia A, Militon C, Polonais V, Wincker P, Jubin C, Delbac F, Peyretaillade E, Peyret P. (2008) The microsporidian pathogen Brachiola algerae shows efficient infectious capacities and harbours a complex genome. Parasitol. Int., 57(1):62-71.

Larmande P, Gay C, Lorieux M, Périn C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C, Martin J, Morel JB, Johnson AA, Bourgis F, Ghesquière A, Ruiz M, Courtois B, Guiderdoni E. (2008) Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res., 36 (Database issue):D1022-7.

Militon C, Biderre C, Peyret P. (2008) New tools for isolation and identification of micro-organisms. Asiatech Publishers, Inc., New Delhi, pp 3-44.

Lepère C, Domaizon I, Debroas D (2007). Community composition of lacustrine small eucaryotes in hyper eutrophic conditions in relation to top-down and bottom-up factors. FEMS Microbiol. Ecol. 61, 483-495.

Enault F, Fremez R, Baranowski E et Faraut T. (2007) - Alvira : comparative genomics of viral strains. Bioinformatics, 23(16):2178-9.

Militon C, Rimour S, Missaoui M, Biderre C, Barra V, Hill D, Moné A, Gagne G, Meier H, Peyretaillade E, Peyret P. (2007) PhylArray : Phylogenetic Probe Design Algorithm For MicroArray. Bioinformatics, 23(19):2550-7.

Cao X, Costa LM., Biderre-Petit C., Kbhaya B., Dey N., Perez P., McCarty DR., Gutierrez-Marcos JF., Becraft PW. (2007) Abscisic acid and stress signals induce viviparous1 (vp1) expression in maize embryos and phloem cells. Plant Physiology, 143 (2) : pp 720-731.

Boucher D., Richardot M., Thénot A., Debroas D (2006). Incorporation of 3H-Thymidine by different prokaryotic groups in relation to temperature and nutrients in a lacustrine ecosystem. Microb. Ecol. 52, 399-407.

Lepère C., D. Boucher, L. Jardillier, I. Domaizon, D. Debroas (2006). Succession and regulation factors of small eukaryote community composition in a lacustrine ecosystem (Lake Pavin). Appl. Environ. Microbiol. 72, 2971-2981

Lemarchand C., Jardillier L., Carrias J-F., Richardot M., Debroas D., Sime-Ngando T., Amblard C (2006). Community composition and activity of prokaryotes associated to detrital particles in two contrasting lake ecosystems. FEMS Microbiol. Ecol. 57, 442-451

Jugnia L.B., M. Richardot, D. Debroas, J. Devaux. Bacterial production in the recently flooded Sep Reservoir (2006). Diel changes in relation to dissolved carbohydrates and combined amino acids. Hydrobiologia 563, 421-430.

Lehours A. C., C. Bardot, A. Thénot, D. Debroas, G. Fonty (2005). Anaerobic microbial community in Lake Pavin : a unique meromictic lake in France. Appl. Environ. Microbiol. 71, 7389-7400

Enault F, Suhre K et Claverie JM. (2005) - Phydbac “Gene Function Predictor” : a gene annotation tool based on genomic context analysis. BMC Bioinformatics, 6:247

Jardillier L., Y. Bettarel, M. Richardot, C. Bardot, C. Amblard, T. Sime-Ngando and D. Debroas (2005). Effects of Viruses and Predators on Prokaryotic Community Composition. Microb. Ecol. 50, 557-569.

Boucher D., Jardillier L., Debroas D. (2005). Succession of bacterial community composition over two consecutive years in two aquatic systems : a natural lake and a lake-reservoir. FEMS Microbiol. Ecol. 55, 79-97

Lefranc M., Thénot A., Lepère C. Debroas D. (2005) Genetic diversity of small eukaryotes in lakes differing by their trophic status. Appl. Environ. Microbiol. 71, 5935-5942

Ludwig Jardillier, Delphine Boucher, Sébastien Personnic, Stéphan Jacquet, Aurélie Thénot, Denis Sargos, Christian Amblard and Didier Debroas (2005). Relative importance of nutrients and mortality factors on prokaryotic community composition in two lakes of different trophic status : Microcosm experiments. FEMS Microbiol. Ecol. 53, 429-443.

Pradeep Ram AS, D. Boucher, T. Sime-Ngando, D. Debroas, JC Romagoux (2005). Phage bacteriolysis, protistan bacterivory potential, and bacterial production in a freshwater reservoir : coupling with temperature. Microb. Ecol., 50, 64-72.

Jugnia L-B. , D. Debroas, J-C. Romagoux, J. Dévaux (2004). Initial results of remediation activities to restore hypereutrophic Villerest Reservoir (Roanne, France). Lakes and Reservoir 9, 109-117.

Mallet C., M. Basset, G. Fonty, C. Desvilettes, G. Bourdier, D. Debroas (2004). Microbial population dynamics in the sediments of a eutrophic lake (Aydat, france) and characterisation of some heterotrophic bacterial isolates. Microb. Ecol. 48, 66-77.

Jardillier L., M. Basset, I. Domaizon, A. Belan, C. Amblard, M. Richardot, D. Debroas (2004) Bottom-up and top-down control of the bacterial community composition in the euphotic zone of a reservoir. Aquat. Microb. Ecol. 35, 259-273.

Enault F, Suhre K, Poirot O, Abergel C et Claverie JM. (2004) - Phydbac2 : improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis. Nucleic Acids Research, 32(Web Server issue):W336-9.

Gutierrez-Marcos JF, Costa LM, Biderre–Petit C, Khbaya B, Perez P and Dickinson HG. (2004) Meg1 is a novel maize endosperm transfer cell-specific gene with a maternal parent-of-origin pattern of expression. Plant Cell, 16, 1288-1301.

Van Gool T, Biderre C, Delbac F, Wentink-Bonnema E, Ron Peek R, Vivarès C. (2004) Journal of Infectious Disease, 12, 2243-2249. Serodiagnostic studies in an immunocompetent individual infected with Encephalitozoon cuniculi. Journal of Infectious Disease, 12, 2243-2249

Thouvenot A., M. richardot, D. Debroas, J. Devaux (2003). Regulation of the abundance and growth of ciliates in a newly flooded reservoir. Arch. Hydrobiol. 157, 195-193.

Tadonleke R., A. Thouvenot, D. Gilbert, T. Sime-Ngando, D. Debroas, J. Devaux (2003). Size-Fractionated Phytoplankton and Relationships with Metazooplankton in a Newly Flooded Reservoir . Internat. Rev. Hydrobiol. 88, 614-634.

Enault F, Suhre K, Poirot O, Abergel C et Claverie JM. (2003) - Phydbac (phylogenomic display of bacterial genes) : an interactive resource for the annotation of bacterial genomes. Nucleic Acids Research, 31(13) :3720-2.

Enault F, Suhre K, poirot O, Abergel C et Claverie JM. (2003) - Annotation of bacterial genomes using improved phylogenomic profiles. Bioinformatics, 19 Suppl. 1 : i105-7.

Bontems F, le Floch P, Duffieux F, Biderre C, Peyret P, Lallemand JY. (2003) Homology modeling and calculation of the cobalt cluster charges of the Encephazlitozoon cuniculi methionine aminopeptidase, a potential target for drug design. Biophysical Chemistry, 105(1), 29-43.

Bronner G, Spataro B, Page M, Gautier C, Rechenmann F. (2002) - Modeling comparative mapping using objects and associations. Comput. Chem, 26:413-420.

Jugnia L-B., R. Taonleke, T. Sime-Ngando, D. Debroas, J. Dévaux (2001) Bacteria-phytoplankton relationships in a recently formed reservoir (Sep, France). Verh. Internat. Verein. Limnol. 27, 3820-3824.

Richardot M., D. Debroas , A.Thouvenot, D. Sargos, J-L. Berthon, J. Dévaux (2001). Influence of cladoceran grazing activity on dissolved organic matter, enzymatic hydrolysis and bacterial growth. J. Plankton Res. 23, 1249-1261.

Roué A, M. Richardot, A. Thouvenot, D. Debroas, J. Dévaux, M. Poulin (2001). Functionning of a lacustrine ecosystem in a newly flooded reservoir (Sep, Puy de Dôme, France) : modelling of carbon flux between the different food web compartments. Verh Internat Verein Limnol 28, 1253-1258.

Mallet C., D. Debroas (2001). Regulation of a - and b - glycolytic activities in the sediments of a eutrophic lake. Microb. Ecol. 41, 106-113.

Bronner G, Gautier C, Rechenmann F. (2001) - The GeMCore model for comparative mapping. Bio-ontologies, ISMB satellite meeting, 26 juillet 2001 - Copenhague.

Bronner G, Spataro B, Page M, Gautier C, Rechenmann F. (2001) - GeMCore, a knowledge base dedicated to the genomic mapping of mammalian genomes. LNCS : 2066, 11-8.

Jugnia L-B., M. Richardot, D. Debroas, T. Sime-Ngando, R. Tadonleke, J. Dévaux (2000) Variations in the numbers of active bacteria in the euphotic zone of a recently flooded reservoir. Aquat. Microb. Ecol. 22, 251-259.

Domaizon I., C. Desvilettes, D. Debroas, G. Bourdier (2000). Influence of zooplankton and phytoplankton on the fatty acid composition of digesta and tissue lipids of silver carp : mesocosm experiment. J. Fish Biol. 57, 417-432.

Mallet C., D. Debroas (2000) Regulation of aminopeptidase activity in the sediments of a eutrophic lake. Archiv. Hydrobiol.149, 327-335.

Richardot M., D. Debroas, L-B. Jugnia, R. Tadonleke, J-L.Berthon, J. Dévaux (2000). Changes in bacterial processing and composition of dissolved organic matter in a newly-flooded reservoir (a three-year study). Archiv. Hydrobiol. 148, 231-248.

Thouvenot A., D. Debroas, M. Richardot, L-B. Jugnia, J. Dévaux (2000). Study of changes between years in the structure of plankton community in a newly-flooded reservoir. Arch. Hydrobiol. 149, 131-152.

Biderre C, Babin F, Vivarès CP. (2000) Fatty acid composition of four microsporidian species compared to that of their vertebrate hosts (fishes). Journal of Eukaryotic Microbiology, 47, 7-10.

Richardot M., D. Debroas, A. Thouvenot, J-C. Romagoux, J-L. Berthon, J. Dévaux (1999). Proteolytic and glycolytic activities in size-fractionated surface water samples from of an oligotrophic reservoir in relation to plankton communities. Aquatic. Sci. 61, 279-292.

Thouvenot A., M. Richardot, D. Debroas, J. Dévaux (1999b). Bacterivory of metazooplankton, ciliates and flagellates in a newly-flooded reservoir. J. Plankton Res. 21, 1659-1679.

Mallet C., D. Debroas (1999). Relations between organic matter and bacterial proteolytic activity in the superficial sediment layer of a eutrophic lake (Lake Aydat, Puy-de-Dôme, France). Arch. Hydrobiol. 147, 39-56.

Thouvenot A., D. Debroas, M. Richardot, J. Dévaux (1999a). Impact of natural metazooplankton assemblage on planktonic microbial communities in a newly-flooded reservoir. J. Plankton Res. 21, 179-199.

Biderre C, Canning EU, Méténier G, Vivarès CP. (1999) Comparison of two isolates of Encephalitozoon hellem and E. intestinalis (Microspora) by pulsed-field gel electrophoresis. European Journal of Protistology, 35, 194-196.

Biderre C, Mathis A, Deplazes P, Weber R, Méténier G, Vivarès CP. (1999) Molecular karyotype diversity in the microsporidian Encephalitozoon cuniculi. Parasitology, 118, 439-445.

Biderre C, Peyretaillade E, Peyret P, Duffieux F, Méténier G, Gouy M, Michot B, Vivarès CP. (1998) Microsporidian Encephalitozoon cuniculi, a unicellular eukaryote, with a unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core. Nucleic Acids Research, 26, 3513-3520 (les 2 premiers auteurs sont co-auteurs).

Biderre C, Méténier G, Vivarès CP. (1998) A spliceosomal-type intron occurs in an r-protein gene of the microsporidian Encephalitozoon cuniculi. Molecular and Biochemical Parasitology, 94, 282-286.

Debroas D. (1998). Decomposition of protein compounds in an eutrophic lake : spatial and temporal distribution of exopeptidase and endopeptidase in various size fractions. Hydrobiologia 382, 161-173.