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Viruses as key reservoirs of antibiotic resistance genes in the environment.

Debroas D, Siguret C.

ISME J. 2019 Nov;13(11):2856-2867. doi: 10.1038/s41396-019-0478-9. Epub 2019 Jul 29.


Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean.

Pereira O, Hochart C, Auguet JC, Debroas D, Galand PE.

Microbiologyopen. 2019 Sep;8(9):e00852. doi: 10.1002/mbo3.852. Epub 2019 Jul 2.


Temporal covariation of epibacterial community and surface metabolome in the Mediterranean seaweed holobiont Taonia atomaria.

Paix B, Othmani A, Debroas D, Culioli G, Briand JF.

Environ Microbiol. 2019 Apr 4. doi: 10.1111/1462-2920.14617. [Epub ahead of print]


Diversity, spatial distribution and activity of fungi in freshwater ecosystems.

Lepère C, Domaizon I, Humbert JF, Jardillier L, Hugoni M, Debroas D.

PeerJ. 2019 Feb 21;7:e6247. doi: 10.7717/peerj.6247. eCollection 2019.


A De Novo Robust Clustering Approach for Amplicon-Based Sequence Data.

Bazin A, Debroas D, Mephu Nguifo E.

J Comput Biol. 2019 Jun;26(6):618-624. doi: 10.1089/cmb.2018.0170. Epub 2018 Dec 5.


New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics.

Biderre-Petit C, Taib N, Gardon H, Hochart C, Debroas D.

FEMS Microbiol Ecol. 2019 Mar 1;95(3). doi: 10.1093/femsec/fiy183.


A strong link between marine microbial community composition and function challenges the idea of functional redundancy.

Galand PE, Pereira O, Hochart C, Auguet JC, Debroas D.

ISME J. 2018 Oct;12(10):2470-2478. doi: 10.1038/s41396-018-0158-1. Epub 2018 Jun 20.


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.

Bisseux M, Colombet J, Mirand A, Roque-Afonso AM, Abravanel F, Izopet J, Archimbaud C, Peigue-Lafeuille H, Debroas D, Bailly JL, Henquell C.

Euro Surveill. 2018 Feb;23(7). doi: 10.2807/1560-7917.ES.2018.23.7.17-00237.


Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems.

Frouin E, Bes M, Ollivier B, Quéméneur M, Postec A, Debroas D, Armougom F, Erauso G.

Front Microbiol. 2018 Feb 6;9:102. doi: 10.3389/fmicb.2018.00102. eCollection 2018.


Active microorganisms thrive among extremely diverse communities in cloud water.

Amato P, Joly M, Besaury L, Oudart A, Taib N, Moné AI, Deguillaume L, Delort AM, Debroas D.

PLoS One. 2017 Aug 8;12(8):e0182869. doi: 10.1371/journal.pone.0182869. eCollection 2017.


Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study.

Lavergne C, Hugoni M, Hubas C, Debroas D, Dupuy C, Agogué H.

Microb Ecol. 2018 Feb;75(2):364-374. doi: 10.1007/s00248-017-1048-1. Epub 2017 Aug 4.


Deciphering biodiversity and interactions between bacteria and microeukaryotes within epilithic biofilms from the Loue River, France.

Zancarini A, Echenique-Subiabre I, Debroas D, Taïb N, Quiblier C, Humbert JF.

Sci Rep. 2017 Jun 28;7(1):4344. doi: 10.1038/s41598-017-04016-w.


Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming.

Capo E, Debroas D, Arnaud F, Perga ME, Chardon C, Domaizon I.

Environ Microbiol. 2017 Jul;19(7):2873-2892. doi: 10.1111/1462-2920.13815. Epub 2017 Jun 22.


Plastics in the North Atlantic garbage patch: A boat-microbe for hitchhikers and plastic degraders.

Debroas D, Mone A, Ter Halle A.

Sci Total Environ. 2017 Dec 1;599-600:1222-1232. doi: 10.1016/j.scitotenv.2017.05.059. Epub 2017 May 13.


Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments.

Briand JF, Barani A, Garnier C, Réhel K, Urvois F, LePoupon C, Bouchez A, Debroas D, Bressy C.

Microb Ecol. 2017 Oct;74(3):585-598. doi: 10.1007/s00248-017-0966-2. Epub 2017 Apr 3.


Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data.

Debroas D, Domaizon I, Humbert JF, Jardillier L, Lepère C, Oudart A, Taïb N.

FEMS Microbiol Ecol. 2017 Apr 1;93(4). doi: 10.1093/femsec/fix023.


Bacterial Communities Associated with Four Cyanobacterial Genera Display Structural and Functional Differences: Evidence from an Experimental Approach.

Zhu L, Zancarini A, Louati I, De Cesare S, Duval C, Tambosco K, Bernard C, Debroas D, Song L, Leloup J, Humbert JF.

Front Microbiol. 2016 Oct 24;7:1662. eCollection 2016.


Long-term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA.

Capo E, Debroas D, Arnaud F, Guillemot T, Bichet V, Millet L, Gauthier E, Massa C, Develle AL, Pignol C, Lejzerowicz F, Domaizon I.

Mol Ecol. 2016 Dec;25(23):5925-5943. doi: 10.1111/mec.13893. Epub 2016 Nov 10.


Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments.

Jeanbille M, Gury J, Duran R, Tronczynski J, Ghiglione JF, Agogué H, Saïd OB, Taïb N, Debroas D, Garnier C, Auguet JC.

Front Microbiol. 2016 Aug 19;7:1303. doi: 10.3389/fmicb.2016.01303. eCollection 2016.


Diversity and Dynamics of Active Small Microbial Eukaryotes in the Anoxic Zone of a Freshwater Meromictic Lake (Pavin, France).

Lepère C, Domaizon I, Hugoni M, Vellet A, Debroas D.

Front Microbiol. 2016 Feb 10;7:130. doi: 10.3389/fmicb.2016.00130. eCollection 2016.


Correction: Structural Diversity of Bacterial Communities Associated with Bloom-Forming Freshwater Cyanobacteria Differs According to the Cyanobacterial Genus.

Louati I, Pascault N, Debroas D, Bernard C, Humbert JF, Leloup J.

PLoS One. 2016 Jan 7;11(1):e0146866. doi: 10.1371/journal.pone.0146866. eCollection 2016. No abstract available.


Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes.

Biderre-Petit C, Dugat-Bony E, Mege M, Parisot N, Adrian L, Moné A, Denonfoux J, Peyretaillade E, Debroas D, Boucher D, Peyret P.

PLoS One. 2016 Jan 6;11(1):e0145558. doi: 10.1371/journal.pone.0145558. eCollection 2016.


Structural Diversity of Bacterial Communities Associated with Bloom-Forming Freshwater Cyanobacteria Differs According to the Cyanobacterial Genus.

Louati I, Pascault N, Debroas D, Bernard C, Humbert JF, Leloup J.

PLoS One. 2015 Nov 18;10(11):e0140614. doi: 10.1371/journal.pone.0140614. eCollection 2015. Erratum in: PLoS One. 2016;11(1):e0146866.


Analysis of metagenomic data reveals common features of halophilic viral communities across continents.

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.

Environ Microbiol. 2016 Mar;18(3):889-903. doi: 10.1111/1462-2920.13084. Epub 2015 Dec 10.


Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity.

Capo E, Debroas D, Arnaud F, Domaizon I.

Microb Ecol. 2015 Nov;70(4):865-75. doi: 10.1007/s00248-015-0627-2. Epub 2015 May 29.


Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea.

Hugoni M, Agogué H, Taib N, Domaizon I, Moné A, Galand PE, Bronner G, Debroas D, Mary I.

Microb Ecol. 2015 Aug;70(2):473-83. doi: 10.1007/s00248-015-0601-z. Epub 2015 Apr 8.


Evidence for an active rare biosphere within freshwater protists community.

Debroas D, Hugoni M, Domaizon I.

Mol Ecol. 2015 Mar;24(6):1236-47. doi: 10.1111/mec.13116.


Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes.

Hugoni M, Domaizon I, Taib N, Biderre-Petit C, Agogué H, Galand PE, Debroas D, Mary I.

Environ Microbiol Rep. 2015 Apr;7(2):321-9. doi: 10.1111/1758-2229.12251. Epub 2015 Jan 23.


Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems.

Pascault N, Loux V, Derozier S, Martin V, Debroas D, Maloufi S, Humbert JF, Leloup J.

Genetica. 2015 Apr;143(2):157-67. doi: 10.1007/s10709-014-9783-4. Epub 2014 Sep 13.


A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole.

Pascault N, Roux S, Artigas J, Pesce S, Leloup J, Tadonleke RD, Debroas D, Bouchez A, Humbert JF.

FEMS Microbiol Ecol. 2014 Dec;90(3):563-74. doi: 10.1111/1574-6941.12416. Epub 2014 Sep 15.


Metavir 2: new tools for viral metagenome comparison and assembled virome analysis.

Roux S, Tournayre J, Mahul A, Debroas D, Enault F.

BMC Bioinformatics. 2014 Mar 19;15:76. doi: 10.1186/1471-2105-15-76.


Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences.

Roux S, Krupovic M, Debroas D, Forterre P, Enault F.

Open Biol. 2013 Dec 11;3(12):130160. doi: 10.1098/rsob.130160.


Bacterial communities associated with Microcystis colonies differ from free-living communities living in the same ecosystem.

Parveen B, Ravet V, Djediat C, Mary I, Quiblier C, Debroas D, Humbert JF.

Environ Microbiol Rep. 2013 Oct;5(5):716-24. doi: 10.1111/1758-2229.12071. Epub 2013 Jun 13.


Comparative sensitivity to the fungicide tebuconazole of biofilm and plankton microbial communities in freshwater ecosystems.

Artigas J, Pascault N, Bouchez A, Chastain J, Debroas D, Humbert JF, Leloup J, Tadonleke RD, ter Halle A, Pesce S.

Sci Total Environ. 2014 Jan 15;468-469:326-36. doi: 10.1016/j.scitotenv.2013.08.074. Epub 2013 Sep 15.


Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters.

Hugoni M, Taib N, Debroas D, Domaizon I, Jouan Dufournel I, Bronner G, Salter I, Agogué H, Mary I, Galand PE.

Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):6004-9. doi: 10.1073/pnas.1216863110. Epub 2013 Mar 27.


Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity.

Taib N, Mangot JF, Domaizon I, Bronner G, Debroas D.

PLoS One. 2013;8(3):e58950. doi: 10.1371/journal.pone.0058950. Epub 2013 Mar 14.


Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems.

Lepère C, Domaizon I, Taïb N, Mangot JF, Bronner G, Boucher D, Debroas D.

FEMS Microbiol Ecol. 2013 Jul;85(1):85-94. doi: 10.1111/1574-6941.12100. Epub 2013 Mar 18.


Dynamics of ammonia-oxidizing Archaea and Bacteria in contrasted freshwater ecosystems.

Hugoni M, Etien S, Bourges A, Lepère C, Domaizon I, Mallet C, Bronner G, Debroas D, Mary I.

Res Microbiol. 2013 May;164(4):360-70. doi: 10.1016/j.resmic.2013.01.004. Epub 2013 Feb 8.


Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes.

Mangot JF, Domaizon I, Taib N, Marouni N, Duffaud E, Bronner G, Debroas D.

Environ Microbiol. 2013 Jun;15(6):1745-58. doi: 10.1111/1462-2920.12065. Epub 2013 Jan 9.


Short-term responses of unicellular planktonic eukaryotes to increases in temperature and UVB radiation.

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.

BMC Microbiol. 2012 Sep 11;12:202. doi: 10.1186/1471-2180-12-202.


Temporal dynamics and phylogenetic diversity of free-living and particle-associated Verrucomicrobia communities in relation to environmental variables in a mesotrophic lake.

Parveen B, Mary I, Vellet A, Ravet V, Debroas D.

FEMS Microbiol Ecol. 2013 Jan;83(1):189-201. doi: 10.1111/j.1574-6941.2012.01469.x. Epub 2012 Sep 19.


Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.

Roux S, Krupovic M, Poulet A, Debroas D, Enault F.

PLoS One. 2012;7(7):e40418. doi: 10.1371/journal.pone.0040418. Epub 2012 Jul 11.


Assessing the diversity and specificity of two freshwater viral communities through metagenomics.

Roux S, Enault F, Robin A, Ravet V, Personnic S, Theil S, Colombet J, Sime-Ngando T, Debroas D.

PLoS One. 2012;7(3):e33641. doi: 10.1371/journal.pone.0033641. Epub 2012 Mar 14.


Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems.

Roux S, Enault F, Bronner G, Debroas D.

FEMS Microbiol Ecol. 2011 Dec;78(3):617-28. doi: 10.1111/j.1574-6941.2011.01190.x. Epub 2011 Sep 19.


Quantitative PCR enumeration of total/toxic Planktothrix rubescens and total cyanobacteria in preserved DNA isolated from lake sediments.

Savichtcheva O, Debroas D, Kurmayer R, Villar C, Jenny JP, Arnaud F, Perga ME, Domaizon I.

Appl Environ Microbiol. 2011 Dec;77(24):8744-53. doi: 10.1128/AEM.06106-11. Epub 2011 Oct 7.


Metavir: a web server dedicated to virome analysis.

Roux S, Faubladier M, Mahul A, Paulhe N, Bernard A, Debroas D, Enault F.

Bioinformatics. 2011 Nov 1;27(21):3074-5. doi: 10.1093/bioinformatics/btr519. Epub 2011 Sep 11.


Diversity and dynamics of free-living and particle-associated Betaproteobacteria and Actinobacteria in relation to phytoplankton and zooplankton communities.

Parveen B, Reveilliez JP, Mary I, Ravet V, Bronner G, Mangot JF, Domaizon I, Debroas D.

FEMS Microbiol Ecol. 2011 Sep;77(3):461-76. doi: 10.1111/j.1574-6941.2011.01130.x. Epub 2011 Jun 16.


Vertical structure of small eukaryotes in three lakes that differ by their trophic status: a quantitative approach.

Lepère C, Masquelier S, Mangot JF, Debroas D, Domaizon I.

ISME J. 2010 Dec;4(12):1509-19. doi: 10.1038/ismej.2010.83. Epub 2010 Jun 24.


Community structure and dynamics of small eukaryotes targeted by new oligonucleotide probes: new insight into the lacustrine microbial food web.

Mangot JF, Lepère C, Bouvier C, Debroas D, Domaizon I.

Appl Environ Microbiol. 2009 Oct;75(19):6373-81. doi: 10.1128/AEM.00607-09. Epub 2009 Aug 7.


Impact of environmental factors on couplings between bacterial community composition and ectoenzymatic activities in a lacustrine ecosystem.

Boucher D, Debroas D.

FEMS Microbiol Ecol. 2009 Oct;70(1):66-78. doi: 10.1111/j.1574-6941.2009.00730.x. Epub 2009 Jun 22.

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