| "The complete genome sequence of elite bread wheat cultivar, ""Sonmez""" | Akpinar BA, Leroy P, Watson-Haigh N, Baumann U, Barbe V and Budak H | |  | | Metatranscriptomics of cheese microbial communities: Efficiency of RNA extraction from various cheese types and of mRNA enrichment | Carbonne C, Labadie K, Cruaud C, Brun E, Barbe V and Monnet C | | | | Microbiological versus Chemical Reductive Sulfidation: An Experimental and Theoretical Study | Della-Negra O, de Bonneville BL, Chaussonnerie S, Le Paslier D, Frison G and Saaidi PL | | | | Genetic Analysis of Citrobacter sp.86 Reveals Involvement of Corrinoids in Chlordecone and Lindane Biotransformations | Barbance A, Della-Negra O, Chaussonnerie S, Delmas V, Muselet D, Ugarte E, Saaidi PL, Weissenbach J, Fischer C, Le Paslier D and Fonknechten N | | | | Transformation of the recalcitrant pesticide chlordecone by Desulfovibrio sp.86 with a switch from ring-opening dechlorination to reductive sulfidation activity | Della-Negra O, Chaussonnerie S, Fonknechten N, Barbance A, Muselet D, Martin DE, Fouteau S, Fischer C, Saaidi PL and Le Paslier D | | | | Colonization kinetics and implantation follow-up of the sewage microbiome in an urban wastewater treatment plant | Morin L, Goubet A, Madigou C, Pernelle JJ, Palmier K, Labadie K, Lemainque A, Michot O, Astoul L, Barbier P, Almayrac JL and Sghir A | | | | In situ metabolic activities of uncultivated Ferrovum sp. CARN8 evidenced by metatranscriptomic analysis | Plewniak F, Koechler S, Le Paslier D, Hery M, Bruneel O and Bertin PN | | | | Natural Chlordecone Degradation Revealed by Numerous Transformation Products Characterized in Key French West Indies Environmental Compartments | Chevallier ML, Della-Negra O, Chaussonnerie S, Barbance A, Muselet D, Lagarde F, Darii E, Ugarte E, Lescop E, Fonknechten N, Weissenbach J, Woignier T, Gallard JF, Vuilleumier S, Imfeld G, Le Paslier D and Saaidi PL | | | | Molecular analysis of methanogen populations and their interactions within anaerobic sludge digesters | Guermazi-Toumi S, Chouari R and Sghir A | | | | Recognition of the persistent organic pollutant chlordecone by a hemicryptophane cage | Long A, Lefevre S, Guy L, Robert V, Dutasta JP, Chevallier ML, Della-Negra O, Saaidi PL and Martinez A | | | | Distinct Carbon Isotope Fractionation Signatures during Biotic and Abiotic Reductive Transformation of Chlordecone | Chevallier ML, Cooper M, Kummel S, Barbance A, Le Paslier D, Richnow HH, Saaidi PL and Adrian L | | | | Screening and Characterization of Novel Polyesterases from Environmental Metagenomes with High Hydrolytic Activity against Synthetic Polyesters | Hajighasemi M, Tchigvintsev A, Nocek B, Flick R, Popovic A, Hai T, Khusnutdinova AN, Brown G, Xu XH, Cui H, Anstett J, Chernikova TN, Bruls T, Le Paslier D, Yakimov MM, Joachimiak A, Golyshina OV, Savchenko A, Golyshin PN, Edwards EA and Yakunin AF | | | | Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms | Kazamia E, Sutak R, Paz-Yepes J, Dorrell RG, Vieira FRJ, Mach J, Morrissey J, Leon S, Lam F, Pelletier E, Camadro JM, Bowler C and Lesuisse E | | | | Eukaryotic molecular diversity at different steps of the wastewater treatment plant process reveals more phylogenetic novel lineages | Chouari R, Leonard M, Bouali M, Guermazi S, Rahli N, Zrafi I, Morin L and Sghir A | | | | Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families | Popovic A, Hai T, Tchigvintsev A, Hajighasemi M, Nocek B, Khusnutdinova AN, Brown G, Glinos J, Flick R, Skarina T, Chernikova TN, Yim V, Bruls T, Le Paslier D, Yakimov MM, Joachimiak A, Ferrer M, Golyshina OV, Savchenko A, Golyshin PN and Yakunin AF | | | | The metagenomic data life-cycle: standards and best practices | ten Hoopen P, Finn RD, Bongo LA, Corre E, Fosso B, Meyer F, Mitchell A, Pelletier E, Pesole G, Santamaria M, Willassen NP and Cochrane G | Gigascience 6 (7), , 2017 | | | Microbial Degradation of a Recalcitrant Pesticide: Chlordecone | Chaussonnerie S, Saaidi PL, Ugarte E, Barbance A, Fossey A, Barbe V, Gyapay G, Bruls T, Chevalier M, Couturat L, Fouteau S, Muselet D, Pateau E, Cohen GN, Fonknechten N, Weissenbach J and Le Paslier D | | | | Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters | Gannoun H, Omri I, Chouari R, Khelifi E, Keskes S, Godon JJ, Hamdi M, Sghir A and Bouallagui H | | | | Microbiotes and metagenomics | Weissenbach J and Sghir A | | | | Microbial Analysis and Efficiency of Biofiltration Packing Systems for Hydrogen Sulfide Removal from Wastewater Off Gas | Chouari R, Dardouri W, Sallami F, Ben Rais M, Le Paslier D and Sghir A | | | | Co-occurence of Crenarchaeota, Thermoplasmata and methanogens in anaerobic sludge digesters | Chouari R, Guermazi S and Sghir A | | | | Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics | Delmont TO, Eren AM, Maccario L, Prestat E, Esen O, Pelletier E, LePaslier D, Simonet P and Vogel TM | | | | 16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage | Fahy A, Giloteaux L, Bertin P, Le Paslier D, Medigue C, Weissenbach J, Duran R and Lauga B | | | | Characterization of functional communities and metabolic pathways during methanogenesis in wastewater sludge by isotopic and molecular analysis | Limam RD, Grossin-Debattista J, Chouari R, Landoulsi A and Sghir A | | | | Determinants of community structure in the global plankton interactome | Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sanchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J and Tara Oceans C | | | | Structure and function of the global ocean microbiome | Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P and Tara Oceans C | | | | Bacterial structure and spatiotemporal distribution in a horizontal subsurface flow constructed wetland | Bouali M, Zrafi I, Bakhrouf A, Chaussonnerie S and Sghir A | | | | Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation | Koch H, Galushko A, Albertsen M, Schintlmeister A, Gruber-Dorninger C, Lucker S, Pelletier E, Le Paslier D, Spieck E, Richter A, Nielsen PH, Wagner M and Daims H | | | | An integrated catalog of reference genes in the human gut microbiome | Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Dore J, Ehrlich SD, Bork P, Wang J and Meta HITC | | | | Members of the uncultured bacterial candidate division WWE1 are implicated in anaerobic digestion of cellulose | Limam RD, Chouari R, Mazeas L, Wu T-D, Li T, Grossin-Debattista J, Guerquin-Kern J-L, Saidi M, Landoulsi A, Sghir A and Bouchez T | | | | Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes | Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto J-M, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Dore J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Leonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sorensen S, Tap J, Tims S, Ussery DW, Yamada T, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD and Meta HITC | | | | Characterization of rhizosphere prokaryotic diversity in a horizontal subsurface flow constructed wetland using a PCR cloning-sequencing based approach | Bouali M, Pelletier E, Chaussonnerie S, Le Paslier D, Bakhrouf A and Sghir A | | | | Gene Capture Coupled to High-Throughput Sequencing as a Strategy for Targeted Metagenome Exploration | Denonfoux J, Parisot N, Dugat-Bony E, Biderre-Petit C, Boucher D, Morgavi DP, Le Paslier D, Peyretaillade E and Peyret P | | | | "Enrichment and Genome Sequence of the Group I. 1a Ammonia-Oxidizing Archaeon ""Ca. Nitrosotenuis uzonensis"" Representing a Clade Globally Distributed in Thermal Habitats" | Lebedeva EV, Hatzenpichler R, Pelletier E, Schuster N, Hauzmayer S, Bulaev A, Grigor'eva NV, Galushko A, Schmid M, Palatinszky M, Le Paslier D, Daims H and Wagner M | | | | The structure and spatio-temporal distribution of the Archaea in a horizontal subsurface flow constructed wetland | Bouali M, Zrafi-Nouira I, Bakhrouf A, Le Paslier D, Chaussonnerie S, Ammar E and Sghir A | | | | Structure, fluctuation and magnitude of a natural grassland soil metagenome | Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, Pelletier E, Hirsch PR, Meyer F, Gilbert JA, Le Paslier D, Simonet P and Vogel TM | | | | Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene | Martin F, Torelli S, Le Paslier D, Barbance A, Martin-Laurent F, Bru D, Geremia R, Blake G and Jouanneau Y | | | | Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi | Sorokin DY, Lucker S, Vejmelkova D, Kostrikina NA, Kleerebezem R, Rijpstra WIC, Damste JSS, Le Paslier D, Muyzer G, Wagner M, van Loosdrecht MCM and Daims H | | | | Enterotypes of the human gut microbiome | Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin JJ, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, Weissenbach J, Ehrlich SD, Bork P and Meta HITC | Nature 473 (7346), 174-180, 2011 | | | Molecular community analysis of magnesium-rich bittern brine recovered from a Tunisian solar saltern | Baati H, Jarboui R, Gharsallah N, Sghir A and Ammar E | Canadian Journal of Microbiology 57 (12), 975-981, 2011 | | | Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics | Bertin PN, Heinrich-Salmeron A, Pelletier E, Goulhen-Chollet F, Arsene-Ploetze F, Gallien S, Lauga B, Casiot C, Calteau A, Vallenet D, Bonnefoy V, Bruneel O, Chane-Woon-Ming B, Cleiss-Arnold J, Duran R, Elbaz-Poulichet F, Fonknechten N, Giloteaux L, Halter D, Koechler S, Marchal M, Mornico D, Schaeffer C, Smith AAT, Van Dorsselaer A, Weissenbach J, Medigue C and Le Paslier D | Isme Journal 5 (11), 1735-1747, 2011 | | | Characterization of the Active Bacterial Community Involved in Natural Attenuation Processes in Arsenic-Rich Creek Sediments | Bruneel O, Volant A, Gallien S, Chaumande B, Casiot C, Carapito C, Bardil A, Morin G, Brown GE, Jr., Personne CJ, Le Paslier D, Schaeffer C, Van Dorsselaer A, Bertin PN, Elbaz-Poulichet F and Arsene-Ploetze F | Microbial Ecology 61 (4), 793-810, 2011 | | | Isolation and Characterization of Moderately Halophilic Bacteria from Tunisian Solar Saltern | Baati H, Amdouni R, Gharsallah N, Sghir A and Ammar E | Current Microbiology 60 (3), 157-161, 2010 | | | Microbial community of salt crystals processed from Mediterranean seawater based on 16S rRNA analysis | Baati H, Guermazi S, Gharsallah N, Sghir A and Ammar E | Canadian Journal of Microbiology 56 (1), 44-51, 2010 | | | Novel prokaryotic diversity in sediments of Tunisian multipond solar saltern | Baati H, Guermazi S, Gharsallah N, Sghir A and Ammar E | Research in Microbiology 161 (7), 573-582, 2010 | | | Molecular Analyses of the Microbial Community Composition of an Anoxic Basin of a Municipal Wastewater Treatment Plant Reveal a Novel Lineage of Proteobacteria | Chouari R, Le Paslier D, Daegelen P, Dauga C, Weissenbach J and Sghir A | Microbial Ecology 60 (2), 272-281, 2010 | | | Nitrite-driven anaerobic methane oxidation by oxygenic bacteria | Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MMM, Schreiber F, Dutilh BE, Zedelius J, de Beer D, Gloerich J, Wessels H, van Alen T, Luesken F, Wu ML, van de Pas-Schoonen KT, den Camp H, Janssen-Megens EM, Francoijs KJ, Stunnenberg H, Weissenbach J, Jetten MSM and Strous M | Nature 464 (7288), 543-U94, 2010 | | | Clostridium sticklandii, a specialist in amino acid degradation: revisiting its metabolism through its genome sequence | Fonknechten N, Chaussonnerie S, Tricot S, Lajus A, Andreesen JR, Perchat N, Pelletier E, Gouyvenoux M, Barbe V, Salanoubat M, Le Paslier D, Weissenbach J, Cohen GN and Kreimeyer A | Bmc Genomics 11 (), 555, 2010 | | | Detection of WWE2-related Lentisphaerae by 16S rRNA gene sequencing and fluorescence in situ hybridization in landfill leachate | Limam RD, Bouchez T, Chouari R, Li TL, Barkallah I, Landoulsi A and Sghir A | Canadian Journal of Microbiology 56 (10), 846-852, 2010 | | | A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria | Lucker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B, Rattei T, Damste JSS, Spieck E, Le Paslier D and Daims H | Proceedings of the National Academy of Sciences of the United States of America 107 (30), 13479-13484, 2010 | | | A human gut microbial gene catalogue established by metagenomic sequencing | Qin JJ, Li RQ, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li JH, Xu JM, Li SC, Li DF, Cao JJ, Wang B, Liang HQ, Zheng HS, Xie YL, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu HM, Yu C, Li ST, Jian M, Zhou Y, Li YR, Zhang XQ, Li SG, Qin N, Yang HM, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD and Meta HITC | Nature 464 (7285), 59-65, 2010 | | | Tracing Ancestors and Relatives of Escherichia coli B, and the Derivation of B Strains REL606 and BL21(DE3) | Daegelen P, Studier FW, Lenski RE, Cure S and Kim JF | Journal of Molecular Biology 394 (4), 634-643, 2009 | | | A Conserved Gene Cluster Rules Anaerobic Oxidative Degradation of L-Ornithine | Fonknechten N, Perret A, Perchat N, Tricot S, Lechaplais C, Vallenet D, Vergne C, Zaparucha A, Le Paslier D, Weissenbach J and Salanoubat M | Journal of Bacteriology 191 (9), 3162-3167, 2009 | | | Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3) | Jeong H, Barbe V, Lee CH, Vallenet D, Yu DS, Choi SH, Couloux A, Lee SW, Yoon SH, Cattolico L, Hur CG, Park HS, Segurens B, Kim SC, Oh TK, Lenski RE, Studier FW, Daegelen P and Kim JF | Journal of Molecular Biology 394 (4), 644-652, 2009 | | | Insights into networks of functional microbes catalysing methanization of cellulose under mesophilic conditions | Li TL, Mazeas L, Sghir A, Leblon G and Bouchez T | Environmental Microbiology 11 (4), 889-904, 2009 | | | Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes | Loy A, Duller S, Baranyi C, Mussmann M, Ott J, Sharon I, Beja O, Le Paslier D, Dahl C and Wagner M | Environmental Microbiology 11 (2), 289-299, 2009 | | | Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge | Riviere D, Desvignes V, Pelletier E, Chaussonnerie S, Guermazi S, Weissenbach J, Li T, Camacho P and Sghir A | Isme Journal 3 (6), 700-714, 2009 | | | Broad-range PCR, cloning and sequencing of the full 16S rRNA gene for detection of bacterial DNA in synovial fluid samples of Tunisian patients with reactive and undifferentiated arthritis | Siala M, Gdoura R, Fourati H, Rihl M, Jaulhac B, Younes M, Sibilia J, Baklouti S, Bargaoui N, Sellami S, Sghir A and Hammami A | Arthritis Research & Therapy 11 (4), 11, 2009 | | | Understanding the Differences between Genome Sequences of Escherichia coli B Strains REL606 and BL21(DE3) and Comparison of the E-coli B and K-12 Genomes | Studier FW, Daegelen P, Lenski RE, Maslov S and Kim JF | Journal of Molecular Biology 394 (4), 653-680, 2009 | | | Towards the human intestinal microbiota phylogenetic core | Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Munoz-Tamayo R, Paslier DLE, Nalin R, Dore J and Leclerc M | Environmental Microbiology 11 (10), 2574-2584, 2009 | | | Molecular diversity analysis and bacterial population dynamics of an adapted seawater microbiota during the degradation of Tunisian zarzatine oil | Zrafi-Nouira I, Guermazi S, Chouari R, Safi NMD, Pelletier E, Bakhrouf A, Saidane-Mosbahi D and Sghir A | Biodegradation 20 (4), 467-486, 2009 | | | Prokaryotic diversity of a Tunisian multipond solar saltern | Baati H, Guermazi S, Amdouni R, Gharsallah N, Sghir A and Ammar E | Extremophiles 12 (4), 505-518, 2008 | | | Cloacibacillus evryensis gen. nov., sp nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum 'Synergistetes', isolated from an anaerobic sludge digester | Ganesan A, Chaussonnerie S, Tarrade A, Dauga C, Bouchez T, Pelletier E, Le Paslier D and Sghir A | International Journal of Systematic and Evolutionary Microbiology 58 (), 2003-2012, 2008 | | | Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach | Guermazi S, Daegelen P, Dauga C, Riviere D, Bouchez T, Godon JJ, Gyapay G, Sghir A, Pelletier E, Weissenbach J and Le Paslier D | Environmental Microbiology 10 (8), 2111-2123, 2008 | | | Environmental genomics reveals a functional chlorite dismutase in the nitrite-oxidizing bacterium 'Candidatus Nitrospira defluvii' | Maixner F, Wagner M, Lucker S, Pelletier E, Schmitz-Esser S, Hace K, Spieck E, Konrat R, Le Paslier D and Daims H | Environmental Microbiology 10 (11), 3043-3056, 2008 | |
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