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Metagenomics of prokaryotes


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Published on 21 December 2021
"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