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Metagenomics of prokaryotes



Published on 21 December 2021

The Laboratory for the Metagenomics of Prokaryotes (LMP) is currently focusing much of its activity on the study of recalcitrant xenobiotic degradation including that of chlordecone.

The LMP initiated the "Cloaca maxima" project designed to study the biodiversity of the microorganisms involved in waste water treatment. The LMP has set up environmental genomic and metagenomic methods for that purpose. The aim of the program was to inventory the microorganisms, genes and enzymes responsible for the principal stages in water treatment and use that metagenomic resource to characterize new enzymes and metabolic pathways of particular interest with respect to anaerobic metabolism.

The LMP is also addressing the diversity of eukaryotes present in sewage plants, in particular through the Pegasus project.


The LMP has contributed to national and international metagenomic projects:  microorganisms essential in the nitrogen cycle, sediment contaminated by arsenic, human intestinal microbiome and soil microbiome.

Nitrogen cycle 

The Laboratory has also contributed to sequencing key microorganisms in the nitrogen cycle. In most cases, the bacteria had never been isolated in pure cultures and had thus retained "Candidatus" status.

The work was implemented in cooperation with the teams of :

 -  Marc Strous and Mike Jetten 


 - Holger Daims and Michael Wagner 


"Candidatus Kuenenia stuttgartiensis"

Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes H-W, Weissenbach J, Jetten MSM, Wagner M, Le Paslier D. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. 2006. Nature. 440:790-4.

 "Candidatus Methylomirabilis oxyfera"

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 HJCT, van Alen T, Luesken F, Wu ML, van de Pas-Schoonen KT, Op den Camp HJM, Janssen-Megens EM, Francoijs K-J, Stunnenberg H, Weissenbach J, Jetten MSM, Strous M. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. 2010. Nature. 464:543-8.

 "Candidatus Nitrospira defluvii"

Maixner F, Wagner M, Lücker S, Pelletier E, Schmitz-Esser S, Hace K, Spieck E, Konrat R, Le Paslier D, Daims H. Environmental genomics reveals a functional chlorite dismutase in the nitrite-oxidizing bacterium 'Candidatus Nitrospira defluvii'. 2008. Environ Microbiol. 10:3043-56.
Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B, Rattei T, Damsté JSS, Spieck E, Le Paslier D, Daims H. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. 2010. Proc Natl Acad Sci USA. 107:13479-84.

Nitrolancetus hollandicus

Sorokin DY, Lucker S, Vejmelkova D, Kostrikina NA, Kleerebezem R, Rijpstra WI, Damste JS, Le Paslier D, Muyzer G, Wagner M, van Loosdrecht MC, Daims H. Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. 2012. The ISME journal. 6:2245-56.

"Candidatus Nitrosotenuis uzonensis"

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, Wagner M. Enrichment and genome sequence of the group I.1a ammonia-oxidizing archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats. 2013. PlosOne 8(11): e80835.

Nitrospira moscoviensis

Koch H, Galushko A, Albertsen M, Schintlmeister A, Dorninger C, Lücker S, Pelletier E, Le Paslier D, Spieck E, Richter A, Nielsen PH, Wagner M, Daims H. Growth of Nitrite-Oxidizing Bacteria by the Knallgas metabolism. 2014. Science. 345:1052-4.

Arsenic-contaminated sediment          

The project was implemented in cooperation with Philippe Bertin, University of Strasbourg, and received financing from the National Research Agency (ANR).


Bertin PN, Heinrich-Salmeron A, Pelletier E, Goulhen-Chollet F, Arsène-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, Médigue C, Le Paslier D. Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics. 2011. The ISME journal. 5:1735-47.


The work was conducted in cooperation with Tim Vogel and Pascal Simonet, Ecole Centrale, Lyon, and received ANR financing.   


​Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LF, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P. Back to the Future of Soil Metagenomics. 2016. Front Microbiol. 7:73.
Delmont TO, Eren AM, Maccario L, Prestat E, Esen ÖC, Pelletier E, Le Paslier D, Simonet P, Vogel TM. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. 2015. Front Microbiol.  Apr 30;6:358. doi: 10.3389/fmicb.2015.00358. eCollection 2015.
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, Vogel TM. Structure, fluctuation and magnitude of a natural grassland soil metagenome. 2012. The ISME journal. 6:1677-87.


 MetaHit Human intestinal microbiome:  MicroObes and MetaHit projects

The work was conducted in cooperation with Joël Doré and Dusko Ehrlich, INRA, Jouy-en-Josas.​


​Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Igor Costea P, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J; MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. 2015. Nature 528:262-6.
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, Doré J, Ehrlich SD; MetaHIT Consortium, Bork P, Wang J. An integrated catalog of reference genes in the human gut microbiome. 2014. Nat Biotechnol. 32:834-41
Nielsen  H, Almeida M, Juncker A, Rasmussen S, Li J, Sunagawa S, Plichta D, Gautier L, Pedersen A, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto J-M, Bertalan M, Blom N, Borruel N, Burgdorf K, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas R, Kennedy S, Kristiansen K, Kultima J, Leonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery D, Yamada T, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Ehrlich S. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. 2014. Nature Biotechnology. 32:822-8.
Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N, Le Chatelier E, Almeida M, Quinquis B, Levenez F, Galleron N, Gougis S, Rizkalla S, Batto JM, Renault P, ANR MicroObes consortium, Doré J, Zucker JD, Clément K, Ehrlich SD. Dietary intervention impact on gut microbial gene richness. 2013. Nature 500:585-8.


Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O. Richness of human gut microbiome correlates with metabolic markers. 2013. Nature 500:541-6.
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J-M, 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 J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F,​ Pedersen O, de Vos WM, Brunak S, Doré J, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'Rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P. Enterotypes of the human gut microbiome. 2011. Nature. 473:174-80.
Brüls T, Weissenbach J. The human metagenome: our other genome? 2011. Hum Mol Genet. 20:R142-8.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto J-M, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J. A human gut microbial gene catalogue established by metagenomic sequencing. 2010. Nature. 464:59-65.