MGPS & l'INRA
The microbiota in human health
and well being.

Publications

2018

26/11/2018

Prediction of the intestinal resistome by a three-dimensional structure-based method

Etienne Ruppé, Amine Ghozlane, Julien Tap, Nicolas Pons, Anne-Sophie Alvarez, Nicolas Maziers, Trinidad Cuesta, Sara Hernando-Amado, Irene Clares, Jose Luís Martínez, Teresa M. Coque, Fernando Baquero, Val F. Lanza, Luis Máiz, Tiphaine Goulenok, Victoire de Lastours, Nawal Amor, Bruno Fantin, Ingrid Wieder, Antoine Andremont, Willem van Schaik, Malbert Rogers, Xinglin Zhang, Rob J. L. Willems, Alexandre G. de Brevern, Jean-Michel Batto, Hervé M. Blottière, Pierre Léonard, Véronique Léjard, Aline Letur, Florence Levenez, Kevin Weiszer, Florence Haimet, Joël Doré, Sean P. Kennedy & S. Dusko Ehrlich

 

 DOI: 10.1038/s41564-018-0292-6

25/09/2018

MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data

Florian Plaza Oñate, Emmanuelle Le Chatelier, Mathieu Almeida, Alessandra C L Cervino, Franck Gauthier, Frédéric Magoulès, S Dusko Ehrlich, Matthieu Pichaud

 

 DOI: 10.1093/bioinformatics/bty830

10/07/2018

Major microbiota dysbiosis in severe obesity: fate after bariatric surgery

Judith Aron-Wisnewsky, Edi Prifti, Eugeni Belda, Farid Ichou, Brandon D Kayser, Maria Carlota Dao, Eric O Verger, Lyamine Hedjazi, Jean-Luc Bouillot, Jean-Marc Chevallier, Nicolas Pons, Emmanuelle Le Chatelier, Florence Levenez, Stanislav Dusko Ehrlich, Joel Dore, Jean-Daniel Zucker, Karine Clément

 

 DOI: 10.1136/gutjnl-2018-316103

02/05/2018

Microbial ecology perturbation in human IgA deficiency

Jehane Fadlallah, Hela El Kafsi, Delphine Sterlin, Catherine Juste, Christophe Parizo2, Karim Dorgham, Gaëlle Autaa, Doriane Gouas, Mathieu Almeida, Patricia Lepage, Nicolas Pons, Emmanuelle Le Chatelier, Florence Levenez, Sean Kennedy, Nathalie Galleron, Jean-Paul Pais de Barros, Marion Malphettes, Lionel Galicier, David Boutboul, Alexis Mathian, Makoto Miyara, Eric Oksenhendler, Zahir Amoura, Joel Doré, Claire Fieschi, S. Dusko Ehrlich, Martin Larsen and Guy Gorochov

 

 DOI: 10.1126/scitranslmed.aan1217

05/01/2018

Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors

Bertrand Routy, Emmanuelle Le Chatelier, Lisa Derosa, Connie P. M. Duong, Maryam Tidjani Alou, Romain Daillère, Aurélie Fluckiger, Meriem Messaoudene, Conrad Rauber, Maria P. Roberti, Marine Fidelle, Caroline Flament, Vichnou Poirier-Colame, Paule Opolon, Christophe Klein, Kristina Iribarren, Laura Mondragón, Nicolas Jacquelot, Bo Qu, Gladys Ferrere, Céline Clémenson, Laura Mezquita, Jordi Remon Masip, Charles Naltet, Solenn Brosseau, Coureche Kaderbhai, Corentin Richard, Hira Rizvi, Florence Levenez, Nathalie Galleron, Benoit Quinquis, Nicolas Pons, Bernhard Ryffel, Véronique Minard-Colin, Patrick Gonin, Jean-Charles Soria, Eric Deutsch, Yohann Loriot, François Ghiringhelli, Gérard Zalcman, François Goldwasser, Bernard Escudier, Matthew D. Hellmann, Alexander Eggermont, Didier Raoult, Laurence Albiges, Guido Kroemer, Laurence Zitvogel

 

 DOI: 10.1126/science.aan3706


2017

02/10/2017

Towards standards for human fecal sample processing in metagenomic studies

Paul I Costea, Georg Zeller, Shinichi Sunagawa, Eric Pelletier, Adriana Alberti, Florence Levenez, Melanie Tramontano, Marja Driessen, Rajna Hercog, Ferris-Elias Jung, Jens Roat Kultima, Matthew R Hayward, Luis Pedro Coelho, Emma Allen-Vercoe, Laurie Bertrand, Michael Blaut, Jillian R M Brown, Thomas Carton, Stéphanie Cools-Portier, Michelle Daigneault, Muriel Derrien, Anne Druesne, Willem M de Vos, B Brett Finlay, Harry J Flint, Francisco Guarner, Masahira Hattori, Hans Heilig, Ruth Ann Luna, Johan van Hylckama Vlieg, Jana Junick, Ingeborg Klymiuk, Philippe Langella, Emmanuelle Le Chatelier, Volker Mai, Chaysavanh Manichanh, Jennifer C Martin, Clémentine Mery, Hidetoshi Morita, Paul W O'Toole, Céline Orvain, Kiran Raosaheb Patil, John Penders, Søren Persson, Nicolas Pons, Milena Popova, Anne Salonen, Delphine Saulnier, Karen P Scott, Bhagirath Singh, Kathleen Slezak, Patrick Veiga, James Versalovic, Liping Zhao, Erwin G Zoetendal, S Dusko Ehrlich, Joel Dore & Peer Bork

 

 DOI: 10.1038/nbt.3960

27/07/2017

Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis

Chengping Wen, Zhijun Zheng, Tiejuan Shao, Lin Liu, Zhijun Xie, Emmanuelle Le Chatelier, Zhixing He, Wendi Zhong, Yongsheng Fan, Linshuang Zhang, Haichang Li, Chunyan Wu, Changfeng Hu, Qian Xu, Jia Zhou, Shunfeng Cai, Dawei Wang, Yun Huang, Maxime Breban, Nan Qin and Stanislav Dusko Ehrlich

 

 DOI: 10.1186/s13059-017-1271-6


2016

22/09/2016

A reference gene catalogue of the pig gut microbiome

Liang Xiao, Jordi Estellé, Pia Kiilerich, Yuliaxis Ramayo-Caldas, Zhongkui Xia, Qiang Feng, Suisha Liang, Anni Øyan Pedersen, Niels Jørgen Kjeldsen, Chuan Liu, Emmanuelle Maguin, Joël Doré, Nicolas Pons, Emmanuelle Le Chatelier, Edi Prifti, Junhua Li, Huijue Jia, Xin Liu, Xun Xu, Stanislav D. Ehrlich, Lise Madsen, Karsten Kristiansen, Claire Rogel-Gaillard & Jun Wang

 

 DOI: 10.1038/nmicrobiol.2016.161 [Communiqué de presse/ press release]

26/08/2016

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

D.R. Plichta, A.S. Juncker, M. Bertalan, E. Rettedal, L. Gautier, E. Varela, C. Manichanh, C. Fouqueray, F. Levenez, T. Nielsen, J. Doré, A. M. Dantas Machado, M.C. Rodriguez de Evgrafov, T. Hansen, T. Jørgensen, P. Bork, F. Guarner, O. Pedersen, Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium, M.O.A. Sommer, S.D. Ehrlich, T. Sicheritz-Pontén, S. Brunak and H. B Nielsen 

 

doi:10.1038/nmicrobiol.2016.152

13/07/2016

Human gut microbes impact host serum metabolome and insulin sensitivity

Helle Krogh Pedersen, Valborg Gudmundsdottir, Henrik Bjørn Nielsen, Tuulia Hyotylainen, Trine Nielsen, Benjamin A. H.Jensen, Kristoffer Forslund, Falk Hildebrand, Edi Prifti, Gwen Falony, Emmanuelle Le Chatelier, Florence Levenez, Joel Doré et al.

 

 DOI: 10.1038/nature18646 [Communiqué de presse/ press release]

25/05/2016

The human gut microbiome impacts health and disease.

S.D. Ehrlich 

 

doi:10.1016/j.crvi.2016.04.008 

15/04/2016

Tongue Coating and the Salivary Microbial Communities Vary in Children with Halitosis

W. Ren, Z. Xun, Z. Wang, Q. Zhang, X. Liu, H. Zheng, Q. Zhang, Y. Zhang, L. Zhang, C. Wu, S. Zheng, N. Qin, S.D. Ehrlich, Y. Li, X. He, T. Xu T. Chen, and F. Chen 

 

 doi: 10.1038/srep24481

04/03/2016

Capturing the most wanted taxa through cross-sample correlations

M. Almeida, M. Pop, E. Le Chatelier, E. Prifti, N. Pons, A. Ghozlane, and S.D. Ehrlich

 

doi: 10.1038/ismej.2016.35

03/2016

Intestinal carriage of the mcr-1 gene

E. Ruppé, E. Le Chatelier, N. Pons, A. Andremont, S.D. Ehrlich.

 

doi: 10.1016/S1473-3099(16)00066-9


2015

02/12/2015

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

Kristoffer Forslund, Falk Hildebrand, Trine Nielsen, Gwen Falony, Emmanuelle Le Chatelier, Shinichi Sunagawa, Edi Prifti, Sara Vieira-Silva, Valborg Gudmundsdottir, Helle Krogh Pedersen, Manimozhiyan Arumugam, Karsten Kristiansen, Anita Yvonne Voigt, Henrik Vestergaard, Rajna Hercog, Paul Igor Costea, Jens Roat Kultima, Junhua Li, Torben Jørgensen, Florence Levenez, Joël Dore, MetaHIT consortium, H. Bjørn Nielsen, Søren Brunak, Jeroen Raes, Torben Hansen, Jun Wang, S. Dusko Ehrlich, Peer Bork & Oluf Pedersen DOI:10.1038/nature15766

28/09/2015

A catalog of the mouse gut metagenome

L. Xiao, Q. Feng, S. Liang, S. B. Sonne, Z. Xia, X. Qiu, X. Li, H. Long, J. Zhang, D. Zhang, C. Liu, Z. Fang, J. Chou, J. Glanville, Q. Hao, D. Kotowska, C. Colding, T.R. Licht, D. Wu, J. Yu, J.J.Y. Sung, Q. Liang, J. Li, H. Jia, Z. Lan, V. Tremaroli, P. Dworzynski, H.B. Nielsen, F. Bäckhed, J. Doré, E. Le Chatelier, S.D. Ehrlich, J.C. Lin, M. Arumugam, J. Wang, L. Madsen, K. Kristiansen on line, DOI:10.1038/nbt.3353

16/09/2015

Qin et al. reply

N. Qin, E. Le Chatelier, J. Guo, E. Prifti, L. Li, S.D. Ehrlich (2015) In reply to J. S. Bajaj, N. S. Betrapally & P. M. Gillevet Nature 525, dx.doi.org/10.1038/nature14851 (2015) Nature 525, on line. DOI:10.1038/nature14852

8/04/2015

Effect of genome and environment on metabolic and inflammatory profiles.

Marina Sirota et al. DOI:10.1371/journal.pone.0120898

14/03/2015

Quality control of microbiota metagenomics by k-mer analysis.

Florian Plaza Onate et al. DOI: 10.1186/s12864-015-1406-7


2014

13/12/2014

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.

Mathieu Almeida et al. DOI:10.1186/1471-2164-15-1101

06/10/2014

Bacterial protein signals are associated with Crohn's disease.

Catherine Juste et al. DOI: 10.1136/gutjnl-2012-303786

11/09/2014

Changes of the human gut microbiome induced by a fermented milk product

Patrick Veiga et al. DOI:10.1038/srep06328 [Communiqué de presse/ Press release]

20/08/2014

A robust and adaptable High throughput screening method to study host-microbiota interactions in the human intestine

Tomas de Wouters et al. DOI:10.1371/journal.pone.0105598

05/08/2014

Genomic encyclopedia of bacteria and archaea: Sequencing a myriad of type strains

Nikos C. Kyrpides et al. doi: 10.1371/journal.pbio.1001920

23/07/2014

Alterations of the human gut microbiome in liver cirrhosis

Nan Qin*, Fengling Yang*, Ang Li*, Edi Prifti*, Yanfei Chen*, Li Shao* et al. - These authors contributed equally to this work. DOI:10.1038/nature13568 [Communiqué de presse/ press release]

06/07/2014

An integrated catalog of reference genes in the human gut microbiome

Junhua Li*, Huijue Jia*, Xianghang Cai*,Huanzi Zhong*, Qiang Feng* et al. - These authors contributed equally to this work. DOI:10.1038/nbt.2942 [Abstract]

06/07/2014

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

H Bjorn Nielsen*, Mathieu Almeida* et al. - *These authors contributed equally to this work. DOI:10.1038/nbt.2939 [Communiqué de presse /Press release]


2013

20/10/2013

Metagenomic species profiling using universal phylogenetic marker genes

Shinichi Sunagawa et al. DOI:10.1038/nmeth.2693 [Abstract]

29/08/2013

Richness of human gut microbiome correlates with metabolic markers

Emmanuelle Le Chatelier*, Trine Nielsen*, Junjie Qin*, Edi Prifti* et al. - *These authors contributed equally to this work. DOI:10.1038/nature12506 [Communiqué de presse /Press release]

29/08/2013

Dietary intervention impact on gut microbial gene richness

Aurélie Cotillard*, Sean P Kennedy*, Ling Chun Kond*, Edi Prifti*, Nicolas Pons* et al. - *These authors contributed equally to this work. DOI:10.1038/nature12480 [Communiqué de presse /Press release]

29/08/2013

Microbiology: Wealth management in the gut

Sungsoon Fang & Ronald M Evans. DOI:10.1038/500538a

06/2013

Human intestinal metagenomics: state of the art and future

Hervé Blottière, Willemen de Vos, Dusko Ehrlich & Joël Doré. DOI:10.1016/j.mib 2013.06.006

30/07/2013

Hot topics in gut microbiota

Doré J et al.

07/2013

Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes

Kong LC et al. DOI:10.3945/ajcn.113.058743

04/2013

Translating the human microbiome

Brown J. et al. DOI:10.1038/nbt.2543

14/06/2013

High-throughput system for the presentation of secreted and surface exposed proteins from Gram-positive bacteria in functional metagenomics

Dobrijevic D. et al. DOI:10.1371/journal.pone.0065956

06/2013

ANGPTL4 expression induced by butyrate and rosiglitazone in human intestinal epithelial cells utilize independent pathways

Korecka A. et al. DOI:10.1152/ajpgi.00293.2012

04/2013

The NK-kB binding site located in the proximal region of the TSLP promoter is critical for TSLP modulation in human intestinal epithelial cells

Cultrone A. et al. DOI:10.1002/eji.201142340

01/2013

A metagenomic insight into our gut's microbiome

Lepage P. et al. DOI:10.1136/gutjnl-2011-301805


2012

2012

Modification de la flore intestinale après chirurgie bariatrique : état des connaissances et mécanismes impliqués - Microbiota changes after bariatric surgery : state of the art and mechanisms

J Aron et al. - e-memoires de l'Académie Nationale de Chirurgie 2012, 11 (4) : 069-076

2012

Does our food (environment) change our gut microbiome ("in-vironment"): a potential role for inflammatory bowel disease ?

de Wouters T. et al. DOI: 10.1159/000342595

04/2012

Anti-inflammatory properties of dairy lactobacilli

Santos Rocha C. et al. DOI:10.1002/ibd.21834

04/10/2012

A metagenome-wide association study of gut microbiota in type 2 diabetes

Junjie Qin*, Yingrui Li*, Zhiming Cai*, Shenghui Li*, Jianfeng Zhu*, Fan Zhang* et al. * These authors contributed equally to this work - DOI:10.1038/nature11450

12/2012

Butyrate produced by commensal bacteria potentiates phorbol esters induced AP-1 response in human intestinal epithelial cells

Malgorzata Nepelska et al. DOI:10.1371/journal.pone.0052869


2011

06/2011

Identification of NF-kB modulation capabilities within human intestinal commensal bacteria

Lakhdari O. et al. DOI:10.1155/2011/282356

07/2011

Inhibition of the NF-kB pathway in human intestinal epithelial cells by commensal streptococcus salivarius

Kaci G. et al. DOI:10.1128/AEM.03021-10

05/2011

Enterotypes of the human gut microbiome

Arumugam M.*, Raes J* et al. * These authors contributed equally to this work - DOI:10.1038/nature09944


2010

09/2010

Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-kB modulation in the human gut

Lakhdari O. et al. DOI:10.1371/journal.pone.0013092

03/2010

A human gut microbial gene catalogue established by metagenomic sequencing

Qin J.*, Li R* et al. * These authors contributed equally to this work - DOI:10.1038/nature08821