Publications

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

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

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

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

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]

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

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]

The human gut microbiome impacts health and disease.

S.D. Ehrlich 

doi:10.1016/j.crvi.2016.04.008 

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

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

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

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

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

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]

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]

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]

Metagenomic species profiling using universal phylogenetic marker genes

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

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]

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]

Microbiology: Wealth management in the gut

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

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

Hot topics in gut microbiota

Doré J et al.

Translating the human microbiome

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

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

A metagenomic insight into our gut's microbiome

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

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

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

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

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

Enterotypes of the human gut microbiome

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

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