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

Publications

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

08/04/2015

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