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1.

Combinatorial, additive and dose-dependent drug-microbiome associations.

Forslund, Sofia K; Chakaroun, Rima; Zimmermann-Kogadeeva, Maria; Markó, Lajos; Aron-Wisnewsky, Judith; Nielsen, Trine; Moitinho-Silva, Lucas; Schmidt, Thomas S B; Falony, Gwen; Vieira-Silva, Sara; Adriouch, Solia; Alves, Renato J; Assmann, Karen; Bastard, Jean-Philippe; Birkner, Till; Caesar, Robert; Chilloux, Julien; Coelho, Luis Pedro; Fezeu, Leopold; Galleron, Nathalie; Helft, Gerard; Isnard, Richard; Ji, Boyang; Kuhn, Michael; Le Chatelier, Emmanuelle; Myridakis, Antonis; Olsson, Lisa; Pons, Nicolas; Prifti, Edi; Quinquis, Benoit; Roume, Hugo; Salem, Joe-Elie; Sokolovska, Nataliya; Tremaroli, Valentina; Valles-Colomer, Mireia; Lewinter, Christian; Søndertoft, Nadja B; Pedersen, Helle Krogh; Hansen, Tue H; Gøtze, Jens Peter; Køber, Lars; Vestergaard, Henrik; Hansen, Torben; Zucker, Jean-Daniel; Hercberg, Serge; Oppert, Jean-Michel; Letunic, Ivica; Nielsen, Jens; Bäckhed, Fredrik; Ehrlich, S Dusko.

Nature; 600(7889): 500-505, 2021 12.

Artículo en Inglés | MEDLINE | ID: mdl-34880489

2.

Human gut microbes impact host serum metabolome and insulin sensitivity.

Pedersen, Helle Krogh; Gudmundsdottir, Valborg; Nielsen, Henrik Bjørn; Hyotylainen, Tuulia; Nielsen, Trine; Jensen, Benjamin A H; Forslund, Kristoffer; Hildebrand, Falk; Prifti, Edi; Falony, Gwen; Le Chatelier, Emmanuelle; Levenez, Florence; Doré, Joel; Mattila, Ismo; Plichta, Damian R; Pöhö, Päivi; Hellgren, Lars I; Arumugam, Manimozhiyan; Sunagawa, Shinichi; Vieira-Silva, Sara; Jørgensen, Torben; Holm, Jacob Bak; Trost, Kajetan; Kristiansen, Karsten; Brix, Susanne; Raes, Jeroen; Wang, Jun; Hansen, Torben; Bork, Peer; Brunak, Søren; Oresic, Matej; Ehrlich, S Dusko; Pedersen, Oluf.

Nature; 535(7612): 376-81, 2016 07 21.

Artículo en Inglés | MEDLINE | ID: mdl-27409811

3.

Effects of Low FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial.

Cox, Selina R; Lindsay, James O; Fromentin, Sébastien; Stagg, Andrew J; McCarthy, Neil E; Galleron, Nathalie; Ibraim, Samar B; Roume, Hugo; Levenez, Florence; Pons, Nicolas; Maziers, Nicolas; Lomer, Miranda C; Ehrlich, S Dusko; Irving, Peter M; Whelan, Kevin.

Gastroenterology; 158(1): 176-188.e7, 2020 01.

Artículo en Inglés | MEDLINE | ID: mdl-31586453

4.

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

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

Nature; 528(7581): 262-266, 2015 Dec 10.

Artículo en Inglés | MEDLINE | ID: mdl-26633628

5.

Commensal Hafnia alvei strain reduces food intake and fat mass in obese mice-a new potential probiotic for appetite and body weight management.

Legrand, Romain; Lucas, Nicolas; Dominique, Manon; Azhar, Saida; Deroissart, Camille; Le Solliec, Marie-Anne; Rondeaux, Julie; Nobis, Séverine; Guérin, Charlène; Léon, Fatima; do Rego, Jean-Claude; Pons, Nicolas; Le Chatelier, Emmanuelle; Ehrlich, S Dusko; Lambert, Gregory; Déchelotte, Pierre; Fetissov, Sergueï O.

Int J Obes (Lond); 44(5): 1041-1051, 2020 05.

Artículo en Inglés | MEDLINE | ID: mdl-31911661

6.

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

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

Bioinformatics; 35(9): 1544-1552, 2019 05 01.

Artículo en Inglés | MEDLINE | ID: mdl-30252023

7.

Alterations of the human gut microbiome in liver cirrhosis.

Qin, Nan; Yang, Fengling; Li, Ang; Prifti, Edi; Chen, Yanfei; Shao, Li; Guo, Jing; Le Chatelier, Emmanuelle; Yao, Jian; Wu, Lingjiao; Zhou, Jiawei; Ni, Shujun; Liu, Lin; Pons, Nicolas; Batto, Jean Michel; Kennedy, Sean P; Leonard, Pierre; Yuan, Chunhui; Ding, Wenchao; Chen, Yuanting; Hu, Xinjun; Zheng, Beiwen; Qian, Guirong; Xu, Wei; Ehrlich, S Dusko; Zheng, Shusen; Li, Lanjuan.

Nature; 513(7516): 59-64, 2014 Sep 04.

Artículo en Inglés | MEDLINE | ID: mdl-25079328

8.

Richness of human gut microbiome correlates with metabolic markers.

Le Chatelier, Emmanuelle; Nielsen, Trine; Qin, Junjie; Prifti, Edi; Hildebrand, Falk; Falony, Gwen; Almeida, Mathieu; Arumugam, Manimozhiyan; Batto, Jean-Michel; Kennedy, Sean; Leonard, Pierre; Li, Junhua; Burgdorf, Kristoffer; Grarup, Niels; Jørgensen, Torben; Brandslund, Ivan; Nielsen, Henrik Bjørn; Juncker, Agnieszka S; Bertalan, Marcelo; Levenez, Florence; Pons, Nicolas; Rasmussen, Simon; Sunagawa, Shinichi; Tap, Julien; Tims, Sebastian; Zoetendal, Erwin G; Brunak, Søren; Clément, Karine; Doré, Joël; Kleerebezem, Michiel; Kristiansen, Karsten; Renault, Pierre; Sicheritz-Ponten, Thomas; de Vos, Willem M; Zucker, Jean-Daniel; Raes, Jeroen; Hansen, Torben; Bork, Peer; Wang, Jun; Ehrlich, S Dusko; Pedersen, Oluf.

Nature; 500(7464): 541-6, 2013 Aug 29.

Artículo en Inglés | MEDLINE | ID: mdl-23985870

9.

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

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

Nature; 545(7652): 116, 2017 05 03.

Artículo en Inglés | MEDLINE | ID: mdl-28470190

10.

Metagenomic species profiling using universal phylogenetic marker genes.

Sunagawa, Shinichi; Mende, Daniel R; Zeller, Georg; Izquierdo-Carrasco, Fernando; Berger, Simon A; Kultima, Jens Roat; Coelho, Luis Pedro; Arumugam, Manimozhiyan; Tap, Julien; Nielsen, Henrik Bjørn; Rasmussen, Simon; Brunak, Søren; Pedersen, Oluf; Guarner, Francisco; de Vos, Willem M; Wang, Jun; Li, Junhua; Doré, Joël; Ehrlich, S Dusko; Stamatakis, Alexandros; Bork, Peer.

Nat Methods; 10(12): 1196-9, 2013 Dec.

Artículo en Inglés | MEDLINE | ID: mdl-24141494

11.

Qin et al. reply.

Qin, Nan; Le Chatelier, Emmanuelle; Guo, Jing; Prifti, Edi; Li, Lanjuan; Ehrlich, S Dusko.

Nature; 525(7569): E2-3, 2015 Sep 17.

Artículo en Inglés | MEDLINE | ID: mdl-26381989

12.

Quality control of microbiota metagenomics by k-mer analysis.

Plaza Onate, Florian; Batto, Jean-Michel; Juste, Catherine; Fadlallah, Jehane; Fougeroux, Cyrielle; Gouas, Doriane; Pons, Nicolas; Kennedy, Sean; Levenez, Florence; Dore, Joel; Ehrlich, S Dusko; Gorochov, Guy; Larsen, Martin.

BMC Genomics; 16: 183, 2015 Mar 14.

Artículo en Inglés | MEDLINE | ID: mdl-25887914

13.

Dietary modulation of the gut microbiota--a randomised controlled trial in obese postmenopausal women.

Brahe, Lena K; Le Chatelier, Emmanuelle; Prifti, Edi; Pons, Nicolas; Kennedy, Sean; Blædel, Trine; Håkansson, Janet; Dalsgaard, Trine Kastrup; Hansen, Torben; Pedersen, Oluf; Astrup, Arne; Ehrlich, S Dusko; Larsen, Lesli H.

Br J Nutr; 114(3): 406-17, 2015 Aug 14.

Artículo en Inglés | MEDLINE | ID: mdl-26134388

14.

Prepublication data sharing.

Birney, Ewan; Hudson, Thomas J; Green, Eric D; Gunter, Chris; Eddy, Sean; Rogers, Jane; Harris, Jennifer R; Ehrlich, S Dusko; Apweiler, Rolf; Austin, Christopher P; Berglund, Lisa; Bobrow, Martin; Bountra, Chas; Brookes, Anthony J; Cambon-Thomsen, Anne; Carter, Nigel P; Chisholm, Rex L; Contreras, Jorge L; Cooke, Robert M; Crosby, William L; Dewar, Ken; Durbin, Richard; Dyke, Stephanie O M; Ecker, Joseph R; El Emam, Khaled; Feuk, Lars; Gabriel, Stacey B; Gallacher, John; Gelbart, William M; Granell, Antoni; Guarner, Francisco; Hubbard, Tim; Jackson, Scott A; Jennings, Jennifer L; Joly, Yann; Jones, Steven M; Kaye, Jane; Kennedy, Karen L; Knoppers, Bartha Maria; Kyrpides, Nikos C; Lowrance, William W; Luo, Jingchu; MacKay, John J; Martín-Rivera, Luis; McCombie, W Richard; McPherson, John D; Miller, Linda; Miller, Webb; Moerman, Don; Mooser, Vincent.

Nature; 461(7261): 168-70, 2009 Sep 10.

Artículo en Inglés | MEDLINE | ID: mdl-19741685

15.

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model.

Tanaka, Kosei; Henry, Christopher S; Zinner, Jenifer F; Jolivet, Edmond; Cohoon, Matthew P; Xia, Fangfang; Bidnenko, Vladimir; Ehrlich, S Dusko; Stevens, Rick L; Noirot, Philippe.

Nucleic Acids Res; 41(1): 687-99, 2013 Jan 07.

Artículo en Inglés | MEDLINE | ID: mdl-23109554

16.

Bacterial protein signals are associated with Crohn's disease.

Juste, Catherine; Kreil, David P; Beauvallet, Christian; Guillot, Alain; Vaca, Sebastian; Carapito, Christine; Mondot, Stanislas; Sykacek, Peter; Sokol, Harry; Blon, Florence; Lepercq, Pascale; Levenez, Florence; Valot, Benoît; Carré, Wilfrid; Loux, Valentin; Pons, Nicolas; David, Olivier; Schaeffer, Brigitte; Lepage, Patricia; Martin, Patrice; Monnet, Véronique; Seksik, Philippe; Beaugerie, Laurent; Ehrlich, S Dusko; Gibrat, Jean-François; Van Dorsselaer, Alain; Doré, Joël.

Gut; 63(10): 1566-77, 2014 Oct.

Artículo en Inglés | MEDLINE | ID: mdl-24436141

17.

Anti-inflammatory properties of Streptococcus salivarius, a commensal bacterium of the oral cavity and digestive tract.

Kaci, Ghalia; Goudercourt, Denise; Dennin, Véronique; Pot, Bruno; Doré, Joël; Ehrlich, S Dusko; Renault, Pierre; Blottière, Hervé M; Daniel, Catherine; Delorme, Christine.

Appl Environ Microbiol; 80(3): 928-34, 2014 Feb.

Artículo en Inglés | MEDLINE | ID: mdl-24271166

18.

In Vitro Modelling of Oral Microbial Invasion in the Human Colon.

Etienne-Mesmin, Lucie; Meslier, Victoria; Uriot, Ophélie; Fournier, Elora; Deschamps, Charlotte; Denis, Sylvain; David, Aymeric; Jegou, Sarah; Morabito, Christian; Quinquis, Benoit; Thirion, Florence; Plaza Oñate, Florian; Le Chatelier, Emmanuelle; Ehrlich, S Dusko; Blanquet-Diot, Stéphanie; Almeida, Mathieu.

Microbiol Spectr; : e0434422, 2023 Mar 27.

Artículo en Inglés | MEDLINE | ID: mdl-36971547

19.

Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics.

Meslier, Victoria; Menozzi, Elisa; David, Aymeric; Morabito, Christian; Lucas Del Pozo, Sara; Famechon, Alexandre; North, Janet; Quinquis, Benoit; Koletsi, Sofia; Macnaughtan, Jane; Mezabrovschi, Roxana; Ehrlich, S Dusko; Schapira, Anthony H V; Almeida, Mathieu.

Biomolecules; 13(10)2023 10 11.

Artículo en Inglés | MEDLINE | ID: mdl-37892187

20.

The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice.

Fan, Yong; Støving, René Klinkby; Berreira Ibraim, Samar; Hyötyläinen, Tuulia; Thirion, Florence; Arora, Tulika; Lyu, Liwei; Stankevic, Evelina; Hansen, Tue Haldor; Déchelotte, Pierre; Sinioja, Tim; Ragnarsdottir, Oddny; Pons, Nicolas; Galleron, Nathalie; Quinquis, Benoît; Levenez, Florence; Roume, Hugo; Falony, Gwen; Vieira-Silva, Sara; Raes, Jeroen; Clausen, Loa; Telléus, Gry Kjaersdam; Bäckhed, Fredrik; Oresic, Matej; Ehrlich, S Dusko; Pedersen, Oluf.

Nat Microbiol; 8(5): 787-802, 2023 05.

Artículo en Inglés | MEDLINE | ID: mdl-37069399

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