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Chemouny JM, Gleeson PJ, Abbad L, Lauriero G, Boedec E, Le Roux K, Monot C, Bredel M, Bex-Coudrat J, Sannier A, Daugas E, Vrtovsnik F, Gesualdo L, Leclerc M, Berthelot L, Ben Mkaddem S, Lepage P, Monteiro RC. Modulation of the microbiota by oral antibiotics treats immunoglobulin A nephropathy in humanized mice.
Nephrol Dial Transplant. 2018 Nov 20. doi: 10.1093/ndt/gfy323. [Epub ahead of print] PubMed PMID: 30462346.

Soularue E, Lepage P, Colombel JF, Coutzac C, Faleck D, Marthey L, Collins M, Chaput N, Robert C, Carbonnel F. Enterocolitis due to immune checkpoint inhibitors: a systematic review. Gut. 2018 Aug 21. pii: gutjnl-2018-316948. doi: 10.1136/gutjnl-2018-316948. [Epub ahead of print] Review. PubMed PMID: 30131322.

Just S, Mondot S, Ecker J, Wegner K, Rath E, Gau L, Streidl T, Hery-Arnaud G, Schmidt S, Lesker TR, Bieth V, Dunkel A, Strowig T, Hofmann T, Haller D, Liebisch G, Gérard P, Rohn S, Lepage P, Clavel T. The gut microbiota drives the impact of bile acids and fat source in diet on mouse metabolism. Microbiome. 2018 Aug 2;6(1):134. doi: 10.1186/s40168-018-0510-8. PubMed PMID: 30071904; PubMed Central PMCID: PMC6091023.

Maroilley T, Berri M, Lemonnier G, Esquerré D, Chevaleyre C, Mélo S, Meurens F, Coville JL, Leplat JJ, Rau A, Bed'hom B, Vincent-Naulleau S, Mercat MJ, Billon Y, Lepage P, Rogel-Gaillard C, Estellé J. Immunome differences between porcine ileal and jejunal Peyer's patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues. Sci Rep. 2018 Jun 13;8(1):9077. doi: 10.1038/s41598-018-27019-7. PubMed PMID: 29899562; PubMed Central PMCID: PMC5998120.

Fadlallah J, El Kafsi H, Sterlin D, Juste C, Parizot C, Dorgham K, Autaa G, Gouas D, Almeida M, Lepage P, Pons N, Le Chatelier E, Levenez F, Kennedy S, Galleron N, de Barros JP, Malphettes M, Galicier L, Boutboul D, Mathian A, Miyara M, Oksenhendler E, Amoura Z, Doré J, Fieschi C, Ehrlich SD, Larsen M, Gorochov G. Microbial ecology perturbation in human IgA deficiency. Sci Transl Med. 2018 May 2;10(439). pii: eaan1217. doi: 10.1126/scitranslmed.aan1217. PubMed PMID: 29720448.

Darnaud M, Dos Santos A, Gonzalez P, Augui S, Lacoste C, Desterke C, De Hertogh G, Valentino E, Braun E, Zheng J, Boisgard R, Neut C, Dubuquoy L, Chiappini F, Samuel D, Lepage P, Guerrieri F, Doré J, Bréchot C, Moniaux N, Faivre J. Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis. Gastroenterology. 2018 Mar;154(4):1009-1023.e14. doi: 10.1053/j.gastro.2017.11.003. Epub 2017 Nov 11. PubMed PMID: 29133078

Oberli M, Douard V, Beaumont M, Jaoui D, Devime F, Laurent S, Chaumontet C, Mat D, Le Feunteun S, Michon C, Davila AM, Fromentin G, Tomé D, Souchon I, Leclerc M, Gaudichon C, Blachier F. Lipo-Protein Emulsion Structure in the Diet Affects Protein Digestion Kinetics, Intestinal Mucosa Parameters and Microbiota Composition. Mol Nutr Food Res. 2018 Jan;62(2). doi: 10.1002/mnfr.201700570. Epub 2018 Jan 2. PubMed PMID: 28994235

Kökten T, Gibot S, Lepage P, D'Alessio S, Hablot J, Ndiaye NC, Busby-Venner H, Monot C, Garnier B, Moulin D, Jouzeau JY, Hansmannel F, Danese S, Guéant JL, Muller S, Peyrin-Biroulet L. TREM-1 Inhibition Restores Impaired Autophagy Activity and Reduces Colitis in Mice. J Crohns Colitis. 2018 Jan 24;12(2):230-244. doi: 10.1093/ecco-jcc/jjx129. PubMed PMID: 28961797


Lepage P. [The human gut microbiota: Interactions with the host and dysfunctions]. Rev Mal Respir. 2017 Dec;34(10):1085-1090. doi: 10.1016/j.rmr.2016.11.003. Epub 2017 May 12. French. PubMed PMID: 28506730

Coutzac C, Adam J, Soularue E, Collins M, Racine A, Mussini C, Boselli L, Kamsukom N, Mateus C, Charrier M, Cassard L, Planchard D, Ribrag V, Fizazi K, Loriot Y, Lepage P, Scoazec JY, Robert C, Carbonnel F, Chaput N. Colon Immune-Related Adverse Events: Anti-CTLA-4 and Anti-PD-1 Blockade Induce Distinct Immunopathological Entities. J Crohns Colitis. 2017 Oct 1;11(10):1238-1246. doi: 10.1093/ecco-jcc/jjx081. PubMed PMID: 28967957

Beaumont M*, Jaoui D*, Douard V, Mat D, Koeth F, Goustard B, Mayeur C, Mondot S, Hovaghimian A, Le Feunteun S, Chaumontet C, Davila AM, Tomé D, Souchon I, Michon C, Fromentin G, Blachier F, Leclerc M. Structure of protein emulsion in food impacts intestinal microbiota, caecal luminal content composition and distal intestine characteristics in rats. Mol Nutr Food Res. 2017 Oct;61(10). doi: 10.1002/mnfr.201700078. Epub 2017 Jul 5. PubMed PMID: 28512779

De Arcangelis A, Hamade H, Alpy F, Normand S, Bruyère E, Lefebvre O, Méchine-Neuville A, Siebert S, Pfister V, Lepage P, Laquerriere P, Dembele D, Delanoye-Crespin A, Rodius S, Robine S, Kedinger M, Van Seuningen I, Simon-Assmann P, Chamaillard M, Labouesse M, Georges-Labouesse E. Hemidesmosome integrity protects the colon against colitis and colorectal cancer. Gut. 2017 Oct;66(10):1748-1760. doi: 10.1136/gutjnl-2015-310847. Epub 2016 Jul 1. PubMed PMID: 27371534; PubMed Central PMCID: PMC5595104

Rozé JC, Ancel PY, Lepage P, Martin-Marchand L, Al Nabhani Z, Delannoy J, Picaud JC, Lapillonne A, Aires J, Durox M, Darmaun D, Neu J, Butel MJ; Nutrition EPIPAGE 2 study group and the EPIFLORE Study Group. Nutritional strategies and gut microbiota composition as risk factors for necrotizing enterocolitis in very-preterm infants. Am J Clin Nutr. 2017 Sep;106(3):821-830. doi: 10.3945/ajcn.117.152967. Epub 2017 Jun 28. PubMed PMID: 28659297; PubMed Central PMCID: PMC5573022

Chaput N, Lepage P, Coutzac C, Soularue E, Le Roux K, Monot C, Boselli L, Routier E, Cassard L, Collins M, Vaysse T, Marthey L, Eggermont A, Asvatourian V, Lanoy E, Mateus C, Robert C, Carbonnel F. Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab. Ann Oncol. 2017 Jun 1;28(6):1368-1379. doi: 10.1093/annonc/mdx108. PubMed PMID: 28368458

Gillard L, Mayeur C, Robert V, Pingenot I, Le Beyec J, Bado A, Lepage P, Thomas M, Joly F. Microbiota Is Involved in Post-resection Adaptation in Humans with Short Bowel Syndrome. Front Physiol. 2017 Apr 19;8:224. doi: 10.3389/fphys.2017.00224. eCollection 2017. PubMed PMID: 28469580; PubMed Central PMCID: PMC5395573

Carbonnel F, Soularue E, Coutzac C, Chaput N, Mateus C, Lepage P, Robert C. Inflammatory bowel disease and cancer response due to anti-CTLA-4: is it in the flora? Semin Immunopathol. 2017 Apr;39(3):327-331. doi: 10.1007/s00281-016-0613-x. Epub 2017 Jan 16. Review. PubMed PMID: 28093620

Wegner K, Just S, Gau L, Mueller H, Gérard P, Lepage P, Clavel T, Rohn S. Rapid analysis of bile acids in different biological matrices using LC-ESI-MS/MS for the investigation of bile acid transformation by mammalian gut bacteria. Anal Bioanal Chem. 2017 Feb;409(5):1231-1245. doi: 10.1007/s00216-016-0048-1. Epub 2016 Nov 7. PubMed PMID: 27822648

Patrascu O, Béguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc M, Klopp C, Terrapon N, Henrissat B, Blottière HM, Doré J, Béra-Maillet C. A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Sci Rep. 2017 Jan 16;7:40248. doi: 10.1038/srep40248. PubMed PMID: 28091525; PubMed Central PMCID: PMC5238381

Guinet-Charpentier C, Lepage P, Morali A, Chamaillard M, Peyrin-Biroulet L. Effects of enteral polymeric diet on gut microbiota in children with Crohn's disease. Gut. 2017 Jan;66(1):194-195. doi: 10.1136/gutjnl-2015-311058. Epub 2016 Jan 27. PubMed PMID: 26818618


Raguideau S, Plancade S, Pons N, Leclerc M, Laroche B. Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota. PLoS Comput Biol. 2016 Dec 16;12(12):e1005252. doi: 10.1371/journal.pcbi.1005252. eCollection 2016 Dec. PubMed PMID: 27984592; PubMed Central PMCID: PMC5161307

Ramayo-Caldas Y, Mach N, Lepage P, Levenez F, Denis C, Lemonnier G, Leplat JJ, Billon Y, Berri M, Doré J, Rogel-Gaillard C, Estellé J. Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits. ISME J. 2016 Dec;10(12):2973-2977. doi: 10.1038/ismej.2016.77. Epub 2016 May 13. PubMed PMID: 27177190; PubMed Central PMCID: PMC5148198

Al Nabhani Z, Lepage P, Mauny P, Montcuquet N, Roy M, Le Roux K, Dussaillant M, Berrebi D, Hugot JP, Barreau F. Nod2 Deficiency Leads to a Specific and Transmissible Mucosa-associated Microbial Dysbiosis Which Is Independent of the Mucosal Barrier Defect. J Crohns Colitis. 2016 Dec;10(12):1428-1436. Epub 2016 May 4. PubMed PMID: 27147452

Daillère R, Vétizou M, Waldschmitt N, Yamazaki T, Isnard C, Poirier-Colame V, Duong CPM, Flament C, Lepage P, Roberti MP, Routy B, Jacquelot N, Apetoh L, Becharef S, Rusakiewicz S, Langella P, Sokol H, Kroemer G, Enot D, Roux A, Eggermont A, Tartour E, Johannes L, Woerther PL, Chachaty E, Soria JC, Golden E, Formenti S, Plebanski M, Madondo M, Rosenstiel P, Raoult D, Cattoir V, Boneca IG, Chamaillard M, Zitvogel L. Enterococcus hirae and Barnesiella intestinihominis Facilitate Cyclophosphamide-Induced Therapeutic Immunomodulatory Effects. Immunity. 2016 Oct 18;45(4):931-943. doi: 10.1016/j.immuni.2016.09.009. Epub 2016 Oct 4. PubMed PMID: 27717798

Raguideau S, Laroche B, Leclerc M, Plancade S. A Constrained NMF Approach to Analyze Quantitative Metagenomic Data. IFAC-PapersOnLine, Volume 49, Issue 26, 2016, Pages 71-76

Zantow J, Just S, Lagkouvardos I, Kisling S, Dübel S, Lepage P, Clavel T, Hust M. Mining gut microbiome oligopeptides by functional metaproteome display. Sci Rep. 2016 Oct 5;6:34337. doi: 10.1038/srep34337. PubMed PMID: 27703179; PubMed Central PMCID: PMC5050496

Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K; MetaHIT Consortium, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. 2016 Jul 21;535(7612):376-81. Epub 2016 Jul 13. PubMed PMID: 27409811

Pitt JM, Vétizou M, Daillère R, Roberti MP, Yamazaki T, Routy B, Lepage P, Boneca IG, Chamaillard M, Kroemer G, Zitvogel L. Resistance Mechanisms to Immune-Checkpoint Blockade in Cancer: Tumor-Intrinsic and -Extrinsic Factors. Immunity. 2016 Jun 21;44(6):1255-69. doi: 10.1016/j.immuni.2016.06.001. Review. PubMed PMID: 27332730

Mondot S, Lepage P, Seksik P, Allez M, Tréton X, Bouhnik Y, Colombel JF, Leclerc M, Pochart P, Doré J, Marteau P; GETAID. Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery. Gut. 2016 Jun;65(6):954-62. doi: 10.1136/gutjnl-2015-309184. Epub 2015 Dec 1. PubMed PMID: 26628508; PubMed Central PMCID: PMC4893116

Mondot S, Lepage P. The human gut microbiome and its dysfunctions through the meta-omics prism. Ann N Y Acad Sci. 2016 May;1372(1):9-19. doi: 10.1111/nyas.13033. Epub 2016 Mar 4. PubMed PMID: 26945826

Llopis M, Cassard AM, Wrzosek L, Boschat L, Bruneau A, Ferrere G, Puchois V, Martin JC, Lepage P, Le Roy T, Lefèvre L, Langelier B, Cailleux F, González-Castro AM, Rabot S, Gaudin F, Agostini H, Prévot S, Berrebi D, Ciocan D, Jousse C, Naveau S, Gérard P, Perlemuter G. Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease. Gut. 2016 May;65(5):830-9. doi: 10.1136/gutjnl-2015-310585. Epub 2015 Dec 7. PubMed PMID: 26642859

Alnabhani Z, Hugot JP, Montcuquet N, Le Roux K, Dussaillant M, Roy M, Leclerc M, Cerf-Bensussan N, Lepage P*, Barreau F*. Respective Roles of Hematopoietic and Nonhematopoietic Nod2 on the Gut Microbiota and Mucosal Homeostasis. Inflamm Bowel Dis. 2016 Apr;22(4):763-73. doi: 10.1097/MIB.0000000000000749. PubMed PMID: 26963567

Mosca A, Leclerc M, Hugot JP. Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem? Front Microbiol. 2016 Mar 31;7:455. doi: 10.3389/fmicb.2016.00455. eCollection 2016. PubMed PMID: 27065999; PubMed Central PMCID: PMC4815357

Dao MC, Everard A, Aron-Wisnewsky J, Sokolovska N, Prifti E, Verger EO, Kayser BD, Levenez F, Chilloux J, Hoyles L; MICRO-Obes Consortium, Dumas ME, Rizkalla SW, Doré J, Cani PD, Clément K. Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut. 2016 Mar;65(3):426-36. doi: 10.1136/gutjnl-2014-308778. Epub 2015 Jun 22. PubMed PMID: 26100928

Pitt JM, Vétizou M, Gomperts Boneca I, Lepage P, Chamaillard M, Zitvogel L. Enhancing the clinical coverage and anticancer efficacy of immune checkpoint blockade through manipulation of the gut microbiota. Oncoimmunology. 2016 Feb 18;6(1):e1132137. doi: 10.1080/2162402X.2015.1132137. eCollection 2017. PubMed PMID: 28197360; PubMed Central PMCID: PMC5283646


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. Nature. 2015 Dec 10;528(7581):262-6. doi: 10.1038/nature15766. Epub 2015 Dec 2. PubMed PMID: 26633628; PubMed Central PMCID: PMC4681099

Tap J, Furet JP, Bensaada M, Philippe C, Roth H, Rabot S, Lakhdari O, Lombard V, Henrissat B, Corthier G, Fontaine E, Doré J, Leclerc M. Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environ Microbiol. 2015 Dec;17(12):4954-64. doi: 10.1111/1462-2920.13006. Epub 2015 Sep 3. PubMed PMID: 26235304

Vétizou M, Pitt JM, Daillère R, Lepage P, Waldschmitt N, Flament C, Rusakiewicz S, Routy B, Roberti MP, Duong CP, Poirier-Colame V, Roux A, Becharef S, Formenti S, Golden E, Cording S, Eberl G, Schlitzer A, Ginhoux F, Mani S, Yamazaki T, Jacquelot N, Enot DP, Bérard M, Nigou J, Opolon P, Eggermont A, Woerther PL, Chachaty E, Chaput N, Robert C, Mateus C, Kroemer G, Raoult D, Boneca IG, Carbonnel F, Chamaillard M, Zitvogel L. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science. 2015 Nov 27;350(6264):1079-84. doi: 10.1126/science.aad1329. Epub 2015 Nov 5. PubMed PMID: 26541610

Shoaie S, Ghaffari P, Kovatcheva-Datchary P, Mardinoglu A, Sen P, Pujos-Guillot E, de Wouters T, Juste C, Rizkalla S, Chilloux J, Hoyles L, Nicholson JK; MICRO-Obes Consortium, Dore J, Dumas ME, Clement K, Bäckhed F, Nielsen J. Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome. Cell Metab. 2015 Aug 4;22(2):320-31. doi: 10.1016/j.cmet.2015.07.001. PubMed PMID: 26244934

Lévy J, Cacheux W, Bara MA, L'Hermitte A, Lepage P, Fraudeau M, Trentesaux C, Lemarchand J, Durand A, Crain AM, Marchiol C, Renault G, Dumont F, Letourneur F, Delacre M, Schmitt A, Terris B, Perret C, Chamaillard M, Couty JP, Romagnolo B. Intestinal inhibition of Atg7 prevents tumour initiation through a microbiome-influenced immune response and suppresses tumour growth. Nat Cell Biol. 2015 Aug;17(8):1062-73. doi: 10.1038/ncb3206. Epub 2015 Jul 27. PubMed PMID: 26214133

Mach N, Berri M, Estellé J, Levenez F, Lemonnier G, Denis C, Leplat JJ, Chevaleyre C, Billon Y, Doré J, Rogel-Gaillard C, Lepage P. Early-life establishment of the swine gut microbiome and impact on host phenotypes. Environ Microbiol Rep. 2015 Jun;7(3):554-69. doi: 10.1111/1758-2229.12285. Epub 2015 May 6. PubMed PMID: 25727666

Miquel S, Leclerc M, Martin R, Chain F, Lenoir M, Raguideau S, Hudault S, Bridonneau C, Northen T, Bowen B, Bermúdez-Humarán LG, Sokol H, Thomas M, Langella P. Identification of Metabolic Signatures Linked to Anti-Inflammatory Effects of Faecalibacterium prausnitzii. MBio. 2015 Apr 21;6(2). pii: e00300-15. doi: 10.1128/mBio.00300-15. PubMed PMID: 25900655

Martin C, Burgel PR, Lepage P, Andréjak C, Blic J, Bourdin A, Brouard J, Chanez P, Dalphin JC, Deslée G, Deschildre A, Gosset P, Touqui L, Dusser D. Host-microbe interactions in distal airways: relevance to chronic airway diseases. Eur Respir Rev. 2015 Mar;24(135):78-91. Review. PubMed PMID: 25726559

Viaud S, Daillère R, Boneca IG, Lepage P, Langella P, Chamaillard M, Pittet MJ, Ghiringhelli F, Trinchieri G, Goldszmid R, Zitvogel L. Gut microbiome and anticancer immune response: really hot Sh*t! Cell Death Differ. 2015 Feb;22(2):199-214. doi: 10.1038/cdd.2014.56. Epub 2014 May 16. Review. PubMed PMID: 24832470; PubMed Central PMCID: PMC4291500


Juste C, Kreil DP, Beauvallet C, Guillot A, Vaca S, Carapito C, Mondot S, Sykacek P, Sokol H, Blon F, Lepercq P, Levenez F, Valot B, Carré W, Loux V, Pons  N, David O, Schaeffer B, Lepage P, Martin P, Monnet V, Seksik P, Beaugerie L, Ehrlich SD, Gibrat JF, Van Dorsselaer A, Doré J. Bacterial protein signals are associated with Crohn's disease. Gut. 2014 Oct;63(10):1566-77. doi: 10.1136/gutjnl-2012-303786. Epub 2014 Jan 16. PubMed PMID: 24436141; PubMed Central PMCID: PMC4173658

Viaud S, Daillère R, Boneca IG, Lepage P, Pittet MJ, Ghiringhelli F, Trinchieri G, Goldszmid R, Zitvogel L. Harnessing the intestinal microbiome for optimal therapeutic immunomodulation. Cancer Res. 2014 Aug 15;74(16):4217-21. doi: 10.1158/0008-5472.CAN-14-0987. Epub 2014 Jul 29. PubMed PMID: 25074615

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; MetaHIT Consortium. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol. 2014 Aug;32(8):834-41. doi: 10.1038/nbt.2942. Epub 2014 Jul 6. PubMed PMID: 24997786

Clavel T, Desmarchelier C, Haller D, Gérard P, Rohn S, Lepage P, Daniel H. Intestinal microbiota in metabolic diseases: From bacterial community structure and functions to species of pathophysiological relevance. Gut Microbes. 2014 Jul  1;5(4):544-51. doi: 10.4161/gmic.29331. Epub 2014 Jul 8. PubMed PMID: 25003516

Duca FA, Sakar Y, Lepage P, Devime F, Langelier B, Doré J, Covasa M. Replication of obesity and associated signaling pathways through transfer of microbiota from obese-prone rats. Diabetes. 2014 May;63(5):1624-36. doi: 10.2337/db13-1526. Epub 2014 Jan 15. PubMed PMID: 24430437

Duca F, Gérard P, Covasa M, Lepage P. Metabolic interplay between gut bacteria and their host. Front Horm Res. 2014;42:73-82. doi: 10.1159/000358315. Epub 2014  Apr 7. PubMed PMID: 24732926

De Paepe M, Leclerc M, Tinsley CR, Petit MA. Bacteriophages: an underestimated role in human and animal health? Front Cell Infect Microbiol. 2014 Mar 28;4:39. doi: 10.3389/fcimb.2014.00039. eCollection 2014. Review. PubMed PMID: 24734220; PubMed Central PMCID: PMC3975094

Slezak K, Krupova Z, Rabot S, Loh G, Levenez F, Descamps A, Lepage P, Doré J,  Bellier S, Blaut M. Association of germ-free mice with a simplified human intestinal microbiota results in a shortened intestine. Gut Microbes. 2014 Mar-Apr;5(2):176-82. doi: 10.4161/gmic.28203. Epub 2014 Feb 13. PubMed PMID: 24637599; PubMed Central PMCID: PMC4063842

Mach N, Berri M, Esquerré D, Chevaleyre C, Lemonnier G, Billon Y, Lepage P, Oswald IP, Doré J, Rogel-Gaillard C, Estellé J. Extensive expression differences  along porcine small intestine evidenced by transcriptome sequencing. PLoS One. 2014 Feb 12;9(2):e88515. doi: 10.1371/journal.pone.0088515. eCollection 2014. PubMed PMID: 24533095; PubMed Central PMCID: PMC3922923

Daniel H, Moghaddas Gholami A, Berry D, Desmarchelier C, Hahne H, Loh G, Mondot S, Lepage P, Rothballer M, Walker A, Böhm C, Wenning M, Wagner M, Blaut M, Schmitt-Kopplin P, Kuster B, Haller D, Clavel T. High-fat diet alters gut microbiota physiology in mice. ISME J. 2014 Feb;8(2):295-308. doi: 10.1038/ismej.2013.155. Epub 2013 Sep 12. PubMed PMID: 24030595; PubMed Central PMCID: PMC3906816

Viaud S, Daillère R, Yamazaki T, Lepage P, Boneca I, Goldszmid R, Trinchieri G, Zitvogel L. Why should we need the gut microbiota to respond to cancer therapies? Oncoimmunology. 2014 Jan 1;3(1):e27574. Epub 2014 Jan 17. PubMed PMID: 24800167; PubMed Central PMCID: PMC4006853


Le Roy T, Llopis M, Lepage P, Bruneau A, Rabot S, Bevilacqua C, Martin P, Philippe C, Walker F, Bado A, Perlemuter G, Cassard-Doulcier AM, Gérard P. Intestinal microbiota determines development of non-alcoholic fatty liver disease in mice. Gut. 2013 Dec;62(12):1787-94. doi: 10.1136/gutjnl-2012-303816. Epub 2012 Nov 29. PubMed PMID: 23197411

Viaud S, Saccheri F, Mignot G, Yamazaki T, Daillère R, Hannani D, Enot DP, Pfirschke C, Engblom C, Pittet MJ, Schlitzer A, Ginhoux F, Apetoh L, Chachaty E,  Woerther PL, Eberl G, Bérard M, Ecobichon C, Clermont D, Bizet C, Gaboriau-Routhiau V, Cerf-Bensussan N, Opolon P, Yessaad N, Vivier E, Ryffel B, Elson CO, Doré J, Kroemer G, Lepage P, Boneca IG, Ghiringhelli F, Zitvogel L. The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science. 2013 Nov 22;342(6161):971-6. doi: 10.1126/science.1240537. PubMed PMID: 24264990; PubMed Central PMCID: PMC4048947

Mondot S, de Wouters T, Doré J, Lepage P. The human gut microbiome and its dysfunctions. Dig Dis. 2013;31(3-4):278-85. doi: 10.1159/000354678. Epub 2013 Nov 14. Review. PubMed PMID: 24246975

Cecchini DA, Laville E, Laguerre S, Robe P, Leclerc M, Doré J, Henrissat B, Remaud-Siméon M, Monsan P, Potocki-Véronèse G. Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. PLoS One. 2013 Sep 16;8(9):e72766. doi: 10.1371/journal.pone.0072766. eCollection 2013. PubMed PMID: 24066026; PubMed Central PMCID: PMC3774763

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. Nature. 2013 Aug 29;500(7464):585-8. doi: 10.1038/nature12480. Erratum in: Nature. 2013 Oct 24;502(7472)580. PubMed PMID: 23985875

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. Nature. 2013 Aug 29;500(7464):541-6. doi: 10.1038/nature12506. PubMed PMID: 23985870

Lepage P, Leclerc MC, Joossens M, Mondot S, Blottière HM, Raes J, Ehrlich D, Doré J. A metagenomic insight into our gut's microbiome. Gut. 2013 Jan;62(1):146-58. doi: 10.1136/gutjnl-2011-301805. Epub 2012 Apr 23. Review. PubMed PMID: 22525886


de Wouters T, Doré J, Lepage P. Does our food (environment) change our gut microbiome ('in-vironment'): a potential role for inflammatory bowel disease? Dig Dis. 2012;30 Suppl 3:33-9. doi: 10.1159/000342595. Epub 2013 Jan 3. Review. PubMed PMID: 23295690

Mondot S, Barreau F, Al Nabhani Z, Dussaillant M, Le Roux K, Doré J, Leclerc M, Hugot JP, Lepage P. Altered gut microbiota composition in immune-impaired Nod2(-/-) mice. Gut. 2012 Apr;61(4):634-5. doi: 10.1136/gutjnl-2011-300478. Epub 2011 Aug 25. PubMed PMID: 21868489


Amar J, Serino M, Lange C, Chabo C, Iacovoni J, Mondot S, Lepage P, Klopp C, Mariette J, Bouchez O, Perez L, Courtney M, Marre M, Klopp P, Lantieri O, Doré J, Charles M, Balkau B, Burcelin R; D.E.S.I.R. Study Group. Involvement of tissue bacteria in the onset of diabetes in humans: evidence for a concept. Diabetologia. 2011 Dec;54(12):3055-61. doi: 10.1007/s00125-011-2329-8. PubMed PMID: 21976140

Lepage P, Häsler R, Spehlmann ME, Rehman A, Zvirbliene A, Begun A, Ott S, Kupcinskas L, Doré J, Raedler A, Schreiber S. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology. 2011 Jul;141(1):227-36. doi: 10.1053/j.gastro.2011.04.011. Epub 2011 Apr 16. PubMed PMID: 21621540

Muñoz-Tamayo R, Laroche B, Walter E, Doré J, Duncan SH, Flint HJ, Leclerc M. Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species. FEMS Microbiol Ecol. 2011 Jun;76(3):615-24. doi: 10.1111/j.1574-6941.2011.01085.x. Epub 2011 Apr 18. PubMed PMID: 21388423

 Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, 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; MetaHIT Consortium, 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. Nature. 2011 May 12;473(7346):174-80. doi: 10.1038/nature09944. Epub 2011 Apr 20. Erratum in: Nature. 2011 Jun 30;474(7353):666. Nature. 2014 Feb 27;506(7489):516. PubMed PMID: 21508958; PubMed Central PMCID: PMC3728647

Rousseau C, Levenez F, Fouqueray C, Doré J, Collignon A, Lepage P. Clostridium difficile colonization in early infancy is accompanied by changes in intestinal microbiota composition. J Clin Microbiol. 2011 Mar;49(3):858-65. doi: 10.1128/JCM.01507-10. Epub 2010 Dec 22. PubMed PMID: 21177896; PubMed Central PMCID: PMC3067754

Gloux K, Berteau O, El Oumami H, Béguet F, Leclerc M, Doré J. A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome. Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4539-46. doi: 10.1073/pnas.1000066107. Epub 2010 Jun 25. PubMed PMID: 20615998; PubMed Central PMCID: PMC3063586

Mondot S, Kang S, Furet JP, Aguirre de Carcer D, McSweeney C, Morrison M, Marteau P, Doré J, Leclerc M. Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm Bowel Dis. 2011 Jan;17(1):185-92. doi: 10.1002/ibd.21436. Epub 2010 Aug 18. PubMed PMID: 20722058


Kang S, Denman SE, Morrison M, Yu Z, Dore J, Leclerc M, McSweeney CS. Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflamm Bowel Dis. 2010 Dec;16(12):2034-42. doi: 10.1002/ibd.21319. PubMed PMID: 20848492

Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Doré J, Monsan P, Remaud-Simeon M, Potocki-Veronese G. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res. 2010 Nov;20(11):1605-12. doi: 10.1101/gr.108332.110. Epub 2010 Sep 14. PubMed PMID: 20841432; PubMed Central PMCID: PMC2963823

Dusko Ehrlich S; MetaHIT consortium. [Metagenomics of the intestinal microbiota: potential applications]. Gastroenterol Clin Biol. 2010 Sep;34 Suppl 1:S23-8. doi: 10.1016/S0399-8320(10)70017-8. French. PubMed PMID: 20889001

Muñoz-Tamayo R, Laroche B, Walter E, Doré J, Leclerc M. Mathematical modelling of carbohydrate degradation by human colonic microbiota. J Theor Biol. 2010 Sep 7;266(1):189-201. doi: 10.1016/j.jtbi.2010.05.040. Epub 2010 Jun 16. PubMed PMID: 20561534

Rehman A, Lepage P, Nolte A, Hellmig S, Schreiber S, Ott SJ. Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients. J Med Microbiol. 2010 Sep;59(Pt 9):1114-22. doi: 10.1099/jmm.0.021170-0. Epub 2010 Jun 3. PubMed PMID: 20522625

Donnet-Hughes A, Perez PF, Doré J, Leclerc M, Levenez F, Benyacoub J, Serrant P, Segura-Roggero I, Schiffrin EJ. Potential role of the intestinal microbiota of the mother in neonatal immune education. Proc Nutr Soc. 2010 Aug;69(3):407-15. doi: 10.1017/S0029665110001898. PubMed PMID: 20633308

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 JM, 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; MetaHIT Consortium, Bork P, Ehrlich SD, Wang J. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010 Mar 4;464(7285):59-65. doi: 10.1038/nature08821. PubMed PMID: 20203603; PubMed Central PMCID: PMC3779803


Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Muñoz-Tamayo R, Paslier DL, Nalin R, Dore J, Leclerc M. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol. 2009 Oct;11(10):2574-84. doi: 10.1111/j.1462-2920.2009.01982.x. Epub 2009 Jul 6. PubMed PMID: 19601958

Furet JP, Firmesse O, Gourmelon M, Bridonneau C, Tap J, Mondot S, Doré J, Corthier G. Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. FEMS Microbiol Ecol. 2009 Jun;68(3):351-62. doi: 10.1111/j.1574-6941.2009.00671.x. Epub 2009 Mar 19. PubMed PMID: 19302550


Kuehbacher T, Rehman A, Lepage P, Hellmig S, Fölsch UR, Schreiber S, Ott SJ. Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease. J Med Microbiol. 2008 Dec;57(Pt 12):1569-76. doi: 10.1099/jmm.0.47719-0. PubMed PMID: 19018031

Spehlmann ME, Begun AZ, Burghardt J, Lepage P, Raedler A, Schreiber S. Epidemiology of inflammatory bowel disease in a German twin cohort: results of a nationwide study. Inflamm Bowel Dis. 2008 Jul;14(7):968-76. doi: 10.1002/ibd.20380. PubMed PMID: 18253950

Lepage P, Colombet J, Marteau P, Sime-Ngando T, Doré J, Leclerc M. Dysbiosis in inflammatory bowel disease: a role for bacteriophages? Gut. 2008 Mar;57(3):424-5. doi: 10.1136/gut.2007.134668. PubMed PMID: 18268057


Gérard P, Lepercq P, Leclerc M, Gavini F, Raibaud P, Juste C. Bacteroides sp. strain D8, the first cholesterol-reducing bacterium isolated from human feces. Appl Environ Microbiol. 2007 Sep;73(18):5742-9. Epub 2007 Jul 6. PubMed PMID: 17616613; PubMed Central PMCID: PMC2074900

Chassard C, Goumy V, Leclerc M, Del'homme C, Bernalier-Donadille A. Characterization of the xylan-degrading microbial community from human faeces. FEMS Microbiol Ecol. 2007 Jul;61(1):121-31. Epub 2007 Mar 28. PubMed PMID: 17391327

Gloux K, Leclerc M, Iliozer H, L'Haridon R, Manichanh C, Corthier G, Nalin R, Blottière HM, Doré J. Development of high-throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth. Appl Environ Microbiol. 2007 Jun;73(11):3734-7. Epub 2007 Mar 30. PubMed PMID: 17400773; PubMed Central PMCID: PMC1932692

Vasquez N, Mangin I, Lepage P, Seksik P, Duong JP, Blum S, Schiffrin E, Suau A, Allez M, Vernier G, Tréton X, Doré J, Marteau P, Pochart P. Patchy distribution of mucosal lesions in ileal Crohn's disease is not linked to differences in the dominant mucosa-associated bacteria: a study using fluorescence in situ hybridization and temporal temperature gradient gel electrophoresis. Inflamm Bowel Dis. 2007 Jun;13(6):684-92. PubMed PMID: 17206669

Perez PF, Doré J, Leclerc M, Levenez F, Benyacoub J, Serrant P, Segura-Roggero I, Schiffrin EJ, Donnet-Hughes A. Bacterial imprinting of the neonatal immune system: lessons from maternal cells? Pediatrics. 2007 Mar;119(3):e724-32. PubMed PMID: 17332189

Sokol H, Lepage P, Seksik P, Doré J, Marteau P. Molecular comparison of dominant microbiota associated with injured versus healthy mucosa in ulcerative colitis. Gut. 2007 Jan;56(1):152-4. PubMed PMID: 17172591; PubMed Central PMCID: PMC1856643


Seksik P, Sokol H, Lepage P, Vasquez N, Manichanh C, Mangin I, Pochart P, Doré J, Marteau P. Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease. Aliment Pharmacol Ther. 2006 Oct;24 Suppl 3:11-8. Review. PubMed PMID: 16961738

Sokol H, Lepage P, Seksik P, Doré J, Marteau P. Temperature gradient gel electrophoresis of fecal 16S rRNA reveals active Escherichia coli in the microbiota of patients with ulcerative colitis. J Clin Microbiol. 2006 Sep;44(9):3172-7. PubMed PMID: 16954244; PubMed Central PMCID: PMC1594675

Sokol H, Seksik P, Rigottier-Gois L, Lay C, Lepage P, Podglajen I, Marteau P, Doré J. Specificities of the fecal microbiota in inflammatory bowel disease. Inflamm Bowel Dis. 2006 Feb;12(2):106-11. PubMed PMID: 16432374


Clavel T, Fallani M, Lepage P, Levenez F, Mathey J, Rochet V, Sérézat M, Sutren M, Henderson G, Bennetau-Pelissero C, Tondu F, Blaut M, Doré J, Coxam V. Isoflavones and functional foods alter the dominant intestinal microbiota in postmenopausal women. J Nutr. 2005 Dec;135(12):2786-92. PubMed PMID: 16317121

De La Cochetière MF, Durand T, Lepage P, Bourreille A, Galmiche JP, Doré J. Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. J Clin Microbiol. 2005 Nov;43(11):5588-92. PubMed PMID: 16272491; PubMed Central PMCID: PMC1287787

Seksik P, Lepage P, de la Cochetière MF, Bourreille A, Sutren M, Galmiche JP, Doré J, Marteau P. Search for localized dysbiosis in Crohn's disease ulcerations by temporal temperature gradient gel electrophoresis of 16S rRNA. J Clin Microbiol. 2005 Sep;43(9):4654-8. PubMed PMID: 16145122; PubMed Central PMCID: PMC1234104

Lepage P, Seksik P, Sutren M, de la Cochetière MF, Jian R, Marteau P, Doré J. Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD. Inflamm Bowel Dis. 2005 May;11(5):473-80. PubMed PMID: 15867587


Marteau P, Seksik P, Lepage P, Doré J. Cellular and physiological effects of probiotics and prebiotics. Mini Rev Med Chem. 2004 Oct;4(8):889-96. Review. PubMed PMID: 15544550

Marteau P, Lepage P, Mangin I, Suau A, Doré J, Pochart P, Seksik P. Review article: gut flora and inflammatory bowel disease. Aliment Pharmacol Ther. 2004 Oct;20 Suppl 4:18-23. Review. PubMed PMID: 15352889

Leclerc M, Delgènes JP, Godon JJ. Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing. Environ Microbiol. 2004 Aug;6(8):809-19. PubMed PMID: 15250883


Béjà O, Spudich EN, Spudich JL, Leclerc M, DeLong EF. Proteorhodopsin phototrophy in the ocean. Nature. 2001 Jun 14;411(6839):786-9. PubMed PMID: 11459054

Delbès C, Leclerc M, Zumstein E, Godon JJ, Moletta R. A molecular method to study population and activity dynamics in anaerobic digestors. Water Sci Technol. 2001;43(1):51-7. PubMed PMID: 11379112

Leclerc M, Delbes C, Moletta R, Godon J. Single strand conformation polymorphism monitoring of 16S rDNA Archaea during start-up of an anaerobic digester. FEMS Microbiol Ecol. 2001 Jan;34(3):213-220. PubMed PMID: 11137601

Leclerc M, Elfoul-Bensaid L, Bernalier A. Effect of yeast extract on growth and metabolism of H2-utilizing acetogenic bacteria from the human colon. Curr Microbiol. 1998 Sep;37(3):166-71. PubMed PMID: 9688815

Leclerc M, Bernalier A, Donadille G, Lelait M. H2/CO2 metabolism in acetogenic bacteria isolated from the human colon. Anaerobe. 1997 Oct;3(5):307-15. PubMed PMID: 16887606

Leclerc M, Bernalier A, Lelait M, Grivet JP. 13C-NMR study of glucose and pyruvate catabolism in four acetogenic species isolated from the human colon. FEMS Microbiol Lett. 1997 Jan 15;146(2):199-204. PubMed PMID: 9011041

Bernalier A, Willems A, Leclerc M, Rochet V, Collins MD. Ruminococcus hydrogenotrophicus sp. nov., a new H2/CO2-utilizing acetogenic bacterium isolated from human feces. Arch Microbiol. 1996 Sep;166(3):176-83. PubMed PMID: 8703194

Bernalier A, Rochet V, Leclerc M, Doré J, Pochart P. Diversity of H2/CO2-utilizing acetogenic bacteria from feces of non-methane-producing humans. Curr Microbiol. 1996 Aug;33(2):94-9. PubMed PMID: 8662179