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PUBLICATIONS 2017

-Beaumont M*, Jaoui D*, Douard V, Mat D, Koeth F, Goustard B, Mayeur C, Mondot S, Hovaghimian A, Feunteun SL, 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 May 17. doi: 10.1002/mnfr.201700078. [Epub ahead of print]

-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 Jan 16. doi: 10.1007/s00281-016-0613-x. [Epub ahead of print].

-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

-Patrascu O, Beguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc M, Klopp C, Terrapon N, Henrissat B, Blottiere HM, et al: A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Sci Rep. 2017 Jan 17, 7:40248.

PUBLICATIONS 2016

16. 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. 2016 Jan 27. pii: gutjnl-2015-311058.

15. 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, 12:e1005252.

14. Daillère R, Vétizou M, Waldschmitt N, Yamazaki T, Isnard C, Poirier-Colame V, Duong CP, 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

13. 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. 2016 Jul 1. pii: gutjnl-2015-310847. doi: 10.1136/gutjnl-2015-310847. [Epub ahead of print]

12. 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. 8. 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

11. 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

10. 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

9. Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, MetaHIT consortium et al: Human gut microbes impact host serum metabolome and insulin sensitivity. Nature 2016, 535:376-381.

8. Raguideau S, Laroche B, Leclerc M, Plancade S. A Constrained NMF approach to analyze quantitative metagenomic data. IFAG-OninePapers 2016, 49:71-76.

7. Al Nabhani 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.

6. 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. 

5. Mosca A, Leclerc M, Hugot JP: Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem? Front Microbiol 2016, 7:455.

4. Quereda JJ, Dussurget O, Nahori MA, Ghozlane A, Volant S, Dillies MA, Regnault B, Kennedy S, Mondot S, Villoing B, Cossart P, Pizarro-Cerda J. Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection. Proc Natl Acad Sci U S A. 2016 May 17;113(20):5706-11. doi: 10.1073/pnas.1523899113. PubMed PMID: 27140611; PubMed Central PMCID: PMC487851

3.  Mondot S, Boudinot P, Lantz O: MAIT, MR1, microbes and riboflavin: a paradigm for the co-evolution of invariant TCRs and restricting MHCI-like molecules?Immunogenetics 2016, 68:537-548.

2. Boudinot P, Mondot S, Jouneau L, Teyton L, Lefranc MP, Lantz O: Restricting nonclassical MHC genes coevolve with TRAV genes used by innate-like T cells in mammals.Proc Natl Acad Sci U S A 2016, 113:E2983-2992.

1. Rankin LC, Girard-Madoux MJ, Seillet C, Mielke LA, Kerdiles Y, Fenis A, Wieduwild E, Putoczki T, Mondot S, Lantz O, et al: Complementarity and redundancy of IL-22-producing innate lymphoid cells.Nat Immunol 2016, 17:179-186.

PUBLICATIONS 2015

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. 2015 Dec 7. pii: gutjnl-2015-310585. doi: 10.1136/gutjnl-2015-310585. [Epub ahead of print] PubMed PMID: 26642859

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

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. 2015 Dec 1. pii: gutjnl-2015-309184. doi: 10.1136/gutjnl-2015-309184. [Epub ahead of print] PubMed PMID: 26628508

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

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 fiber intake in healthy adults. Environ Microbiol. 2015 Jul 31. doi: 10.1111/1462-2920.13006. [Epub ahead of print] PubMed PMID: 26235304.

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.

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. 2015 Jun 22. pii: gutjnl-2014-308778. doi: 10.1136/gutjnl-2014-308778. [Epub ahead of print] PubMed PMID: 26100928.

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.

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 Mar 1. doi: 10.1111/1758-2229.12285. [Epub ahead of print] PubMed PMID: 25727666

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

PUBLICATIONS 2014

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.

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.

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.

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. 2014 May 16. doi: 10.1038/cdd.2014.56. [Epub ahead of print] PubMed PMID: 24832470.

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.

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.

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.

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.

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.

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.

PUBLICATIONS 2013

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.

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.

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.

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.

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.

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.

PUBLICATIONS 2012

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.

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.

PUBLICATIONS 2011

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.

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.

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.

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.

PUBLICATIONS 2010

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.

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.

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.

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.

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.

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.

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.

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.

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.

PUBLICATIONS 2009

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.

PUBLICATIONS 2008

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.

PUBLICATIONS 2007

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.

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.

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.

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.

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.

PUBLICATIONS 2006

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.

PUBLICATIONS 2005

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.

PUBLICATIONS 2004

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.

PUBLICATIONS ANTERIEURES

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.