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Micalis

Publications from the FInE team

Publication since 2008

2018

Aron-Wisnewsky J, Prifti E, Belda E, Ichou F, Kayser BD, Dao MC, Verger EO, Hedjazi L, Bouillot JL, Chevallier JM, Pons N, Le Chatelier E, Levenez F, Ehrlich SD, Doré J, Zucker JD, Clément K. Major microbiota dysbiosis in severe obesity: fate after bariatric surgery. Gut. 2018 Jun 13. pii: gutjnl-2018-316103. doi: 10.1136/gutjnl-2018-316103

Bennet SMP, Sundin J, Magnusson MK, Strid H, Tap J, Derrien M, Le Nevé B, Doré J, Törnblom H, Simrén M, Öhman L. Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation  Neurogastroenterol Motil. 2018 Sep 17:e13468. doi: 10.1111/nmo.13468.

Couvigny B, Kulakauskas S, Pons N, Quinquis B, Abraham AL, Meylheuc T, Delorme C, Renault P, Briandet R, Lapaque N, Guédon E. Identification of New Factors Modulating Adhesion Abilities of the Pioneer Commensal Bacterium Streptococcus salivarius. Front Microbiol. 2018 Feb 20;9:273. doi: 10.3389/fmicb.2018.00273.

Darnaud M, Santos AD, 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.

Dubuisson JF, Juste C, Fonseca F, Lepage P, Bera-Maillet C, Béguet-Crespel F, Le Roux K, Burz F, Levenez F, Leroux A, Boucinha L, Deprez A, Schwinter C, Dussurgey S, Andrieu T, Affagard H, Blottière H, Bourlioux P, Doré J. Nouveaux dispositifs médicaux et nouveau procédé de fabrication pour un transfert de microbiote fécal par voie rectale, sans risque, standardisé et prêt à l’emploi. J  Pharma Clin 37 : 73-83, 2018.

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, Pais de Barros JP, Malphettes M, Galicier L, Boutboul D, Mathian A, Miyara M, Oksenhendler E, Amoura A, Doré J, Fieschi C, Ehrlich SD, Larsen M, Gorochov G. Microbial ecology perturbation in human IgA deficiency. Science Translational Medicine  02 May 2018: Vol. 10, Issue 439, eaan1217DOI: 10.1126/scitranslmed.aan1217

Girard PM, Peynot N, Lelièvre JM. Differential correlations between changes to glutathione redox state, protein ubiquitination, and stress-inducible HSPA chaperone expression after different types of oxidative stress. Cell Stress Chaperones. 2018 May 12. doi: 10.1007/s12192-018-0909-y.

Larraufie P, Martin-Gallausiaux C, Lapaque N, Dore J, Gribble FM, Reimann F, Blottiere HM. SCFAs strongly stimulate PYY production in human enteroendocrine cells. Sci Rep. 2018 Jan 8;8(1):74. doi: 10.1038/s41598-017-18259-0.

Malard F, Gasc C, Plantamura E, Doré J. High gastrointestinal microbial diversity and clinical outcome in graft-versus-host disease patients. Bone Marrow Transplant. 2018 Jun 14. doi: 10.1038/s41409-018-0254-x.

Martin-Gallausiaux C, Béguet-Crespel F, Marinelli L, Jamet A, Ledue F, Blottière HM, Lapaque N. Butyrate produced by gut commensal bacteria activates TGF-beta1 expression through the transcription factor SP1 in human intestinal epithelial cells. Sci Rep. 2018 Jun 27;8(1):9742. doi: 10.1038/s41598-018-28048-y.

Roume H, Blottière HM. Le microbiote, médiateur des relationq alimentation/physiologie tout au long de la vie. Innovations Agronomiques, 65 : 113-124, 2018.

van de Guchte M, Blottière HM, Doré J. Humans as holobionts: implications for prevention and therapy. Microbiome. 2018 May 1;6(1):81. doi: 10.1186/s40168-018-0466-8.

2017

Arufe S, Chiron H, Doré J, Savary-Auzeloux I, Saulnier L, Della Valle G. Processing & rheological properties of wheat flour dough and bread containing high levels of soluble dietary fibres blends. Food research International 97 (2017) 123-132.

Blottière HM. Chapter 11. The gut microbiota and obesity (2017) In :Romieu I, Dossus L, Willett WC (Eds) IARC Working Group Reports Volume 10: Energy balance and obesity. 

Calder PC, Bosco N, Bourdet-Sicard R, Capuron L, Delzenne N, Doré J, Franceschi C, Lehtinen MJ, Recker T, Salvioli S, Visioli F. Health relevance of the modification of low grade inflammation in ageing (inflammageing) and the role of nutrition. Ageing Res Rev. 2017 Sep 9. pii: S1568-1637(17)30003-X. doi: 10.1016/j.arr.2017.09.001.

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol. 2017 Oct 2. doi: 10.1038/nbt.3960. [Epub ahead of print]

Couvigny B, Lapaque N, Rigottier-Gois L, Guillot A, Chat S, Meylheuc T, Kulakauskas S, Rohde M, Mistou MY, Renault P, Doré J, Briandet R, Serror P, Guédon E. Three glycosylated serine-rich repeat proteins play a pivotal role in adhesion and colonization of the pioneer commensal bacterium, Streptococcus salivarius. Environ Microbiol. 2017 Jul 11. doi: 10.1111/1462-2920.13853. [Epub ahead of print]

Darnaud M, Santos AD, 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. 2017 Nov 11. pii: S0016-5085(17)36349-7. doi: 10.1053/j.gastro.2017.11.003.

Doré J, Multon MC, Béhier JM; les participants à la table ronde 2 des Ateliers de Giens XXXII, Affagard H, Andremont A, Barthélémy P, Batista R, Bonneville M, Bonny C, Boyaval G, Chamaillard M, Chevalier MP, Cordaillat-Simmons M, Cournarie F, Diaz I, Guillaume E, Guyard C, Jouvin-Marche E, Martin FP, Petiteau D. Microbiote intestinal : qu’en attendre au plan physiologique et thérapeutique ? Therapie. 2017 Feb;72(1):1-19. doi: 10.1016/j.therap.2017.01.001.

Doré J, Multon MC, Béhier JM; participants of Giens XXXII, Round Table No. 2. The human gut microbiome as source of innovation for health: Which physiological and therapeutic outcomes could we expect? Therapie. 2017 Feb;72(1):21-38. doi: 10.1016/j.therap.2016.12.007.

El Kafsi H, Loux V , Mariadassou M , Blin C, Chiapello H, Abraham AL, Maguin E, van de Guchte M. Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue. Sci Rep. 2017 Mar 10;7:44331. doi: 10.1038/srep44331.

Jamet A, Dervyn R, Lapaque N, Bugli F, Perez-Cortez NG, Blottière HM , Twizere JC, Sanguinetti M, Posteraro B, Serror P, Maguin E. The Enterococcus faecalis virulence factor ElrA interacts with the human Four-and-a-Half LIM Domains Protein 2. Scientific RepoRts | 7: 4581 | DOI:10.1038/s41598-017-04875-3

Nepelska M, de Wouters T, Jacouton E, Béguet-Crespel F, Lapaque N, Doré J, Arulampalam V, Blottière HM. Commensal gut bacteria modulate phosphorylation-dependent PPARγ transcriptional activity in human intestinal epithelial cells. Sci Rep. 2017 Mar 7;7:43199. doi: 10.1038/srep43199.

O Cuiv P, de Wouters T, Giri R, Mondot S, Smith WJ, Blottière HM, Morrison M. The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in a human gut epithelial cell line in a strain and growth phase dependent manner. Anaerobe 47 (2017) 209-217

Patrascu O, Béguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc M, Klopp C, Terrapon N, Henrissat B, Blottière HM, DoréJ, Béra-Maillet C. A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic Scientific Reports 7, Article number: 40248 (2017) doi:10.1038/srep40248

Romieu I, Dossus L, Barquera S, Blottière HM, Franks PW, Gunter M, Hwalla N, Hursting SD, Leitzmann M, Margetts B, Nishida C, Potischman N, Seidell J, Stepien M, Wang Y, Westerterp K, Winichagoon P, Wiseman M, Willett WC;IARC working group on Energy Balance and Obesity. Energy balance and obesity: what are the main drivers? Cancer Causes Control 2017 Feb 17. doi: 10.1007/s10552-017-0869-z.

Tauzin, A., Laville, E., Cecchini, D., Blottiere, H., Leclerc, M., Dore, J., Veronese, G. (2017). Human gut metagenomics: success and limits of the activity-based approaches. In: Charles TC, Liles MR, Sessitsch (Eds)" Functional Metagenomics: Tools and Applications" . Editions Springer. November 6, 2017.

Van de Guchte M. Horizontal Gene Transfer and Ecosystem Function Dynamics. Trends Microbiol. 2017 Sep;25(9):699-700. doi: 10.1016/j.tim.2017.07.002. Epub 2017 Jul 24.

Versalovic J, Dore J, Guarner F, Luna RA, Ringel Y. Microbiome-Based Diagnostics: Ready for Applications in Laboratory Medicine?
Clin Chem. 2017 Sep 7. pii: clinchem.2016.264473. doi: 10.1373/clinchem.2016.264473.

2016

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 (2016) Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut, 65(3):426-36.

Dobrijevic D, Abraham AL, Jamet A, Maguin E, van de Guchte M. Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment. PLoS One. 2016 Jul 14;11(7):e0159030. doi: 10.1371/journal.pone.0159030.

Duca FA, Sakar Y, Lepage P, Devime F, Langelier B, Doré J, Covasa M. Statement of Retraction. Replication of Obesity and Associated Signaling Pathways Through Transfer of Microbiota From Obese-Prone Rats. Diabetes 2014;63:1624-1636. DOI: 10.2337/db13-1526. Diabetes. 2016 May;65(5):1447. doi: 10.2337/db16-rt05.

Hoffmann TW, Pham HP, Bridonneau C, Aubry C, Lamas B, Martin-Gallausiaux C, Moroldo M, Rainteau D, Lapaque N, Six A, Richard ML, Fargier E, Le Guern ME, Langella P, Sokol H. (2016). Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice. ISME J. 2016 Feb;10(2):460-77. doi: 10.1038/ismej.2015.127. Epub 2015 Jul 28.

Larraufie P, Doré J, Lapaque N, Blottière HM. TLR Ligands and Butyrate Increase Pyy Expression through Two Distinct but Inter-regulated Pathways. Cell Microbiol. 2016 Jul 12. doi: 10.1111/cmi.12648. [Epub ahead of print]

Mondot S, Lepage P, Seksik P, Allez M, Tréton X, Bouhnik Y, Colombel JF, Leclerc M, Pochart P, Doré J, Marteau P; GETAID. (2016). 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.

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.

Plé C, Breton J, Richoux R, Nurdin M, Deutsch SM, Falentin H, Hervé C, Chuat V, Lemée R, Maguin E, Jan G, Van de Guchte M, Foligné B. Combining selected immunomodulatory Propionibacterium freudenreichii and Lactobacillus delbrueckii strains: Reverse engineering development of an anti-inflammatory cheese. Mol Nutr Food Res. 2016 Apr;60(4):935-48. doi: 10.1002/mnfr.201500580. Epub 2015 Dec 29.

Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Doré J, Machado AM, de Evgrafov MC, Hansen T, Jørgensen T, Bork P, Guarner F, Pedersen O; Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium, Sommer MO, Ehrlich SD, Sicheritz-Pontén T, Brunak S, Nielsen HB. (2016) Transcriptional interactions suggest niche segregation among microorganisms in the human gut. Nature Microbiology ARTICLE NUMBER: 1615 DOI:10.1038/NMICROBIOL.2016.152

Putignani L1, Del Chierico F, Vernocchi P, Cicala M, Cucchiara S, Dallapiccola B; Dysbiotrack Study Group. Alisi A, Altomare A, Aloi M, Belzer C, Cavalieri D, Carapito C, Comera C, De Angelis P, Delaere F, De Filippo C, de Vos W, Doré J, Donati C, Furlanello C, Gasbarrini A, Gil C, Guarino M, Hugot JP, Juste C, Knol J, Koletzko B, Monnet V, Nobili V, Oozeer R, Scaldaferri F, Stensvold CR, Stronati L, Tack J, Theodoridis G, Torre G, Urbani A. (2016) Gut Microbiota Dysbiosis as Risk and Premorbid Factors of IBD and IBS Along the Childhood-Adulthood Transition. Inflamm Bowel Dis. 2016 Feb;22(2):487-504. doi: 10.1097/MIB.0000000000000602.

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 May 13. doi: 10.1038/ismej.2016.77. [Epub ahead of print]

Sakar Y, Duca FA, Langelier B, Devime F, Blottiere H, Delorme C, Renault P, Covasa M.  Retraction: Impact of high-fat feeding on basic helix-loop-helix transcription factors controlling enteroendocrine cell differentiation. Int J Obes (Lond). 2016 Jul 6. doi: 10.1038/ijo.2016.118. [Epub ahead of print]

Xiao L, Estellé J, Kiilerich P, Ramayo-Caldas Y, Xia Z, Feng Q, Liang S, Pedersen AØ, Kjeldsen NJ, Liu C, Maguin E, Doré J, Pons N, Le Chatelier E, Prifti E, Li J, Jia H, Liu X, Xu X, Ehrlich SD, Madsen L, Kristiansen K, Rogel-Gaillard C, Wang J. A reference gene catalogue of the pig gut microbiome. Nature Microbiology ARTICLE NUMBER: 16161 DOI: 10.1038/NMICROBIOL.2016.161

Zhang C, Derrien M, Levenez F, Brazeilles R, Ballal SA, Kim J, Degivry MC, Quéré G, Garault P, van Hylckama Vlieg JE, Garrett WS, Doré J, Veiga P. (2016) Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes. ISME J. 2016 Mar 8. doi: 10.1038/ismej.2016.13. [Epub ahead of print]

2015

Chatterjee A, Gogolak P, Blottière HM, Rajnavölgyi E. (2015) The impact of colonic epithelial cell-derived stimuli on myeloid cells and T-lymphocytes. Mediat Inflamm, Vol 2015, article ID 579830, 14 pages.

Couvigny B, de Wouters T, Kaci G, Jacouton E, Delorme C, Doré J, Renault P, Blottière HM, Guédon E, Lapaque N. (2015) Commensal Streptococcus salivarius Modulates PPARγ Transcriptional Activity in Human Intestinal Epithelial Cells. PLoS One. 2015 May 6;10(5):e0125371.

Cultrone A, Tap J, Lapaque N, Doré J, Blottière HM. (2015) Metagenomics of the human intestinal tract: from who is there to what is done there. Curr Opin Food Sci, 4: 64-68.

Doré J, Blottière H. (2015) The influence of diet on the gut microbiota and its consequences for health. Curr Opin Biotechnol, 20;32C:195-199.

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. (2015) Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. 528(7581):262-6.

Jacouton E, Mach N,Cadiou J, Lapaque N, Clément K, Doré J, van Hylckama Vlieg JET, Smokvina T, Blottière HM. (2015) Lactobacillus rhamnosus CNCMI-4317 Modulates Fiaf/Angptl4 in Intestinal Epithelial Cells and Circulating Level in Mice. PLoS One. 2015 October 6; 10(10):e0138880.

Larraufie P, de Wouters T, Veronese G, Blottière HM, Doré J. (2015) Functional Metagenomics to decipher food-microbe-host crosstalk. Proc Nutr Soc, 74(1):1-4.

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. (2015) Early life establishment of the swine gut microbiome and impact on host phenotypes. Environ Microbiol Rep, 7(3):554-69.

Mondot S, Lepage P, Seksik P, Allez M, Tréton X, Bouhnik Y, Colombel JF, Leclerc M, Pochart P, Doré J, Marteau P; GETAID. (2015). Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery. Gut  Dec 1. pii: gutjnl-2015-309184. doi: 10.1136/gutjnl-2015-309184. [Epub ahead of print]

Plaza Onate F, Batto JM, Juste C, Fadlallah J, Fougeroux C, Gouas D, Pons N, Kennedy S, Levenez F, Doré J, Ehrlich SD, Gorochov, G, Larsen M. (2015) Quality control of microbiota metagenomics by k-mer analysis. BMC Genomics, 16(1):183.

Saraiva TD, Morais K, Pereira VB, de Azevedo M, Rocha CS, Prosperi CC, Gomes-Santos AC, Bermudez-Humaran L, Faria AM, Blottiere HM, Langella P, Miyoshi A, de LeBlanc AD, LeBlanc JG, Azevedo V. (2015) Milk Fermented with a 15-Lipoxygenase-1-Producing Lactococcus Lactis Alleviates Symptoms of colitis in a Murine Model. Curr Pharm Biotechnol, 16(5):424-9.

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, Doré J, Dumas ME, Clement K, Bäckhed F, Nielsen J. (2015) Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome. Cell Metabolism, 22 (2), 320–31.

Sokolovska N, Teytaud O, Rizkalla S; MicroObese consortium, Clément K, Zucker JD. (2015) Sparse Zero-Sum Games as Stable Functional Feature Selection. PLoS One. 2015 Sep 1;10(9):e0134683.

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. (2015) Gut microbiota richness promotes its stability upon increased dietary fiber intake in healthy adults. Environ Microbiol, 17(12):4954-64.

Thomas V, Clark J, Doré J. (2015) Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies. Future Microbiol, 10(9):1485-504.

Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, Kotowska D, Colding C, Licht TR, Wu D, Yu J, Sung JJ, Liang Q, Li J, Jia H, Lan Z, Tremaroli V, Dworzynski P, Nielsen HB, Bäckhed F, Doré J, Le Chatelier E, Ehrlich SD, Lin JC, Arumugam M, Wang J, Madsen L, Kristiansen K. (2015) A catalog of the mouse gut metagenome. Nat Biotechnol. 33(10):1103-8.

Zhang C, Yin A, Li H, Wang R, Wu G, Shen J, Zhang M, Wang L, Hou Y, Ouyang H, Zhang Y, Zheng Y, Wang J, Lv X, Wang Y, Zhang F, Zeng B, Li W, Yan F, Zhao Y, Pang X, Zhang X, Fu H, Chen F, Zhao N, Hamaker BR, Bridgewater LC, Weinkove D, Clement K, Dore J, Holmes E, Xiao H, Zhao G, Yang S, Bork P, Nicholson JK, Wei H, Tang H, Zhang X, Zhao L. (2015) Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children. EBioMedicine. 2(8):966-82.

2014

Bolotin A, de Wouters T, Schnupf P, Bouchier C, Loux V, Rhimi M, Jamet A, Dervyn R, Boudebbouze S, Blottière HM, Sorokin A, Snel J, Cerf-Bensussan N, Gaboriau-Routhiau V, van de Guchte M, Maguin E. (2014) Genome Sequence of "Candidatus Arthromitus" sp. Strain SFB-Mouse-NL, a Commensal Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions. Genome Announc., 2:e00705-14.

de Wouters T, Ledue F, Nepelska M, Doré J, Blottière HM, Lapaque N. (2014) A Robust and Adaptable High Throughput Screening Method to study Host-Microbiota interactions in the Human Intestine. PLoS One, 9:e105598.

de Wouters, T, Lapaque N, Maguin E, Doré J, Blottière HM. (2014) Functional Metagenomics of Bacterial-Cell Crosstalk. In "Encyclopedia of Metagenomics" Nelson KE (ed) Springer New York. pp1-6, DOI 10.1007/978-1-4614-6418-1_773-1.

Doré J, Clément K. (2014) Reply to C Matuchansky. Am J Clin NutrReply 99(3):650-1.

El Aidy S, Derrien M, Aardema R, Hooiveld G, Richards SE, Dane A, Dekker J, Vreeken R, Levenez F, Doré J, Zoetendal EG, van Baarlen P, Kleerebezem M. (2014) Transient inflammatory-like state and microbial dysbiosis are pivotal in establishment of mucosal homeostasis during colonisation of germ-free mice. Benef Microbes 5:67-77.

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. (2014) Bacterial protein signals are associated with Crohn's disease. Gut 63 :1566-77.

Kaci G, Goudercourt D, Dennin V, Pot B, Doré J, Ehrlich SD, Renault P, Blottière HM, Daniel C, Delorme C. (2014) Anti-inflammatory properties of Streptococcus salivarius, a commensal bacterium of the oral cavity and digestive tract. Appl Environ Microbiol, 80 :928-934.

Kong LC, Holmes BA, Cotillard A, Habi-Rachedi F, Brazeilles R, Gougis S, Gausserès N, Cani PD, Fellahi S, Bastard JP, Kennedy SP, Doré J, Ehrlich SD, Zucker JD, Rizkalla SW, Clément K. (2014) Dietary patterns differently associate with inflammation and gut microbiota in overweight and obese subjects. PLoS One, 9:e109434.

Lécuyer E, Rakotobe S, Lengliné-Garnier H, Lebreton C, Picard M, Juste C, Fritzen R, Eberl G, McCoy KD, Macpherson AJ, Reynaud CA, Cerf-Bensussan N, Gaboriau-Routhiau V. (2014) Segmented filamentous bacterium uses secondary and tertiary lymphoid tissues to induce gut IgA and specific T helper 17 cell responses. Immunity, 40:608-20.

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. (2014) An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol, 32:834-841.

Petra L, Doré J. (2014) Functional Metagenomics of Human Intestinal Microbiome β-Glucuronidase Activity. In "Encyclopedia of Metagenomics" Nelson, KE (Ed). pp1-8. DOI 10.1007/978-1-4614-6418-1_749-1.

Mach N, Berri M, Esquerré D, Chevaleyre C, Lemonnier G, Billon Y, Lepage P,  Oswald IP, Doré J, Rogel-Gaillard C, Estellé J. (2014). Extensive expression differences along porcine small intestine evidenced by transcriptome sequencing. PLoS One, 9: e88515

Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD. (2014) Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol, 32:822-828.

Santiago A, Panda S, Mengels G, Martinez X, Azpiroz F, Dore J, Guarner F, Manichanh C. (2014) Processing faecal samples: a step forward for standards in microbial community analysis. BMC Microbiol, 14:112.

Slezak K, Krupova Z, Rabot S, Loh G, Levenez F, Descamps A, Lepage P, Doré J, Bellier S, Blaut M. (2014). Association of germ-free mice with a simplified human intestinal microbiota results in a shortened intestine. Gut Microbes, 5:176-82.

Spenlé C, Lefebvre O, Lacroute J, Méchine-Neuville A, Barreau F, Blottière HM, Duclos B, Arnold C, Hussenet T, Hemmerlé J, Gullberg D, Kedinger M, Sorokin L, Orend G, Simon-Assmann P. (2014) The laminin response in inflammatory bowel disease: protection or malignancy?  PLoS One, 9:e111336.

2013

Aziz Q, Doré J, Emmanuel A, Guarner F, Quigley EM. (2013) Gut microbiota and gastrointestinal health: current concepts and future directions. Neurogastroenterol Motil, 25:4-15.

Blottière HM, deVos WM, Ehrlich SD, Doré J (2013) Human intestinal metagenomics – state of the art and future. Curr Opin Microbiol, 16:232-9.

Brown J, de Vos WM, DiStefano PS, Doré J, Huttenhower C, Knight R, Lawley TD, Raes J, Turnbaugh P. (2013) Translating the human microbiome. Nat Biotechnol, 31:304-8.

Cecchini DA, Laville E, Laguerre S, Robe P, Leclerc M, Doré J, Henrissat B, Remaud-Siméon M, Monsan P, Potocki-Véronèse G. (2013) Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. PLoS One, 8:e72766

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 including Blottière HM, Doré J, Zucker JD, Clément K, Ehrlich SD. (2013) Dietary intervention impact on gut microbial gene richness. Nature, 500:585-8

Cultrone A, de Wouters T, Lakhdari O, Kelly D, Mulder I, Logan E, Lapaque N, Doré J, Blottière HM. (2013) The NF-κB binding site located in the proximal region of the TSLP promoter is critical for TSLP modulation in human intestinal epithelial cells. Eur J Immunol. 43:1053-62.

Dobrijevic D, Di Liberto G, Tanaka K, de Wouters T, Dervyn R, Boudebbouze S, Binesse J, Blottière HM, Jamet A, Maguin E, van de Guchte M. (2013) High-throughput system for the presentation of secreted and surface-exposed proteins from gram-positive bacteria in functional metagenomics studies. PLoS One, 8:e65956.

Doré J, Simrén M, Buttle L, Guarner F. (2013) Hot topics in gut microbiota. United European Gastroenterol J, 1:311-8.

Duboc H, Rajca S, Rainteau D, Benarous D, Maubert MA, Quervain E, Thomas G, Barbu V, Humbert L, Despras G, Bridonneau C, Dumetz F, Grill JP, Masliah J, Beaugerie L, Cosnes J, Chazouillères O, Poupon R, Wolf C, Mallet JM, Langella P, Trugnan G, Sokol H, Seksik P. (2013) Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases. Gut, 62:531-9.

El Aidy S, Derrien M, Merrifield CA, Levenez F, Doré J, Boekschoten MV, Dekker J, Holmes E, Zoetendal EG, van Baarlen P, Claus SP, Kleerebezem M. (2013) Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon. ISME J, 7:743-55.

El Aidy S, Merrifield CA, Derrien M, van Baarlen P, Hooiveld G, Levenez F, Doré J, Dekker J, Holmes E, Claus SP, Reijngoud DJ, Kleerebezem M. (2013) The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalization Gut, 62:1306-14.

Jackson NP, Kang YH, Lapaque N, Janssen H, Trowsdale J, Kelly AP. (2013) Salmonella polarises peptide-MHC-II presentation towards an unconventional Type B CD4+ T-cell response. Eur J Immunol, 43:897-906.

Kong LC, Tap J, Aron-Wisnewsky J, Pelloux V, Basdevant A, Bouillot J-L, Zucker J-D, Doré J, Clement K. (2013) Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes. Am J Clin Nutr, 98:16-24.

Kong LC, Wuillemin PH, Bastard JP, Sokolovska N, Gougis S, Fellahi S, Darakhshan F, Bonnefont-Rousselot D, Bittar R, Dore J, Zucker JD, Clement K, Rizkalla S. (2013) Insulin resistance and inflammation predict kinetic body weight changes in response to dietary weight loss and maintenance in overweight and obese subjects by using a Bayesian network approach. Am J Clin Nutr, 98:1385-1394.

Korecka A*, de Wouters T*, Cultrone A, Lapaque N, Pettersson S, Doré J, Blottière HM#, Arulampalam V#. (2013) ANGPTL4 expression induced by butyrate and rosiglitazone in human intestinal epithelial cells utilizes independent pathways. Am J Physiol Gastrointest Liver Physiol, 304:G1025-37. (*, # equal contribution)

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. (2013) Richness of human gut microbiome correlates with metabolic markers. Nature. 500:541-546.

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. (2013) Intestinal microbiota determines development of non-alcoholic fatty liver disease in mice. Gut, 62:1787-94.

Lepage P, Leclerc MC, Joossens M, Mondot S, Blottière HM, Raes J, Ehrlich D, Doré J. (2013) A metagenomic insight into our gut's microbiome. Gut, 62:146–158

Matos RC, Lapaque N, Rigottier-Gois L, Debarbieux L, Meylheuc T, Gonzalez-Zorn B, Repoila F, Lopes Mde F, Serror P. (2013) Enterococcus faecalis Prophage Dynamics and Contributions to Pathogenic Traits. PLoS Genet. 2013 9:e1003539.

Mondot S, de Wouters T, Doré J, Lepage P. (2013) The human gut microbiome and its dysfunctions. Dig Dis, 31:278-85.

Petschow B, Doré J, Hibberd P, Dinan T, Reid G, Blaser M, Cani PD, Degnan FH, Foster J, Gibson G, Hutton J, Klaenhammer TR, Ley R, Nieuwdorp M, Pot B, Relman D, Serazin A, Sanders ME. (2013) Probiotics, prebiotics, and the host microbiome: the science of translation. Ann N Y Acad Sci, 1306:1-17.

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Roat Kultima J, Arumugam M, Tap J, Bjørn Nielsen H, Rasmussen S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A & Bork P. (2013) Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods, 10:1196-9.

Viaud S, Saccheri F, Mignot G, Yamazaki T, Daillere R, Hannani D, Enot DP, Pfirschke C, Engblom C, Pittet MJ, Schlitzer A, Ginhoux F, Apetoh L, Chachaty E, Woerther PL, Eberl G, Berard 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. (2013) The Intestinal Microbiota Modulates the Anticancer Immune Effects of Cyclophosphamide. Science, 342:971-976.

2012

Aron-Wisnewsky J, Doré J, Clement K. (2012) The importance of the gut microbiota after bariatric surgery. Nat Rev Gastroenterol Hepatol. 9:590-8.

Candela T, Dumetz F, Tosi-Couture E, Mock M, Goossens PL, Fouet A. (2012) Cell-wall preparation containing poly-γ-D-glutamate covalently linked to peptidoglycan, a straightforward extractable molecule, protects mice against experimental anthrax infection. Vaccine, 17;31:171-5.

Cardona S, Eck A, Cassellas M, Gallart M, Alastrue C, Dore J, Azpiroz F, Roca J, Guarner F, Manichanh C. (2012) Storage conditions of intestinal microbiota matter in metagenomic analysis. BMC Microbiol, 12:158.

de Wouters T, Doré J, Lepage P. (2012) Does our food (environment) change our gut microbiome ('in-vironment'): a potential role for inflammatory bowel disease ? Dig Dis, Suppl 3:33-9.

El Aidy S, van Baarlen P, Derrien M, Lindenbergh-Kortleve DJ, Hooiveld G, Levenez F, Doré J, Dekker J, Samsom JN, Nieuwenhuis EE, Kleerebezem M. (2012) Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice. Mucosal Immunol, 5:567-79.

Mondot S, Barreau F, Al Nabhani Z, Dussaillant M, Le Roux K, Doré J, Leclerc M, Hugot JP, Lepage P. (2012) Altered gut microbiota composition in immune-impaired Nod2(-/-) mice. Gut. 2012 Apr;61(4):634-5.

Nepelska M, Cultrone A, Béguet-Crespel F, Le Roux K, Doré J, Arulampalam V, Blottière HM. (2012) Butyrate produced by commensal bacteria potentiates phorbol esters induced AP-1 response in human intestinal epithelial cells. PLoS One, 7:e52869.

Santos Rocha C, Lakhdari O, Blottière HM, Blugeon S, Sokol H, Bermúdez-Humarán LG, Azevedo V, Miyoshi A, Doré J, Langella P, Maguin E, van de Guchte M. (2012) Anti-inflammatory properties of dairy lactobacilli. Inflamm Bowel Dis, 18:657-66.

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. (2011) Involvement of tissue bacteria in the onset of diabetes in humans: evidence for a concept. Diabetologia, 54:3055-61.

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. (2011) Enterotypes of the human gut microbiome. Nature, 473:174–180.

Dumetz F, Jouvion G, Khun H, Glomski IJ, Corre JP, Rougeaux C, Tang WJ, Mock M, Huerre M, Goossens PL. (2011) Noninvasive imaging technologies reveal edema toxin as a key virulence factor in anthrax. Am J Pathol, 178(6):2523-35.

Fallani M, Amarri S, Uusijarvi A, Adam R, Khanna S, Aguilera M, Gil A, Vieites JM, Norin E, Young D, Scott JA, Doré J, Edwards CA; INFABIO team. (2011) Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centres. Microbiology 2011 157:1385-92.

Gloux, K., Berteau, O., El Oumami, H., Béguet, F., Leclerc, M., and Dore, J. (2011) A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome. Proc Natl Acad Sci USA, 108 Suppl 1:4539-46.

Guardia S, Konsak B, Combes S, Levenez F, Cauquil L, Guillot JF, Moreau-Vauzelle C, Lessire M, Juin H, Gabriel I. (2011) Effects of stocking density on the growth performance and digestive microbiota of broiler chickens. 2011 Poultry Science 90: 1878–1889.

Kaci G, Lakhdari O, Doré J, Ehrlich SD, Renault P, Blottière HM*, Delorme C*. (2011) Inhibition of the NF-κB pathway in human intestinal epithelial cells by commensal Streptococcus salivarius. Appl Environ Microbiol 2011 77:4681-4684. (*equal contribution)

Lakhdari O, Tap J, Béguet-Crespel F, Le Roux K, de Wouters T, Cultrone A, Nepelska M, Lefèvre F, Doré J, Blottière HM. (2011) Identification of NF-κB modulation capabilities within human intestinal commensal bacteria. J Biomed Biotech 2011, Article ID 282356.

Lepage P, Häsler R, Spehlmann ME, Rehman A, Zvirbliene A, Begun A, Ott S, Kupcinskas L, Doré J, Raedler A, Schreiber S. (2011) Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 2011 141:227-236.

Mondot S, Kang S, Furet JP, Aguirre de Carcer D, McSweeney C, Morrison M, Marteau P, Doré J, Leclerc M. (2011) Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm Bowel Dis  17:185-92.

Muñoz-Tamayo R, Laroche B, Walter E, Doré J, Duncan SH, Flint HJ, Leclerc M. (2011) Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species. FEMS Microbiol Ecol, 76:615-624.

Rooijers K, Kolmeder C, Juste C, Doré J, de Been M, Boeren S, Galan P, Beauvallet C, de Vos WM, Schaap PJ. (2011) An iterative workflow for mining the human intestinal metaproteome. BMC Genomics. 2011 Jan 5;12:6. doi: 10.1186/1471-2164-12-6.

Thompson-Chagoyan OC, Fallani M, Maldonado J, Vieites JM, Khanna S, Edwards C, Doré J, Gil A. (2011) Faecal Microbiota and short-chain fatty acid levels in faeces from infants with cow's milk protein allergy. Int Arch Allergy Immunol 2011 156:325-332.

Rousseau C, Levenez F, Fouqueray C, Doré J, Collignon A, Lepage P. (2011) Clostridium difficile colonization in early infancy is accompanied by changes in intestinal microbiota composition. J Clin Microbiol, 49:858-65.

van Duynhoven J, Vaughan EE, Jacobs DM, Kemperman RA, van Velzen EJJ, Gross G, Roger LC, Possemiers S, Smilde AK, Doré J, Westerhuis JA, Van de Wiele T. (2011) Metabolic fate of polyphenols in the human superorganism. Proc Natl Acad Sci U S A 108 Suppl 1:4531-8.

2010

Benard C, Cultrone A, Michel C, Rosales C, Segain JP, Lahaye M, Galmiche JP, Cherbut C, Blottière HM. (2010) Degraded Carrageenan Causing Colitis in Rats Induces TNF Secretion and ICAM-1 Upregulation in Monocytes through NF-kB Activation. PLoS ONE, 5:e8666.

Corthier G, Doré J. (2010) A new era in gut research concerning interactions between microbiota and human health. Gastroenterol Clin Biol, 34 Suppl 1:S1-6.

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

Doré J, Corthier G. The human intestinal microbiota (2010) Gastroenterol Clin Biol, 34 Suppl 1:S7-15.

Ehrlich SD; MetaHIT consortium. Metagenomics of the intestinal microbiota: potential applications. Gastroenterol Clin Biol 2010 34 Suppl 1:S23-8. French..

Furet JP, Kong LC, Tap J, Poitou C, Basdevant A, Bouillot JL, Mariat D, Corthier G, Doré J, Henegar C, Rizkalla S, Clément K. (2010) Differential adaptation of human gut microbiota to bariatric surgery–induced weight loss. Links with metabolic and low-grade inflammation markers. Diabetes, 59:3049-3057.

Fallani M, Young D, Scott J, Norin E, Amarri S, Adam R, Aguilera M, Khanna S, Gil A, Edwards CA, Doré J; the INFABIO Team. (2010) Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics. J Pediatr Gastroenterol Nutr, 51:77-84.

Lakhdari O, Cultrone A, Tap J, Gloux K, Bernard F, Ehrlich SD, Lefèvre F, Doré J, Blottière HM, (2010) Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-kB modulation in the human gut. PLoS One, 5(9). pii: e13092. Erratum in: PLoS One 2010;5(10).

Madi A, Lakhdari O, Blottière HM, Guyard M, Le Roux K, Svinareff P, Doré J, Orange N, Feuilloley MGJ, Connil N. (2010) The clinical Pseudomonas fluorescens MFN1032 strain exerts cytotoxic effect on epithelial intestinal cells and induces Interleukin-8 via the AP-1 signaling pathway. BMC Microbiol, 10:215.

Mihajlovski A, Doré J, Levenez F, Alric M, Brugère JF. (2010) Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity. Environ Microbiol Rep, 2:272-80.

Mirande C, Kadlecikova E, Matulova M, Capek P, Bernalier-Donadille A, Forano E, Béra-Maillet C. (2010) Dietary fibre degradation and fermentation by two xylanolytic bacteria Bacteroides xylanisolvens XB1AT and Roseburia intestinalis XB6B4 from the human intestine. J Appl Microbiol, 109:451–460.

Mirande C, Mosoni P, Béra-Maillet C, Bernalier-Donadille A, Forano E. (2010) Characterization of Xyn10A, a highly active xylanase from the human gut bacterium Bacteroides xylanisolvens XB1A. Appl Microbiol Biotechnol, 87:2097–2105.

Mondot, S., Kang, S., Furet, J.P., Aguirre de Carcer, D., McSweeney, C., Morrison, M., Marteau, P., Dore, J., and Leclerc, M. (2010) Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm Bowel Dis, 17:185-192.

Muñoz-Tamayo R, Laroche B, Walter E, Doré J, Leclerc M. (2010) Mathematical modelling of carbohydrate degradation by human colonic microbiota. J Theor Biol 266:189-201. Epub 2010 Jun 16.

Qin, J., Ruiqiang, L., Raes, J., Arumugam M., Solvsten, K., Burgdorf, Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D., 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, J. M., Hansen, T., Le Paslier, D., Linneberg, A., Nielsen, H. B., Pelletier, E., Renault, P., Sicheritz-Ponten, T., Turner, K., Zhu, H., Yu, C., Li, S., Jian, M., Zhou, Y., Zhang, X., Li, S., Yang, H., Wang, J., Brunak, S., Doré, J., Guarner, F., Kristiansen, K., Pedersen, O., Parkhill, J., Weissenbach, J., MetaHIT Consortium, Bork, P., Ehrlich, S. D. and Wang, J. (2010) A human gut microbial gene catalog established by deep metagenomic sequencing. Nature 464, 59-65.

Rehman A, Lepage P, Nolte A, HellmigS, Schreiber S, Ott SJ. (2010) Transcriptional activity of dominant gut mucosal microbiota in chronic inflammatory bowel diseases. J Med Microbiol 59:1114-22.

Sun L, Yu Z, Ye X, Zou S, Li H, Yu D, Wu H, Chen Y, Dore J, Clément K, Hu FB, Lin X. (2010) A marker of endotoxemia is associated with obesity and related metabolic disorders in apparently healthy Chinese. Diabetes Care. 33:1925-32.

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. (2010) Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 2010 20:1605-12.

2009

Furet JP, Firmesse O, Gourmelon M, Bridonneau C, Tap J, Mondot S, Doré S, Corthier G. Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. FEMS Microbiol Ecol 2009, 68, 351362.

Gao X, Pujos-Guillot E, Martin JF, Galan P, Juste C, Jia W, Sebedio JL. (2009). Metabolite analysis of human fecal water by gas chromatography/mass spectrometry with ethyl chloroformate derivatization. Anal Biochem 393:163-175.

Mariat D, Firmesse O, Levenez F, Guimarăes V, Sokol H, Doré J, Corthier G, Furet JP. (2009) The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol 9:123.

Sokol H, Seksik P, Furet JP, Firmesse O, Nion-larmurier I, Beaugerie L, Cosnes J, Corthier G, Marteau P, Doré J. (2009) Low counts of Faecalibacterium prausnitzii in Colitis Microbiota. Inflamm Bowel Dis15, 1183-1189.

Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Muñoz-TamayoR, Le Paslier D, Nalin R, Doré J, Leclerc M. (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol11, 25742584.

2008

Barc MC, Charrin-Sarnel C, Rochet V, Bourlioux F, Sandré C, Boureau H, Doré J, Collignon A. (2008) Molecular analysis of the digestive microbiota in a gnotobiotic mouse model during antibiotic treatment: Influence of Saccharomyces boulardii. Anaerobe, 14:229-33.

Firmesse O, Alvaro E, Mogenet A, Bresson JL, Lemée R, Le Ruyet P, Bonhomme C, Lambert D, Andrieux C, Doré J, Corthier G, Furet JP, Rigottier-Gois L. (2008) Fate and effects of Camembert cheese micro-organisms in the human colonic microbiota of healthy volunteers after regular Camembert consumption. Int J Food Microbiol, 125:176-81.

Guigoz Y, Doré J, Schiffrin EJ. (2008) The inflammatory status of old age can be nurtured from the intestinal environment. Curr Opin Clin Nutr Metab Care, 11:13-20.

Lepage P, Colombet J, Marteau P, Sime-Ngando T, Doré J, Leclerc M. (2008) Dysbiosis in inflammatory bowel disease: a role for bacteriophages? Gut 57:424-5.

Manichanh C, Chapple CE, Frangeul L, Gloux K, Guigo R, Dore J. (2008) A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res, 36:5180-8.

Manichanh C, Varela E, Martinez C, Antolin M, Llopis M, Doré J, Giralt J, Guarner F, Malagelada JR. (2008) The gut microbiota predispose to the pathophysiology of acute postradiotherapy diarrhea. Am J Gastroenterol, 103:1754-61.

Rochet V, Rigottier-Gois L, Ledaire A, Andrieux C, Sutren M, Rabot S, Mogenet A, Bresson JL, Cools S, Picard C, Goupil-Feuillerat N, Doré J. (2008) Survival of bifidobacterium animalis DN-173010 in the faecal microbiota after administration in lyophilised form or in fermented product - A randomised study in healthy adults.J Mol Microbiol Biotech, 14:128-36.

Rochet V, Rigottier-Gois L, Levenez F, Cadiou J, Marteau P, Bresson JL, Goupil-Feillerat N, Doré J. (2008) Modulation of Lactobacillus casei in ileal and fecal samples from healthy volunteers after consumption of a fermented milk containing Lactobacillus casei DN-114 001Rif. Can J Microbiol, 54:660-7.

Spehlmann ME, Begun AZ, Burghardt J, Lepage P, Raedler A, Schreiber S. (2008) Epidemiology of inflammatory bowel disease in a German twin cohort: Results of a nationwide study. Inflamm Bowel Dis, 14:968-976.

Sokol H, Pigneur B,Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux J-J, Blugeon S, Bridonneau C, Furet J-P, Corthier G, Grangette C, Vasquez N, Pochart Ph, Trugnan G, Thomas G, Blottière HM, Doré J, Marteau P, Seksik P & Langella P. (2008) Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn's diease patients. Proc Nat Acad Sci USA, 105:16731-16736.

Spehlmann ME, Begun AZ, Burghardt J, Lepage P, Andreas Raedler, Stefan Schreiber. (2008) Epidemiology of Inflammatory Bowel Disease in a German Twin Cohort: Results of a Nationwide Study. Inflamm Bowel Dis, 14:968-976.